GEMM RIBOSWITCHES, STRUCTURE-BASED COMPOUND DESIGN WITH GEMM RIBOSWITCHES, AND METHODS AND COMPOSITIONS FOR USE OF AND WITH GEMM RIBOSWITCHES

FIELD OF THE INVENTION

The disclosed invention is generally in the field of gene expression and specifically in the area of regulation of gene expression.

BACKGROUND OF THE INVENTION

Precision genetic control is an essential feature of living systems, as cells must respond to a multitude of biochemical signals and environmental cues by varying genetic expression patterns. Most known mechanisms of genetic control involve the use of protein factors that sense chemical or physical stimuli and then modulate gene expression by selectively interacting with the relevant DNA or messenger RNA sequence. Proteins can adopt complex shapes and carry out a variety of functions that permit living systems to sense accurately their chemical and physical environments. Protein factors that respond to metabolites typically act by binding DNA to modulate transcription initiation (e.g. the lac repressor protein; Matthews, K. S., and Nichols, J. C., 1998, Prog. Nucleic Acids Res. Mol. Biol. 58, 127-164) or by binding RNA to control either transcription termination (e.g. the PyrR protein; Switzer, R. L., et al., 1999, Prog. Nucleic Acids Res. Mol. Biol. 62, 329-367) or translation (e.g. the TRAP protein; Babitzke, P., and Gollnick, P., 2001, J. Bacteriol. 183, 5795-5802). Protein factors respond to environmental stimuli by various mechanisms such as allosteric modulation or post-translational modification, and are adept at exploiting these mechanisms to serve as highly responsive genetic switches (e.g. see Ptashne, M., and Gann, A. (2002). Genes and Signals. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

In addition to the widespread participation of protein factors in genetic control, it is also known that RNA can take an active role in genetic regulation. Recent studies have begun to reveal the substantial role that small non-coding RNAs play in selectively targeting mRNAs for destruction, which results in down-regulation of gene expression (e.g. see Hannon, G. J. 2002, Nature 418, 244-251 and references therein). This process of RNA interference takes advantage of the ability of short RNAs to recognize the intended mRNA target selectively via Watson-Crick base complementation, after which the bound mRNAs are destroyed by the action of proteins. RNAs are ideal agents for molecular recognition in this system because it is far easier to generate new target-specific RNA factors through evolutionary processes than it would be to generate protein factors with novel but highly specific RNA binding sites.

Although proteins fulfill most requirements that biology has for enzyme, receptor and structural functions, RNA also can serve in these capacities. For example, RNA has sufficient structural plasticity to form numerous ribozyme domains (Cech & Golden, Building a catalytic active site using only RNA. In: The RNA World R. F. Gesteland, T. R. Cech, J. F. Atkins, eds., pp. 321-350 (1998); Breaker, In vitro selection of catalytic polynucleotides. Chem. Rev. 97, 371-390 (1997)) and receptor domains (Osborne & Ellington, Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97, 349-370 (1997); Hermann & Patel, Adaptive recognition by nucleic acid aptamers. Science 287, 820-825 (2000)) that exhibit considerable enzymatic power and precise molecular recognition. Furthermore, these activities can be combined to create allosteric ribozymes (Soukup & Breaker, Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA 96, 3584-3589 (1999); Seetharaman et al., Immobilized riboswitches for the analysis of complex chemical and biological mixtures. Nature Biotechnol. 19, 336-341 (2001)) that are selectively modulated by effector molecules.

BRIEF SUMMARY OF THE INVENTION

Disclosed is the crystal structure of a GEMM riboswitch from V. cholerae bound to cyclic diguanosine monophosphate (c-di-GMP). The crystal structures show that the RNA binds the ligand within a three helix junction that involves base pairing and extensive base stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to the both the bases and the backbone. Also disclosed are GEMM riboswitches engineered to preferentially bind the signaling molecule c-di-AMP over c-di-GMP.

Also disclosed are methods of identifying compounds that interact with, modulates, inhibits, blocks, deactivates, and/or activates a GEMM riboswitch. The method can comprise, for example, modeling the atomic structure of the GEMM riboswitch with a test compound and determining if the test compound interacts with, modulates, inhibits, blocks, deactivates, and/or activates the riboswitch. This can be done by, for example, determining the atomic contacts of the riboswitch and test compound. Furthermore, analogs of a compound known or identified to interact with, modulate, inhibit, block, deactivate, and/or activate a riboswitch can be generated by, for example, analyzing the atomic contacts and then optimizing the atomic structure of the analog to maximize interaction. These methods can be used, for example, with a high throughput screen.

Further disclosed are methods of identifying a compound that interacts with, modulates, inhibits, blocks, deactivates, and/or activates a GEMM riboswitch. The method can comprise modeling the atomic structure of a GEMM riboswitch with a test compound and determining if the test compound interacts with, modulates, inhibits, blocks, deactivates, and/or activates the GEMM riboswitch. Determining if the test compound interacts with, modulates, inhibits, blocks, deactivates, and/or activates the riboswitch can be accomplished by, for example, determining a predicted minimum interaction energy, a predicted binding constant, a predicted dissociation constant, or a combination, for the test compound in the model of the GEMM riboswitch. Determining if the test compound interacts with, modulates, inhibits, blocks, deactivates, and/or activates the riboswitch can be accomplished by, for example, determining one or more predicted bonds, one or more predicted interactions, or a combination, of the test compound with the model of the riboswitch. Atomic contacts of the compound can be determined, thereby determining the interaction of the test compound with the riboswitch. The method of identifying a compound that interacts with, modulates, inhibits, blocks, deactivates, and/or activates a GEMM riboswitch can further comprise, for example, identifying analogs of the test compound and determining if the analogs of the test compound interact with, modulate, inhibit, blocks, deactivates, and/or activate the GEMM riboswitch.

Further disclosed are methods of killing or inhibiting the growth of bacteria, The method can comprise, for example, contacting the bacteria with a compound identified and/or confirmed by any of the methods disclosed herein. Further disclosed are methods of killing bacteria. The method can comprise, for example, contacting the bacteria with a compound identified and/or confirmed by any of the methods disclosed herein. The disclosed methods can be performed in a variety of ways and using different options or combinations of features and components. As an example, a gel-based assay or a chip-based assay can be used to determine if the test compound interacts with, modulates, inhibits, blocks, deactivates, and/or activates the GEMM riboswitch. The test compound can interact in any manner, such as, for example, via van der Waals interactions, hydrogen bonds, electrostatic interactions, hydrophobic interactions, or a combination. The GEMM riboswitch can comprise an RNA cleaving ribozyme, for example. A fluorescent signal can be generated when a nucleic acid comprising a quenching moiety is cleaved. Molecular beacon technology can be employed to generate the fluorescent signal. The methods disclosed herein can be carried out using a high throughput screen.

Also disclosed are compositions and methods for selecting and identifying compounds that can activate, deactivate or block a GEMM riboswitch.

Also disclosed are method of inhibiting growth of a cell, such as a bacterial cell, that is in a subject. The method can comprise administering to the subject an effective amount of a compound identified and/or confirmed in any of the methods described herein. This can result in the compound being brought into contact with the cell. The subject can have, for example, a bacterial infection, and the bacterial cells can be the cells to be inhibited by the compound. The bacteria can be any bacteria, such as bacteria from the genus Bacillus or Staphylococcus, for example. Bacterial growth can also be inhibited in any context in which bacteria are found. For example, bacterial growth in fluids, biofilms, and on surfaces can be inhibited. The compounds disclosed herein can be administered or used in combination with any other compound or composition. For example, the disclosed compounds can be administered or used in combination with another antimicrobial compound.

Disclosed is the atomic structure of a GEMM riboswitch from V. cholerae. The atomic structure comprises the atomic coordinates listed in Table 2. The atomic structure is also depicted in the ribbon diagram in FIG. 1. Also disclosed are portions of the atomic structure of a GEMM riboswitch from V. cholerae. For example, the atomic structure can comprise the binding pocket atomic structure.

Also disclosed are methods of identifying compounds that interact with a riboswitch. The method can comprise (a) modeling the atomic structure of any of claim 1 or 2 with a test compound, and (b) determining if the test compound interacts with the riboswitch.

Also disclosed are methods of killing or inhibiting the growth of bacteria. The method can comprise contacting the bacteria with an analog identified by any of the method disclosed herein. Also disclosed are methods of inhibiting gene expression. The method can comprise bringing into contact a compound and a cell, wherein the compound is identified by any of the disclosed methods.

Also disclosed are methods comprising: (a) testing a compound identified by any of the disclosed methods for inhibition of gene expression of a gene encoding an RNA comprising a GEMM riboswitch, wherein the inhibition is via the riboswitch; and (b) inhibiting gene expression by bringing into contact a cell and a compound that inhibited gene expression in step (a). The cell can comprise a gene encoding an RNA comprising a target riboswitch, wherein the target riboswitch is a GEMM riboswitch, wherein the compound inhibits expression of the gene by binding to the target riboswitch.

Also disclosed are compositions comprising a compound identified by any of the disclosed methods and an RNA comprising a GEMM riboswitch. Also disclosed are complexes comprising a GEMM riboswitch and c-di-GMP.

In some forms, determining if the test compound interacts with the riboswitch can comprise determining a predicted minimum interaction energy, a predicted binding constant, a predicted dissociation constant, or a combination, for the test compound in the model of the riboswitch. In some forms, determining if the test compound interacts with the riboswitch can comprise determining one or more predicted bonds, one or more predicted interactions, or a combination, of the test compound with the model of the riboswitch.

In some forms, atomic contacts can be determined, thereby determining the interaction of the test compound with the riboswitch. In some forms, after identifying a compound, the method can further comprise (c) identifying analogs of the test compound; and (d) determining if the analogs of the test compound interact with the riboswitch. In some forms, a gel-based assay can be used to determine if the test compound interacts with the riboswitch. In some forms, a chip-based assay can be used to determine if the test compound interacts with the riboswitch. In some forms, the test compound can interact via van der Waals interactions, hydrogen bonds, electrostatic interactions, hydrophobic interactions, or a combination. In some forms, a fluorescent signal can be generated when a nucleic acid comprising a quenching moiety is cleaved. In some forms, molecular beacon technology can be employed to generate the fluorescent signal. In some forms, the method can be carried out using a high throughput screen.

In some forms, the cell can be identified as being in need of inhibited gene expression. In some forms, the cell can be a bacterial cell. In some forms, the compound can kill or inhibit the growth of the bacterial cell. In some forms, the compound and the cell can be brought into contact by administering the compound to a subject. In some forms, the cell can be a bacterial cell in the subject, wherein the compound can kill or inhibit the growth of the bacterial cell. In some forms, the subject has a bacterial infection. In some forms, the cell can contain a GEMM riboswitch. In some forms, the bacteria is Bacillus or Staphylococcus. In some forms, the compound can be administered in combination with another antimicrobial compound. In some forms, the compound can inhibit bacterial growth in a biofilm.

In some forms, the RNA can be encoded by a nucleic acid molecule, wherein a regulatable gene expression construct comprises the nucleic acid molecule. In some forms, the riboswitch can be operably linked to a coding region, wherein the riboswitch regulates expression of the RNA, wherein the riboswitch and coding region are heterologous. In some forms, the riboswitch can produce a signal when activated by the compound. In some forms, the riboswitch can change conformation when activated by the compound, wherein the change in conformation produces a signal via a conformation dependent label. In some forms, the riboswitch can change conformation when activated by the compound, wherein the change in conformation causes a change in expression of the coding region linked to the riboswitch, wherein the change in expression produces a signal. In some forms, the RNA can comprise an RNA cleaving ribozyme.

In some forms, the c-di-GMP can bind to the GEMM riboswitch and can lock the 3′ end of the riboswitch into a specific conformation through base pairing with C92, initiating the formation of the P1 stem. In some forms, the P1 stem formation can be the molecular switch that affects gene expression levels in response to c-di-GMP levels. In some forms, the binding can affect motility, pathogenesis, or biofilm formation by a microorganism.

Also disclosed are complexes of c-di-GMP bound to a GEMM riboswitch. In the complex, the c-di-GMP locks the 3′ end of the riboswitch into a specific conformation through base pairing with C92, initiating the formation of the P1 stem. Formation of the P1 stem formation is the molecular switch that adjusts/affects gene expression levels in response to c-di-GMP levels. The 3′ end of the riboswitch involved in the P1 stem is, or interacts with, an expression platform domain. Sequestration of the 3′ end of the riboswitch in the P1 stem prevents this sequence form being available for other interactions. The GEMM riboswitch can bind the c-di-GMP within a three helix junction that involves base pairing and extensive base stacking.

Additional advantages of the disclosed method and compositions will be set forth in part in the description which follows, and in part will be understood from the description, or can be learned by practice of the disclosed method and compositions. The advantages of the disclosed method and compositions will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention as claimed.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the disclosed method and compositions and together with the description, serve to explain the principles of the disclosed method and compositions.

FIGS. 1A and 1B show the structure of a GEMM riboswitch from V. cholerae bound to c-di-GMP. FIG. 1A shows the stem, loops, and base interactions of the riboswitch and c-di-GMP based on the crystal structure and secondary structure studies. The GEMM riboswitch is SEQ ID NO:1. FIG. 1B shows a ribbon diagram of the riboswitch based on a 2.7 Å crystal structure of a GEMM riboswitch from V. cholerae bound to c-di-GMP.

FIGS. 2A-2F show the structure and recognition of c-di-GMP by GEMM riboswitch. FIG. 2A shows the orientation and contacts of c-di-GMP with bases G20, A47, and C92 of the GEMM riboswitch. FIG. 2B shows the secondary structure and contacts of c-di-GMP with portions of the GEMM riboswitch. The sequence depicted is nucleotides 4 to 7, 11 to 21, 32 to 40, and 85 to 90 of SEQ ID NO:1. FIG. 2C shows the orientation and contacts of the alpha G of c-di-GMP with bases G20 and A48 of the GEMM riboswitch. FIG. 2D shows the orientation and contacts of the beta G of c-di-GMP with bases A47 and C92 of the GEMM riboswitch. FIG. 2E shows the orientation and contacts of c-di-GMP with metal ions and with bases A18 and A47 of the GEMM riboswitch. FIG. 2F shows the density observed for the interactions shown in FIG. 2E.

FIGS. 3A and 3B show biochemical characterization of wild-type and mutant riboswitches. FIG. 3A is a gel showing gel-shift of radio-labeled c-di-GMP in the presence of increasing concentration of GEMM riboswitch RNA. FIG. 3B shows the binding curve of the binding in FIG. 3A.

DETAILED DESCRIPTION OF THE INVENTION

The disclosed crystal structures, methods, compounds, and compositions can be understood more readily by reference to the following detailed description of particular embodiments and the Examples included therein and to the Figures and their previous and following description.

Messenger RNAs are typically thought of as passive carriers of genetic information that are acted upon by protein- or small RNA-regulatory factors and by ribosomes during the process of translation. It was discovered that certain mRNAs carry natural aptamer domains and that binding of specific metabolites directly to these RNA domains leads to modulation of gene expression. Natural riboswitches exhibit two surprising functions that are not typically associated with natural RNAs. First, the mRNA element can adopt distinct structural states wherein one structure serves as a precise binding pocket for its target metabolite. Second, the metabolite-induced allosteric interconversion between structural states causes a change in the level of gene expression by one of several distinct mechanisms. Riboswitches typically can be dissected into two separate domains: one that selectively binds the target (aptamer domain) and another that influences genetic control (expression platform). It is the dynamic interplay between these two domains that results in metabolite-dependent allosteric control of gene expression.

Distinct classes of riboswitches have been identified and are shown to selectively recognize activating compounds (referred to herein as trigger molecules). For example, coenzyme B₁₂, glycine, thiamine pyrophosphate (TPP), and flavin mononucleotide (FMN) activate riboswitches present in genes encoding key enzymes in metabolic or transport pathways of these compounds. The aptamer domain of each riboswitch class conforms to a highly conserved consensus sequence and structure. Thus, sequence homology searches can be used to identify related riboswitch domains. Riboswitch domains have been discovered in various organisms from bacteria, archaea, and eukarya.

Cyclic diguanosine monophosphate (c-di-GMP) is a second messenger signaling molecule that regulates many vital processes within the bacterial kingdom. c-di-GMP concentrations regulate the transition from a motile, planktonic lifestyle, to a sessile, biofilm-forming state (Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro 7, 263-73 (2009)). In general, when levels of c-di-GMP rise in the cell, biofilm formation is induced, often by upregulating the cellular machinery necessary to create the exopolysaccharide material necessary for the development of a biofilm. Inversely, many species selectively degrade c-di-GMP under conditions conducive to a motile lifestyle, initiating the transition to a planktonic state (Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro 7, 263-73 (2009)). This signaling pathway also plays an important role in controlling the virulence response in many organisms. c-di-GMP has an inhibitory effect on many virulence genes. Levels of c-di-GMP are often decreased during infection, allowing the bacterium to express virulence factors necessary to survive in the host (Tamayo, R., Pratt, J. T. & Camilli, A. Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu. Rev. Microbiol. 61, 131-48 (2007)). c-di-GMP is also involved in broader signaling pathways, as it interacts with both the quorum sensing and cAMP signaling pathways, underscoring the importance and widespread effects of this second messenger (Waters, C. M., Lu, W., Rabinowitz, J. D. & Bassler, B. Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT. Journal of Bacteriology 190, 2527-36 (2008); Fong, J. C. & Yildiz, F. Interplay between cyclic AMP-cyclic AMP receptor protein and cyclic di-GMP signaling in Vibrio cholerae biofilm formation. Journal of Bacteriology 190, 6646-59 (2008)).

Despite many advances in understanding the effects of c-di-GMP signaling, the molecular view of how the interaction of this molecule with downstream targets leads to phenotypic changes is still incomplete (Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro 7, 263-73 (2009)). The PilZ domain family of proteins has been shown to bind c-di-GMP, and several examples of this protein family are important in processes regulated by c-di-GMP. Potential modes of action for the PilZ protein family have been suggested, although no specific mechanisms for signaling have emerged (Tamayo, R., Pratt, J. T. & Camilli, A. Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu. Rev. Microbiol. 61, 131-48 (2007); Jenal, U. & Malone, J. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet. 40, 385-407 (2006); Ryan, R., Fouhy, Y., Lucey, J. & Dow, J. M. Cyclic di-GMP signaling in bacteria: recent advances and new puzzles. Journal of Bacteriology 188, 8327-34 (2006); Ryjenkov, D. A., Simm, R., Romling, U. & Gomelsky, M. The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria. J Biol Chem 281, 30310-4 (2006); Christen, M. et al. DgrA is a member of a new family of cyclic diguanosine monophosphate receptors and controls flagellar motor function in Caulobacter crescentus. Proc Natl Acad Sci USA 104, 4112-7 (2007); Merighi, M., Lee, V., Hyodo, M., Hayakawa, Y. & Lory, S. The second messenger bis-(3′-5′)-cyclic-GMP and its PilZ domain-containing receptor Alg44 are required for alginate biosynthesis in Pseudomonas aeruginosa. Molecular Microbiology 65, 876-95 (2007); Pratt, J., Tamayo, R., Tischler, A. & Camilli, A. PilZ Domain Proteins Bind Cyclic Diguanylate and Regulate Diverse Processes in Vibrio cholerae. Journal of Biological Chemistry 282, 12860-12870 (2007)). Additionally, c-di-GMP binds to the protein PelD in Pseudomonas aeruginosa (Lee, V. et al. A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol Microbiol 65, 1474-1484 (2007)) and to the LapD protein in Pseudomonas fluorescens (Newell, P., Monds, R. & O'toole, G. LapD is a bis-(3′,5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0-1. Proc Natl Acad Sci USA 106, 3461-6 (2009)). These proteins are essential for biofilm formation, but details of how c-di-GMP binding mediates these processes are still missing (Lee, V. et al. A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol Microbiol 65, 1474-1484 (2007); Newell, P., Monds, R. & O'toole, G. LapD is a bis-(3′,5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0-1. Proc Natl Acad Sci USA 106, 3461-6 (2009)). c-di-GMP also binds to and affects the activity of the transcription factor FleQ in P. aeruginosa, but a full view of this interaction is currently unknown (Hickman, J. W. & Harwood, C. S. Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Molecular Microbiology 69, 376-89 (2008)).

Because the effects of c-di-GMP signaling are so widespread and too few protein receptors had been found to explain the global effects of c-di-GMP, it was proposed that an RNA may act as a downstream target in this signaling pathway (Tamayo, R., Pratt, J. T. & Camilli, A. Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu. Rev. Microbiol. 61, 131-48 (2007); Jenal, U. & Malone, J. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet. 40, 385-407 (2006)). A class of riboswitches was recently identified that binds c-di-GMP with an affinity of ˜1 nM and regulates gene expression in response to c-di-GMP binding (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). Riboswitches are RNA elements that reside in the 5′ untranslated region (UTR) of genes and modulate their expression using either transcriptional or translational mechanisms (Roth, A. & Breaker, R. R. The Structural and Functional Diversity of Metabolite-Binding Riboswitches. Annu Rev Biochem (2009)). The riboswitches responsive to c-di-GMP are found upstream of genes that code for the enzymes that synthesize and degrade c-di-GMP, diguanylate cyclases (DGCs) and c-di-GMP specific phosphodiesterases (PDEs), respectively, as well as genes involved in processes known to be regulated by c-di-GMP (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). This riboswitch class was named GEMM (genes for environment, membranes and motility) reflecting the types of genes to which it is often attached. Because the GEMM riboswitch binds c-di-GMP and regulates the expression of a broad spectrum of genes, it is a primary downstream target in the signaling pathway and is the first example of an RNA involved in intracellular signaling (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)).

Over 500 examples of this riboswitch have been found within the 5′ UTR of genes in many bacteria, including the causative agents of anthrax and cholera. Consistent with the observed role of c-di-GMP in biological function, these genes regulate processes including pilus assembly, motility, chemotaxis sensing, and pathogenesis (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). In Vibrio cholerae, c-di-GMP has been shown to influence the switch to the rugose phenotype, a form of V. cholerae that produces an exopolysaccharide matrix (EPS) and exhibits higher degrees of biofilm formation (Lim, B., Beyhan, S., Meir, J. & Yildiz, F. Cyclic-diGMP signal transduction systems in Vibrio cholerae: modulation of rugosity and biofilm formation. Molecular Microbiology 60, 331-48 (2006)). A GEMM riboswitch has been found upstream of the tfoX-like gene in this organism, which has been shown to be upregulated in rugose phenotype mutants. This RNA, Vc2, was found to be an “ON” switch, indicating that when c-di-GMP levels rise, greater expression of this gene would be predicted (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). Examples of “OFF” switches have also been found for this class of riboswitches (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). It is well established that c-di-GMP has an inhibitory effect on motility, suggesting that genes involved in this process must be downregulated under conditions where the concentration of c-di-GMP is high (Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro 7, 263-73 (2009)). In Clostridium difficile, a riboswitch has been found that functions as on “OFF” switch and controls genes involved in assembling the flagella of the bacterium (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)).

The GEMM riboswitch RNA was originally reported as an orphan domain for which the ligand was unknown (Weinberg, Z. et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 35, 4809-19 (2007)). The RNA was predicted to form a conserved secondary structure with two stems, P1 and P2 (now renamed P2 and P3 in FIG. 1), that are flanked by highly conserved nucleotides in the single stranded regions on both sides. These nucleotides are necessary for c-di-GMP binding but the bases closest to the helices are the only ones that are conserved (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008); Weinberg, Z. et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 35, 4809-19 (2007)). The majority of the nucleotides that showed modulations using in-line probing were seen in these flanking regions. From the change in cleavage at these positions upon c-di-GMP addition, it appeared that they became more structured in the ligand-bound form, suggesting a role in c-di-GMP binding (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). What is needed in the art is crystal structure of GEMM riboswitch to ascertain the binding of c-di-GMP to the GEMM riboswitch and to model bonding of compounds to GEMM riboswitches.

A. General Organization of Riboswitch RNAs

Bacterial riboswitch RNAs are genetic control elements that are located primarily within the 5′-untranslated region (5′-UTR) of the main coding region of a particular mRNA. Structural probing studies (discussed further below) reveal that riboswitch elements are generally composed of two domains: a natural aptamer (T. Hermann, D. J. Patel, Science 2000, 287, 820; L. Gold, et al., Annual Review of Biochemistry 1995, 64, 763) that serves as the ligand-binding domain, and an ‘expression platform’ that interfaces with RNA elements that are involved in gene expression (e.g. Shine-Dalgarno (SD) elements; transcription terminator stems). These conclusions are drawn from the observation that aptamer domains synthesized in vitro bind the appropriate ligand in the absence of the expression platform (see Examples 2, 3 and 6 of U.S. Application Publication No. 2005-0053951). Moreover, structural probing investigations indicate that the aptamer domain of most riboswitches adopts a particular secondary- and tertiary-structure fold when examined independently, that is essentially identical to the aptamer structure when examined in the context of the entire 5′ leader RNA. This indicates that, in many cases, the aptamer domain is a modular unit that folds independently of the expression platform (see Examples 2, 3 and 6 of U.S. Application Publication No. 2005-0053951).

Ultimately, the ligand-bound or unbound status of the aptamer domain is interpreted through the expression platform, which is responsible for exerting an influence upon gene expression. The view of a riboswitch as a modular element is further supported by the fact that aptamer domains are highly conserved amongst various organisms (and even between kingdoms as is observed for the TPP riboswitch), (N. Sudarsan, et al., RNA 2003, 9, 644) whereas the expression platform varies in sequence, structure, and in the mechanism by which expression of the appended open reading frame is controlled. For example, ligand binding to the TPP riboswitch of the tenA mRNA of B. subtilis causes transcription termination (A. S. Mironov, et al., Cell 2002, 111, 747). This expression platform is distinct in sequence and structure compared to the expression platform of the TPP riboswitch in the thiM mRNA from E. coli, wherein TPP binding causes inhibition of translation by a SD blocking mechanism (see Example 2 of U.S. Application Publication No. 2005-0053951). The TPP aptamer domain is easily recognizable and of near identical functional character between these two transcriptional units, but the genetic control mechanisms and the expression platforms that carry them out are very different.

Aptamer domains for riboswitch RNAs typically range from ˜70 to 170 nt in length (FIG. 11 of U.S. Application Publication No. 2005-0053951). This observation was somewhat unexpected given that in vitro evolution experiments identified a wide variety of small molecule-binding aptamers, which are considerably shorter in length and structural intricacy (T. Hermann, D. J. Patel, Science 2000, 287, 820; L. Gold, et al., Annual Review of Biochemistry 1995, 64, 763; M. Famulok, Current Opinion in Structural Biology 1999, 9, 324). Although the reasons for the substantial increase in complexity and information content of the natural aptamer sequences relative to artificial aptamers remains to be proven, this complexity is believed required to form RNA receptors that function with high affinity and selectivity. Apparent K_Dvalues for the ligand-riboswitch complexes range from low nanomolar to low micromolar. It is also worth noting that some aptamer domains, when isolated from the appended expression platform, exhibit improved affinity for the target ligand over that of the intact riboswitch. (˜10 to 100-fold) (see Example 2 of U.S. Application Publication No. 2005-0053951). Presumably, there is an energetic cost in sampling the multiple distinct RNA conformations required by a fully intact riboswitch RNA, which is reflected by a loss in ligand affinity. Since the aptamer domain must serve as a molecular switch, this might also add to the functional demands on natural aptamers that might help rationalize their more sophisticated structures.

B. Riboswitch Regulation of Transcription Termination in Bacteria

Bacteria primarily make use of two methods for termination of transcription. Certain genes incorporate a termination signal that is dependent upon the Rho protein, (J. P. Richardson, Biochimica et Biophysica Acta 2002, 1577, 251). while others make use of Rho-independent terminators (intrinsic terminators) to destabilize the transcription elongation complex (I. Gusarov, E. Nudler, Molecular Cell 1999, 3, 495; E. Nudler, M. E. Gottesman, Genes to Cells 2002, 7, 755). The latter RNA elements are composed of a GC-rich stem-loop followed by a stretch of 6-9 uridyl residues. Intrinsic terminators are widespread throughout bacterial genomes (F. Lillo, et al., 2002, 18, 971), and are typically located at the 3′-termini of genes or operons. Interestingly, an increasing number of examples are being observed for intrinsic terminators located within 5′-UTRs.

Amongst the wide variety of genetic regulatory strategies employed by bacteria there is a growing class of examples wherein RNA polymerase responds to a termination signal within the 5′-UTR in a regulated fashion (T. M. Henkin, Current Opinion in Microbiology 2000, 3, 149). During certain conditions the RNA polymerase complex is directed by external signals either to perceive or to ignore the termination signal. Although transcription initiation might occur without regulation, control over mRNA synthesis (and of gene expression) is ultimately dictated by regulation of the intrinsic terminator. Presumably, one of at least two mutually exclusive mRNA conformations results in the formation or disruption of the RNA structure that signals transcription termination. A trans-acting factor, which in some instances is a RNA (F. J. Grundy, et al., Proceedings of the National Academy of Sciences of the United States of America 2002, 99, 11121; T. M. Henkin, C. Yanofsky, Bioessays 2002, 24, 700) and in others is a protein (J. Stulke, Archives of Microbiology 2002, 177, 433), is generally required for receiving a particular intracellular signal and subsequently stabilizing one of the RNA conformations. Riboswitches offer a direct link between RNA structure modulation and the metabolite signals that are interpreted by the genetic control machinery.

Riboswitches must be capable of discriminating against compounds related to their natural ligands to prevent undesirable regulation of metabolic genes. However, it is possible to generate analogs that trigger riboswitch function and inhibit bacterial growth, as has been demonstrated for riboswitches that normally respond to lysine (Sudarsan 2003) and thiamine pyrophosphate (Sudarsan 2006).

Disclosed is the crystal structure of a GEMM riboswitch from V. cholerae bound to c-di-GMP. The crystal structure shows that the RNA binds the ligand within a three helix junction that involves base pairing and extensive base stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to the both the bases and the backbone. Also disclosed are GEMM riboswitches engineered to preferentially bind the signaling molecule c-di-AMP over c-di-GMP. This indicates that the mechanism by which c-di-GMP binding controls gene expression is through the stabilization of the P1 helix, illustrating a direct mode of action for c-di-GMP.

Also disclosed are the crystalline atomic structures of GEMM riboswitches and models of such structures. For example, disclosed is the atomic structure of a GEMM riboswitch comprising an atomic structure comprising the atomic coordinates listed in Table 2, the atomic structure of the active site and binding pocket as depicted in FIG. 1, and the atomic coordinates of the active site and binding pocket depicted in FIG. 1 contained within Table 2. The atomic coordinates, and the structure defined by the atomic coordinates, of the binding pocket depicted in FIG. 1 contained within Table 2 can be referred to herein as the binding pocket atomic structure. The atomic coordinates, and the structure defined by the atomic coordinates, of the active site depicted in FIG. 1 contained within Table 2 can be referred to herein as the active site atomic structure. These structures are useful, for example, in modeling and assessing the interaction of a GEMM riboswitch with a binding ligand. They are also useful in methods of identifying compounds that interact with the GEMM riboswitch. Any useful portion of the structure can be used for purposes and modeling as described herein. In particular, the active site or binding pocket atomic structure, with or without additional surrounding structure, can be modeled and used in the disclosed methods.

Also disclosed are compositions and methods for selecting and identifying compounds that can activate, deactivate or block a GEMM riboswitch. Activation of a GEMM riboswitch refers to the change in state of the riboswitch upon binding of a trigger molecule. A GEMM riboswitch can be activated by compounds other than the trigger molecule and in ways other than binding of a trigger molecule. The term trigger molecule is used herein to refer to molecules and compounds that can activate a riboswitch. This includes the natural or normal trigger molecule for the riboswitch and other compounds that can activate the riboswitch. Natural or normal trigger molecules are the trigger molecule for a given riboswitch in nature or, in the case of some non-natural riboswitches, the trigger molecule for which the riboswitch was designed or with which the riboswitch was selected (as in, for example, in vitro selection or in vitro evolution techniques). Non-natural trigger molecules can be referred to as non-natural trigger molecules.

Deactivation of a riboswitch refers to the change in state of the GEMM riboswitch when the trigger molecule is not bound. A GEMM riboswitch can be deactivated by binding of compounds other than the trigger molecule and in ways other than removal of the trigger molecule. Blocking of a GEMM riboswitch refers to a condition or state of the riboswitch where the presence of the trigger molecule does not activate the riboswitch. Activation of a GEMM riboswitch can be assessed in any suitable manner. For example, the GEMM riboswitch can be linked to a reporter RNA and expression, expression level, or change in expression level of the reporter RNA can be measured in the presence and absence of the test compound. As another example, the GEMM riboswitch can include a conformation dependent label, the signal from which changes depending on the activation state of the GEMM riboswitch. Such a riboswitch preferably uses an aptamer domain from or derived from a naturally occurring riboswitch. As can be seen, assessment of activation of a riboswitch can be performed with the use of a control assay or measurement or without the use of a control assay or measurement. Methods for identifying compounds that deactivate a riboswitch can be performed in analogous ways.

It is to be understood that the disclosed crystal structures, methods and compositions are not limited to specific examples unless otherwise specified, and, as such, can vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.

Materials

Disclosed are materials, compositions, and components that can be used for, can be used in conjunction with, can be used in preparation for, or are products of the disclosed crystal structures, methods and compositions. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference to each of various individual and collective combinations and permutation of these compounds can not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a riboswitch or aptamer domain is disclosed and discussed and a number of modifications that can be made to a number of molecules including the riboswitch or aptamer domain are discussed, each and every combination and permutation of riboswitch or aptamer domain and the modifications that are possible are specifically contemplated unless specifically indicated to the contrary. Thus, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited, each is individually and collectively contemplated. Thus, in this example, each of the combinations A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. Likewise, any subset or combination of these is also specifically contemplated and disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E are specifically contemplated and should be considered disclosed from disclosure of A, B, and C; D, E, and F; and the example combination A-D. This concept applies to all aspects of this application including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods, and that each such combination is specifically contemplated and should be considered disclosed.

A. Riboswitches

Riboswitches are expression control elements that are part of an RNA molecule to be expressed and that change state when bound by a trigger molecule. Riboswitches typically can be dissected into two separate domains: one that selectively binds the target (aptamer domain) and another that influences genetic control (expression platform domain). It is the dynamic interplay between these two domains that results in metabolite-dependent allosteric control of gene expression. Disclosed are isolated and recombinant riboswitches, recombinant constructs containing such riboswitches, heterologous sequences operably linked to such riboswitches, and cells and transgenic organisms harboring such riboswitches, riboswitch recombinant constructs, and riboswitches operably linked to heterologous sequences. The heterologous sequences can be, for example, sequences encoding proteins or peptides of interest, including reporter proteins or peptides. Preferred riboswitches are, or are derived from, naturally occurring riboswitches.

The disclosed riboswitches, including the derivatives and recombinant forms thereof, generally can be from any source, including naturally occurring riboswitches and riboswitches designed de novo. Any such riboswitches can be used in or with the disclosed methods. However, different types of riboswitches can be defined and some such sub-types can be useful in or with particular methods (generally as described elsewhere herein). Types of riboswitches include, for example, naturally occurring riboswitches, derivatives and modified forms of naturally occurring riboswitches, chimeric riboswitches, and recombinant riboswitches. A naturally occurring riboswitch is a riboswitch having the sequence of a riboswitch as found in nature. Such a naturally occurring riboswitch can be an isolated or recombinant form of the naturally occurring riboswitch as it occurs in nature. That is, the riboswitch has the same primary structure but has been isolated or engineered in a new genetic or nucleic acid context. Chimeric riboswitches can be made up of, for example, part of a riboswitch of any or of a particular class or type of riboswitch and part of a different riboswitch of the same or of any different class or type of riboswitch; part of a riboswitch of any or of a particular class or type of riboswitch and any non-riboswitch sequence or component. Recombinant riboswitches are riboswitches that have been isolated or engineered in a new genetic or nucleic acid context.

Riboswitches can have single or multiple aptamer domains. Aptamer domains in riboswitches having multiple aptamer domains can exhibit cooperative binding of trigger molecules or can not exhibit cooperative binding of trigger molecules (that is, the aptamers need not exhibit cooperative binding). In the latter case, the aptamer domains can be said to be independent binders. Riboswitches having multiple aptamers can have one or multiple expression platform domains. For example, a riboswitch having two aptamer domains that exhibit cooperative binding of their trigger molecules can be linked to a single expression platform domain that is regulated by both aptamer domains. Riboswitches having multiple aptamers can have one or more of the aptamers joined via a linker. Where such aptamers exhibit cooperative binding of trigger molecules, the linker can be a cooperative linker.

Aptamer domains can be said to exhibit cooperative binding if they have a Hill coefficient n between x and x−1, where x is the number of aptamer domains (or the number of binding sites on the aptamer domains) that are being analyzed for cooperative binding. Thus, for example, a riboswitch having two aptamer domains (such as glycine-responsive riboswitches) can be said to exhibit cooperative binding if the riboswitch has Hill coefficient between 2 and 1. It should be understood that the value of x used depends on the number of aptamer domains being analyzed for cooperative binding, not necessarily the number of aptamer domains present in the riboswitch. This makes sense because a riboswitch can have multiple aptamer domains where only some exhibit cooperative binding.

Disclosed are chimeric riboswitches containing heterologous aptamer domains and expression platform domains. That is, chimeric riboswitches are made up an aptamer domain from one source and an expression platform domain from another source. The heterologous sources can be from, for example, different specific riboswitches, different types of riboswitches, or different classes of riboswitches. The heterologous aptamers can also come from non-riboswitch aptamers. The heterologous expression platform domains can also come from non-riboswitch sources.

Modified or derivative riboswitches can be produced using in vitro selection and evolution techniques. In general, in vitro evolution techniques as applied to riboswitches involve producing a set of variant riboswitches where part(s) of the riboswitch sequence is varied while other parts of the riboswitch are held constant. Activation, deactivation or blocking (or other functional or structural criteria) of the set of variant riboswitches can then be assessed and those variant riboswitches meeting the criteria of interest are selected for use or further rounds of evolution. Useful base riboswitches for generation of variants are the specific and consensus riboswitches disclosed herein. Consensus riboswitches can be used to inform which part(s) of a riboswitch to vary for in vitro selection and evolution.

Also disclosed are modified riboswitches with altered regulation. The regulation of a riboswitch can be altered by operably linking an aptamer domain to the expression platform domain of the riboswitch (which is a chimeric riboswitch). The aptamer domain can then mediate regulation of the riboswitch through the action of, for example, a trigger molecule for the aptamer domain. Aptamer domains can be operably linked to expression platform domains of riboswitches in any suitable manner, including, for example, by replacing the normal or natural aptamer domain of the riboswitch with the new aptamer domain. Generally, any compound or condition that can activate, deactivate or block the riboswitch from which the aptamer domain is derived can be used to activate, deactivate or block the chimeric riboswitch.

Also disclosed are inactivated riboswitches. Riboswitches can be inactivated by covalently altering the riboswitch (by, for example, crosslinking parts of the riboswitch or coupling a compound to the riboswitch). Inactivation of a riboswitch in this manner can result from, for example, an alteration that prevents the trigger molecule for the riboswitch from binding, that prevents the change in state of the riboswitch upon binding of the trigger molecule, or that prevents the expression platform domain of the riboswitch from affecting expression upon binding of the trigger molecule.

Also disclosed are biosensor riboswitches. Biosensor riboswitches are engineered riboswitches that produce a detectable signal in the presence of their cognate trigger molecule. Useful biosensor riboswitches can be triggered at or above threshold levels of the trigger molecules. Biosensor riboswitches can be designed for use in vivo or in vitro. For example, biosensor riboswitches operably linked to a reporter RNA that encodes a protein that serves as or is involved in producing a signal can be used in vivo by engineering a cell or organism to harbor a nucleic acid construct encoding the riboswitch/reporter RNA. An example of a biosensor riboswitch for use in vitro is a riboswitch that includes a conformation dependent label, the signal from which changes depending on the activation state of the riboswitch. Such a biosensor riboswitch preferably uses an aptamer domain from or derived from a naturally occurring riboswitch. Biosensor riboswitches can be used in various situations and platforms. For example, biosensor riboswitches can be used with solid supports, such as plates, chips, strips and wells.

Also disclosed are modified or derivative riboswitches that recognize new trigger molecules. New riboswitches and/or new aptamers that recognize new trigger molecules can be selected for, designed or derived from known riboswitches. This can be accomplished by, for example, producing a set of aptamer variants in a riboswitch, assessing the activation of the variant riboswitches in the presence of a compound of interest, selecting variant riboswitches that were activated (or, for example, the riboswitches that were the most highly or the most selectively activated), and repeating these steps until a variant riboswitch of a desired activity, specificity, combination of activity and specificity, or other combination of properties results.

In general, any aptamer domain can be adapted for use with any expression platform domain by designing or adapting a regulated strand in the expression platform domain to be complementary to the control strand of the aptamer domain. Alternatively, the sequence of the aptamer and control strands of an aptamer domain can be adapted so that the control strand is complementary to a functionally significant sequence in an expression platform. For example, the control strand can be adapted to be complementary to the Shine-Dalgarno sequence of an RNA such that, upon formation of a stem structure between the control strand and the SD sequence, the SD sequence becomes inaccessible to ribosomes, thus reducing or preventing translation initiation. Note that the aptamer strand would have corresponding changes in sequence to allow formation of a P1 stem in the aptamer domain. In the case of riboswitches having multiple aptamers exhibiting cooperative binding, one the P1 stem of the activating aptamer (the aptamer that interacts with the expression platform domain) need be designed to form a stem structure with the SD sequence.

As another example, a transcription terminator can be added to an RNA molecule (most conveniently in an untranslated region of the RNA) where part of the sequence of the transcription terminator is complementary to the control strand of an aptamer domain (the sequence will be the regulated strand). This will allow the control sequence of the aptamer domain to form alternative stem structures with the aptamer strand and the regulated strand, thus either forming or disrupting a transcription terminator stem upon activation or deactivation of the riboswitch. Any other expression element can be brought under the control of a riboswitch by similar design of alternative stem structures.

For transcription terminators controlled by riboswitches, the speed of transcription and spacing of the riboswitch and expression platform elements can be important for proper control. Transcription speed can be adjusted by, for example, including polymerase pausing elements (e.g., a series of uridine residues) to pause transcription and allow the riboswitch to form and sense trigger molecules.

Disclosed are regulatable gene expression constructs comprising a nucleic acid molecule encoding an RNA comprising a riboswitch operably linked to a coding region, wherein the riboswitch regulates expression of the RNA, wherein the riboswitch and coding region are heterologous. The riboswitch can comprise an aptamer domain and an expression platform domain, wherein the aptamer domain and the expression platform domain are heterologous. The riboswitch can comprise an aptamer domain and an expression platform domain, wherein the aptamer domain comprises a P1 stem, wherein the P1 stem comprises an aptamer strand and a control strand, wherein the expression platform domain comprises a regulated strand, wherein the regulated strand, the control strand, or both have been designed to form a stem structure. The riboswitch can comprise two or more aptamer domains and an expression platform domain, wherein at least one of the aptamer domains and the expression platform domain are heterologous. The riboswitch can comprise two or more aptamer domains and an expression platform domain, wherein at least one of the aptamer domains comprises a P1 stem, wherein the P1 stem comprises an aptamer strand and a control strand, wherein the expression platform domain comprises a regulated strand, wherein the regulated strand, the control strand, or both have been designed to form a stem structure. For GEMM riboswitches of the type the crystal structure of which is disclosed herein, the 5′ sequences that participate in the P1 stem can be considered part of the aptamer domain and/or can be considered a control strand. The 3′ sequences that participate in the P1 stem can be considered part of the expression platform domain and/or can be considered a regulated strand.

1. Aptamer Domains

Aptamers are nucleic acid segments and structures that can bind selectively to particular compounds and classes of compounds. Riboswitches have aptamer domains that, upon binding of a trigger molecule result in a change in the state or structure of the riboswitch. In functional riboswitches, the state or structure of the expression platform domain linked to the aptamer domain changes when the trigger molecule binds to the aptamer domain. Aptamer domains of riboswitches can be derived from any source, including, for example, natural aptamer domains of riboswitches, artificial aptamers, engineered, selected, evolved or derived aptamers or aptamer domains. Aptamers in riboswitches generally have at least one portion that can interact, such as by forming a stem structure, with a portion of the linked expression platform domain. This stem structure will either form or be disrupted upon binding of the trigger molecule.

Consensus aptamer domains of a variety of natural riboswitches are shown in FIG. 11 of U.S. Application Publication No. 2005-0053951 and elsewhere herein. These aptamer domains (including all of the direct variants embodied therein) can be used in riboswitches. The consensus sequences and structures indicate variations in sequence and structure. Aptamer domains that are within the indicated variations are referred to herein as direct variants. These aptamer domains can be modified to produce modified or variant aptamer domains. Conservative modifications include any change in base paired nucleotides such that the nucleotides in the pair remain complementary. Moderate modifications include changes in the length of stems or of loops (for which a length or length range is indicated) of less than or equal to 20% of the length range indicated. Loop and stem lengths are considered to be “indicated” where the consensus structure shows a stem or loop of a particular length or where a range of lengths is listed or depicted. Moderate modifications include changes in the length of stems or of loops (for which a length or length range is not indicated) of less than or equal to 40% of the length range indicated. Moderate modifications also include and functional variants of unspecified portions of the aptamer domain.

The P1 stem and its constituent strands can be modified in adapting aptamer domains for use with expression platforms and RNA molecules. Such modifications, which can be extensive, are referred to herein as P1 modifications. P1 modifications include changes to the sequence and/or length of the P1 stem of an aptamer domain.

Aptamer domains of the disclosed riboswitches can also be used for any other purpose, and in any other context, as aptamers. For example, aptamers can be used to control ribozymes, other molecular switches, and any RNA molecule where a change in structure can affect function of the RNA.

2. Expression Platform Domains

Expression platform domains are a part of riboswitches that affect expression of the RNA molecule that contains the riboswitch. Expression platform domains generally have at least one portion that can interact, such as by forming a stem structure, with a portion of the linked aptamer domain. This stem structure will either form or be disrupted upon binding of the trigger molecule. The stem structure generally either is, or prevents formation of, an expression regulatory structure. An expression regulatory structure is a structure that allows, prevents, enhances or inhibits expression of an RNA molecule containing the structure. Examples include Shine-Dalgarno sequences, initiation codons, transcription terminators, and stability and processing signals.

B. Trigger Molecules

Trigger molecules are molecules and compounds that can activate a riboswitch. This includes the natural or normal trigger molecule for the riboswitch and other compounds that can activate the riboswitch. Natural or normal trigger molecules are the trigger molecule for a given riboswitch in nature or, in the case of some non-natural riboswitches, the trigger molecule for which the riboswitch was designed or with which the riboswitch was selected (as in, for example, in vitro selection or in vitro evolution techniques).

C. Cyclic di-GMP Riboswitch (GEMM Motif)

The disclosed GEMM riboswitch binds c-di-GMP at the junction of three helices. The predicted secondary structure included two stems and conserved but unpaired nucleotides on both the 5′ and 3′ ends. Additional unconserved residues on both ends were required for binding and were observed to become more structured upon ligand binding but were not predicted to participate in secondary structure formation (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). The crystal structure reveals that these 5′ and 3′ flanking residues form an additional helix that includes a canonical base pair with c-di-GMP (FIG. 1). This new helix has been named P1 and the two original helices have been renamed P2 and P3. When the alignment of GEMM riboswitch sequences was reexamined, potential for similar P1 helices was observed in many examples, but was not conserved in sequence, length, or bulges, explaining why it was not found in the initial bioinformatics study. c-di-GMP binds within the three helix junction formed between P1, P2 and P3. Stems P2 and P3 are parallel to each other and are aligned via a tetraloop receptor interaction between a tetraloop in P2 and its receptor in P3. The helical juxtaposition is further stabilized by a phylogenetically conserved but structurally isolated Watson-Crick base pair between bulged resides in each helix. C44 in P2 base pairs with G83 in P3. The extensive interaction network between P2 and P3 suggests that the majority of the aptamer does not change upon ligand binding. This is consistent with the absence of structural modulation in either the P2 or P3 helix as monitored by in line probing.

The c-di-GMP binding pocket is composed of residues from P1 and P2 as well as the J1/2 and J2/3 regions (FIG. 1). c-di-GMP is recognized by the GEMM riboswitch by both Watson-Crick base pairing and contacts to the Hoogsteen face. Additionally, the sugar and phosphate moieties are recognized by hydrogen bonding interactions and contacts with metals. The two guanine bases are vertically aligned with respect to one another and participate in extensive stacking interactions with the riboswitch RNA and one another.

The two guanine bases of c-di-GMP are asymmetrically recognized via specific base pair interactions. The top guanosine, G_α, forms a Hoogsteen pair with G20, the first unpaired nucleotide on the 5′ end of P2 (FIG. 2C). The O6 of G_α hydrogen bonds with the exocyclic amine of G20, and the G_αN7 forms a hydrogen bond with N1 of G20. Additionally, N2 of G_αforms a hydrogen bond with the 3′ OH of A48. Interestingly, the Watson-Crick surface of G_αis not recognized, but instead faces into a large, solvent accessible cavity formed by the junction of the P2 and P3 helices.

The second guanosine of c-di-GMP, G_β, forms a standard Watson-Crick base pair with C92, a highly conserved nucleotide 3′ of P3 (FIG. 2D). The interaction is further supported by a hydrogen bond between the 2′ OH of A47 and the O6 of G_β. This RNA-ligand base pair begins P1, initiating the formation of a helix not predicted in the secondary structure. Including the c-di-GMP/C92 pair, this structure reveals a P1 helix 5 base pairs in length. Inspection of the full length riboswitch sequence suggests that an additional three base pairs could be present in solution, but were not seen here due to the length of the RNA used and the fact that the 5′ end residues were involved in crystal packing interactions.

In addition to hydrogen bonding contacts, the two bases of c-di-GMP participate in an extensive base stacking network that bridges the P1 and P3 helical stacks. G_αand G_βdo not stack directly on each other. Instead A47, a highly conserved base in the J2/3 segment, stacks directly between the two guanine bases (FIGS. 2A and 2B). The result is a continuous three base stack between G_α, A47, and G_β. The stacking interface continues with the G21/C46 base pair above G_αand the G14/C93 base pair below G_β. These interactions could provide the stabilizing contacts necessary to nucleate formation of the P1 helix.

The sugar-phosphate backbone of c-di-GMP is recognized by hydrogen bonding interactions and metal ions, but like the bases, the two phosphates of the symmetric ligand are recognized asymmetrically (FIG. 2E). The phosphate 5′ of G_αis extensively contacted by both a hydrogen bond to the exocyclic amine of A47 and an iridium hexamine. This is an outer sphere contact to a tightly bound, fully hydrated metal ion. The phosphate 5′ of G_β, appears to form contacts with one magnesium and a water molecule. In this case, the phosphate is making an inner sphere contact to the metal. The water molecule appears to satisfy a second ligand for this metal, and forms a hydrogen bond to one of the phosphate oxygens as well. The other ligands of this metal are most likely water molecules as it is solvent exposed and no RNA is at a close enough distance. In the experimental MAD electron density, strong density is observed for c-di-GMP and the metal recognizing the first phosphate. This peak is also observed in native diffraction data. However, only a small peak (˜2σ) is seen for the metal recognizing the second phosphate (FIG. 2F). This may indicate that this metal it not as tightly bound or that the metal is not as localized. This difference in recognition of the two phosphates is an area that could be exploited in the future when designing inhibitors. The 2′-OH of the sugar of G_αis contacted by a non-bridging phosphate oxygen of A47 and the 2′-OH of the sugar of G_β forms a hydrogen bond with the exocyclic amine of A18.

D. Constructs, Vectors and Expression Systems The disclosed GEMM riboswitches can be used with any suitable expression system. Recombinant expression is usefully accomplished using a vector, such as a plasmid. The vector can include a promoter operably linked to riboswitch-encoding sequence and RNA to be expression (e.g., RNA encoding a protein). The vector can also include other elements required for transcription and translation. As used herein, vector refers to any carrier containing exogenous DNA. Thus, vectors are agents that transport the exogenous nucleic acid into a cell without degradation and include a promoter yielding expression of the nucleic acid in the cells into which it is delivered. Vectors include but are not limited to plasmids, viral nucleic acids, viruses, phage nucleic acids, phages, cosmids, and artificial chromosomes. A variety of prokaryotic and eukaryotic expression vectors suitable for carrying riboswitch-regulated constructs can be produced. Such expression vectors include, for example, pET, pET3d, pCR2.1, pBAD, pUC, and yeast vectors. The vectors can be used, for example, in a variety of in vivo and in vitro situation.

Viral vectors include adenovirus, adeno-associated virus, herpes virus, vaccinia virus, polio virus, AIDS virus, neuronal trophic virus, Sindbis and other RNA viruses, including these viruses with the HIV backbone. Also useful are any viral families which share the properties of these viruses which make them suitable for use as vectors. Retroviral vectors, which are described in Verma (1985), include Murine Maloney Leukemia virus, MMLV, and retroviruses that express the desirable properties of MMLV as a vector. Typically, viral vectors contain, nonstructural early genes, structural late genes, an RNA polymerase III transcript, inverted terminal repeats necessary for replication and encapsidation, and promoters to control the transcription and replication of the viral genome. When engineered as vectors, viruses typically have one or more of the early genes removed and a gene or gene/promoter cassette is inserted into the viral genome in place of the removed viral DNA.

A “promoter” is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A “promoter” contains core elements required for basic interaction of RNA polymerase and transcription factors and can contain upstream elements and response elements.

“Enhancer” generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5′ (Laimins, 1981) or 3′ (Lusky et al., 1983) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji et al., 1983) as well as within the coding sequence itself (Osborne et al., 1984). They are usually between 10 and 300 bp in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers, like promoters, also often contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human or nucleated cells) can also contain sequences necessary for the termination of transcription which can affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3′ untranslated regions also include transcription termination sites. It is preferred that the transcription unit also contain a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA. The identification and use of polyadenylation signals in expression constructs is well established. It is preferred that homologous polyadenylation signals be used in the transgene constructs.

The vector can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed. Preferred marker genes are the E. Coli lacZ gene which encodes β-galactosidase and green fluorescent protein.

In some embodiments the marker can be a selectable marker. When such selectable markers are successfully transferred into a host cell, the transformed host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes. The first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media. The second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, (Southern and Berg, 1982), mycophenolic acid, (Mulligan and Berg, 1980) or hygromycin (Sugden et al., 1985).

Gene transfer can be obtained using direct transfer of genetic material, in but not limited to, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, and artificial chromosomes, or via transfer of genetic material in cells or carriers such as cationic liposomes. Such methods are well known in the art and readily adaptable for use in the method described herein. Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53:83-88, (1993)). Appropriate means for transfection, including viral vectors, chemical transfectants, or physico-mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al., Science, 247, 1465-1468, (1990); and Wolff, J. A. Nature, 352, 815-818, (1991).

1. Viral Vectors

Preferred viral vectors are Adenovirus, Adeno-associated virus, Herpes virus, Vaccinia virus, Polio virus, AIDS virus, neuronal trophic virus, Sindbis and other RNA viruses, including these viruses with the HIV backbone. Also preferred are any viral families which share the properties of these viruses which make them suitable for use as vectors. Preferred retroviruses include Murine Maloney Leukemia virus, MMLV, and retroviruses that express the desirable properties of MMLV as a vector. Retroviral vectors are able to carry a larger genetic payload, i.e., a transgene or marker gene, than other viral vectors, and for this reason are a commonly used vector. However, they are not useful in non-proliferating cells. Adenovirus vectors are relatively stable and easy to work with, have high titers, and can be delivered in aerosol formulation, and can transfect non-dividing cells. Pox viral vectors are large and have several sites for inserting genes, they are thermostable and can be stored at room temperature. A preferred embodiment is a viral vector which has been engineered so as to suppress the immune response of the host organism, elicited by the viral antigens. Preferred vectors of this type will carry coding regions for Interleukin 8 or 10.

Viral vectors have higher transaction (ability to introduce genes) abilities than do most chemical or physical methods to introduce genes into cells. Typically, viral vectors contain, nonstructural early genes, structural late genes, an RNA polymerase III transcript, inverted terminal repeats necessary for replication and encapsidation, and promoters to control the transcription and replication of the viral genome. When engineered as vectors, viruses typically have one or more of the early genes removed and a gene or gene/promoter cassette is inserted into the viral genome in place of the removed viral DNA. Constructs of this type can carry up to about 8 kb of foreign genetic material. The necessary functions of the removed early genes are typically supplied by cell lines which have been engineered to express the gene products of the early genes in trans.

i. Retroviral Vectors

A retrovirus is an animal virus belonging to the virus family of Retroviridae, including any types, subfamilies, genus, or tropisms. Retroviral vectors, in general, are described by Verma, I. M., Retroviral vectors for gene transfer. In Microbiology-1985, American Society for Microbiology, pp. 229-232, Washington, (1985), which is incorporated by reference herein. Examples of methods for using retroviral vectors for gene therapy are described in U.S. Pat. Nos. 4,868,116 and 4,980,286; PCT applications WO 90/02806 and WO 89/07136; and Mulligan, (Science 260:926-932 (1993)); the teachings of which are incorporated herein by reference.

A retrovirus is essentially a package which has packed into it nucleic acid cargo. The nucleic acid cargo carries with it a packaging signal, which ensures that the replicated daughter molecules will be efficiently packaged within the package coat. In addition to the package signal, there are a number of molecules which are needed in cis, for the replication, and packaging of the replicated virus. Typically a retroviral genome, contains the gag, pol, and env genes which are involved in the making of the protein coat. It is the gag, pol, and env genes which are typically replaced by the foreign DNA that it is to be transferred to the target cell. Retrovirus vectors typically contain a packaging signal for incorporation into the package coat, a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich sequence 5′ to the 3′ LTR that serve as the priming site for the synthesis of the second strand of DNA synthesis, and specific sequences near the ends of the LTRs that enable the insertion of the DNA state of the retrovirus to insert into the host genome. The removal of the gag, pol, and env genes allows for about 8 kb of foreign sequence to be inserted into the viral genome, become reverse transcribed, and upon replication be packaged into a new retroviral particle. This amount of nucleic acid is sufficient for the delivery of a one to many genes depending on the size of each transcript. It is preferable to include either positive or negative selectable markers along with other genes in the insert.

Since the replication machinery and packaging proteins in most retroviral vectors have been removed (gag, pol, and env), the vectors are typically generated by placing them into a packaging cell line. A packaging cell line is a cell line which has been transfected or transformed with a retrovirus that contains the replication and packaging machinery, but lacks any packaging signal. When the vector carrying the DNA of choice is transfected into these cell lines, the vector containing the gene of interest is replicated and packaged into new retroviral particles, by the machinery provided in cis by the helper cell. The genomes for the machinery are not packaged because they lack the necessary signals.

ii. Adenoviral Vectors

The construction of replication-defective adenoviruses has been described (Berkner et al., J. Virology 61:1213-1220 (1987); Massie et al., Mol. Cell. Biol. 6:2872-2883 (1986); Haj-Ahmad et al., J. Virology 57:267-274 (1986); Davidson et al., J. Virology 61:1226-1239 (1987); Zhang “Generation and identification of recombinant adenovirus by liposome-mediated transfection and PCR analysis” BioTechniques 15:868-872 (1993)). The benefit of the use of these viruses as vectors is that they are limited in the extent to which they can spread to other cell types, since they can replicate within an initial infected cell, but are unable to form new infectious viral particles. Recombinant adenoviruses have been shown to achieve high efficiency gene transfer after direct, in vivo delivery to airway epithelium, hepatocytes, vascular endothelium, CNS parenchyma and a number of other tissue sites (Morsy, J. Clin. Invest. 92:1580-1586 (1993); Kirshenbaum, J. Clin. Invest. 92:381-387 (1993); Roessler, J. Clin. Invest. 92:1085-1092 (1993); Moullier, Nature Genetics 4:154-159 (1993); La Salle, Science 259:988-990 (1993); Gomez-Foix, J. Biol. Chem. 267:25129-25134 (1992); Rich, Human Gene Therapy 4:461-476 (1993); Zabner, Nature Genetics 6:75-83 (1994); Guzman, Circulation Research 73:1201-1207 (1993); Bout, Human Gene Therapy 5:3-10 (1994); Zabner, Cell 75:207-216 (1993); Caillaud, Eur. J. Neuroscience 5:1287-1291 (1993); and Ragot, J. Gen. Virology 74:501-507 (1993)). Recombinant adenoviruses achieve gene transduction by binding to specific cell surface receptors, after which the virus is internalized by receptor-mediated endocytosis, in the same manner as wild type or replication-defective adenovirus (Chardonnet and Dales, Virology 40:462-477 (1970); Brown and Burlingham, J. Virology 12:386-396 (1973); Svensson and Persson, J. Virology 55:442-449 (1985); Seth, et al., J. Virol. 51:650-655 (1984); Seth, et al., Mol. Cell. Biol. 4:1528-1533 (1984); Varga et al., J. Virology 65:6061-6070 (1991); Wickham et al., Cell 73:309-319 (1993)).

A preferred viral vector is one based on an adenovirus which has had the E1 gene removed and these virons are generated in a cell line such as the human 293 cell line. In another preferred embodiment both the E1 and E3 genes are removed from the adenovirus genome.

Another type of viral vector is based on an adeno-associated virus (AAV). This defective parvovirus is a preferred vector because it can infect many cell types and is nonpathogenic to humans. AAV type vectors can transport about 4 to 5 kb and wild type AAV is known to stably insert into chromosome 19. Vectors which contain this site specific integration property are preferred. An especially preferred embodiment of this type of vector is the P4.1 C vector produced by Avigen, San Francisco, Calif., which can contain the herpes simplex virus thymidine kinase gene, HSV-tk, and/or a marker gene, such as the gene encoding the green fluorescent protein, GFP.

The inserted genes in viral and retroviral usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and can contain upstream elements and response elements.

2. Viral Promoters and Enhancers

Preferred promoters controlling transcription from vectors in mammalian host cells can be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. beta actin promoter. The early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al., Nature, 273: 113 (1978)). The immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment (Greenway, P. J. et al., Gene 18: 355-360 (1982)). Of course, promoters from the host cell or related species also are useful herein.

Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5′ (Laimins, L. et al., Proc. Natl. Acad. Sci. 78: 993 (1981)) or 3′ (Lusky, M. L., et al., Mol. Cell. Bio. 3: 1108 (1983)) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji, J. L. et al., Cell 33: 729 (1983)) as well as within the coding sequence itself (Osborne, T. F., et al., Mol. Cell Bio. 4: 1293 (1984)). They are usually between 10 and 300 bp in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus. Preferred examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.

The promoter and/or enhancer can be specifically activated either by light or specific chemical events which trigger their function. Systems can be regulated by reagents such as tetracycline and dexamethasone. There are also ways to enhance viral vector gene expression by exposure to irradiation, such as gamma irradiation, or alkylating chemotherapy drugs.

It is preferred that the promoter and/or enhancer region be active in all eukaryotic cell types. A preferred promoter of this type is the CMV promoter (650 bases). Other preferred promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTF.

It has been shown that all specific regulatory elements can be cloned and used to construct expression vectors that are selectively expressed in specific cell types such as melanoma cells. The glial fibrillary acetic protein (GFAP) promoter has been used to selectively express genes in cells of glial origin.

3. Markers

The vectors can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed. Preferred marker genes are the E. Coli lacZ gene which encodes β-galactosidase and green fluorescent protein.

In some embodiments the marker can be a selectable marker. Examples of suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin. When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes. The first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media. Two examples are: CHO DHFR⁻cells and mouse LTK⁻ cells. These cells lack the ability to grow without the addition of such nutrients as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media. An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non-supplemented media.

The second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, (Southern P. and Berg, P., J. Molec. Appl. Genet. 1: 327 (1982)), mycophenolic acid, (Mulligan, R. C. and Berg, P. Science 209: 1422 (1980)) or hygromycin, (Sugden, B. et al., Mol. Cell. Biol. 5: 410-413 (1985)). The three examples employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively. Others include the neomycin analog G418 and puramycin.

E. Biosensor Riboswitches

Also disclosed are biosensor riboswitches. Biosensor riboswitches are engineered riboswitches that produce a detectable signal in the presence of their cognate trigger molecule. Useful biosensor riboswitches can be triggered at or above threshold levels of the trigger molecules. Biosensor riboswitches can be designed for use in vivo or in vitro. For example, GEMM biosensor riboswitches operably linked to a reporter RNA that encodes a protein that serves as or is involved in producing a signal can be used in vivo by engineering a cell or organism to harbor a nucleic acid construct encoding the GEMM riboswitch/reporter RNA. An example of a biosensor riboswitch for use in vitro is a riboswitch that includes a conformation dependent label, the signal from which changes depending on the activation state of the riboswitch. Such a biosensor riboswitch preferably uses an aptamer domain from or derived from a naturally occurring riboswitch, such as GEMM.

F. Reporter Proteins and Peptides

For assessing activation of a riboswitch, or for biosensor riboswitches, a reporter protein or peptide can be used. The reporter protein or peptide can be encoded by the RNA the expression of which is regulated by the riboswitch. The examples describe the use of some specific reporter proteins. The use of reporter proteins and peptides is well known and can be adapted easily for use with riboswitches. The reporter proteins can be any protein or peptide that can be detected or that produces a detectable signal. Preferably, the presence of the protein or peptide can be detected using standard techniques (e.g., radioimmunoassay, radio-labeling, immunoassay, assay for enzymatic activity, absorbance, fluorescence, luminescence, and Western blot). More preferably, the level of the reporter protein is easily quantifiable using standard techniques even at low levels. Useful reporter proteins include luciferases, green fluorescent proteins and their derivatives, such as firefly luciferase (FL) from Photinus pyralis, and Renilla luciferase (RL) from Renilla reniformis.

G. Conformation Dependent Labels

Conformation dependent labels refer to all labels that produce a change in fluorescence intensity or wavelength based on a change in the form or conformation of the molecule or compound (such as a riboswitch) with which the label is associated. Examples of conformation dependent labels used in the context of probes and primers include molecular beacons, Amplifluors, FRET probes, cleavable FRET probes, TaqMan probes, scorpion primers, fluorescent triplex oligos including but not limited to triplex molecular beacons or triplex FRET probes, fluorescent water-soluble conjugated polymers, PNA probes and QPNA probes. Such labels, and, in particular, the principles of their function, can be adapted for use with riboswitches. Several types of conformation dependent labels are reviewed in Schweitzer and Kingsmore, Curr. Opin. Biotech. 12:21-27 (2001).

Stem quenched labels, a form of conformation dependent labels, are fluorescent labels positioned on a nucleic acid such that when a stem structure forms a quenching moiety is brought into proximity such that fluorescence from the label is quenched. When the stem is disrupted (such as when a riboswitch containing the label is activated), the quenching moiety is no longer in proximity to the fluorescent label and fluorescence increases. Examples of this effect can be found in molecular beacons, fluorescent triplex oligos, triplex molecular beacons, triplex FRET probes, and QPNA probes, the operational principles of which can be adapted for use with riboswitches.

Stem activated labels, a form of conformation dependent labels, are labels or pairs of labels where fluorescence is increased or altered by formation of a stem structure. Stem activated labels can include an acceptor fluorescent label and a donor moiety such that, when the acceptor and donor are in proximity (when the nucleic acid strands containing the labels form a stem structure), fluorescence resonance energy transfer from the donor to the acceptor causes the acceptor to fluoresce. Stem activated labels are typically pairs of labels positioned on nucleic acid molecules (such as riboswitches) such that the acceptor and donor are brought into proximity when a stem structure is formed in the nucleic acid molecule. If the donor moiety of a stem activated label is itself a fluorescent label, it can release energy as fluorescence (typically at a different wavelength than the fluorescence of the acceptor) when not in proximity to an acceptor (that is, when a stem structure is not formed). When the stem structure forms, the overall effect would then be a reduction of donor fluorescence and an increase in acceptor fluorescence. FRET probes are an example of the use of stem activated labels, the operational principles of which can be adapted for use with riboswitches.

H. Detection Labels

To aid in detection and quantitation of riboswitch activation, deactivation or blocking, or expression of nucleic acids or protein produced upon activation, deactivation or blocking of riboswitches, detection labels can be incorporated into detection probes or detection molecules or directly incorporated into expressed nucleic acids or proteins. As used herein, a detection label is any molecule that can be associated with nucleic acid or protein, directly or indirectly, and which results in a measurable, detectable signal, either directly or indirectly. Many such labels are known to those of skill in the art. Examples of detection labels suitable for use in the disclosed method are radioactive isotopes, fluorescent molecules, phosphorescent molecules, enzymes, antibodies, and ligands.

Examples of suitable fluorescent labels include fluorescein isothiocyanate (FITC), 5,6-carboxymethyl fluorescein, Texas red, nitrobenz-2-oxa-1,3-diazol-4-yl (NBD), coumarin, dansyl chloride, rhodamine, amino-methyl coumarin (AMCA), Eosin, Erythrosin, BODIPY®, Cascade Blue®, Oregon Green®, pyrene, lissamine, xanthenes, acridines, oxazines, phycoerythrin, macrocyclic chelates of lanthanide ions such as Quantum Dye™, fluorescent energy transfer dyes, such as thiazole orange-ethidium heterodimer, and the cyanine dyes Cy3, Cy3.5, Cy5, Cy5.5 and Cy7. Examples of other specific fluorescent labels include 3-Hydroxypyrene 5,8,10-Tri Sulfonic acid, 5-Hydroxy Tryptamine (5-HT), Acid Fuchsin, Alizarin Complexon, Alizarin Red, Allophycocyanin, Aminocoumarin, Anthroyl Stearate, Astrazon Brilliant Red 4G, Astrazon Orange R, Astrazon Red 6B, Astrazon Yellow 7 GLL, Atabrine, Auramine, Aurophosphine, Aurophosphine G, BAO 9 (Bisaminophenyloxadiazole), BCECF, Berberine Sulphate, Bisbenzamide, Blancophor FFG Solution, Blancophor SV, Bodipy F1, Brilliant Sulphoflavin FF, Calcien Blue, Calcium Green, Calcofluor RW Solution, Calcofluor White, Calcophor White ABT Solution, Calcophor White Standard Solution, Carbostyryl, Cascade Yellow, Catecholamine, Chinacrine, Coriphosphine O, Coumarin-Phalloidin, CY3.1 8, CY5.1 8, CY7, Dans (1-Dimethyl Amino Naphaline 5 Sulphonic Acid), Dansa (Diamino Naphtyl Sulphonic Acid), Dansyl NH—CH3, Diamino Phenyl Oxydiazole (DAO), Dimethylamino-5-Sulphonic acid, Dipyrrometheneboron Difluoride, Diphenyl Brilliant Flavine 7GFF, Dopamine, Erythrosin ITC, Euchrysin, FIF (Formaldehyde Induced Fluorescence), Flazo Orange, Fluo 3, Fluorescamine, Fura-2, Genacryl Brilliant Red B, Genacryl Brilliant Yellow 10GF, Genacryl Pink 3G, Genacryl Yellow 5GF, Gloxalic Acid, Granular Blue, Haematoporphyrin, Indo-1, Intrawhite Cf Liquid, Leucophor PAF, Leucophor SF, Leucophor WS, Lissamine Rhodamine B200 (RD200), Lucifer Yellow CH, Lucifer Yellow VS, Magdala Red, Marina Blue, Maxilon Brilliant Flavin 10 GFF, Maxilon Brilliant Flavin 8 GFF, MPS (Methyl Green Pyronine Stilbene), Mithramycin, NBD Amine, Nitrobenzoxadidole, Noradrenaline, Nuclear Fast Red, Nuclear Yellow, Nylosan Brilliant Flavin E8G, Oxadiazole, Pacific Blue, Pararosaniline (Feulgen), Phorwite AR Solution, Phorwite BKL, Phorwite Rev, Phorwite RPA, Phosphine 3R, Phthalocyanine, Phycoerythrin R, Polyazaindacene Pontochrome Blue Black, Porphyrin, Primuline, Procion Yellow, Pyronine, Pyronine B, Pyrozal Brilliant Flavin 7GF, Quinacrine Mustard, Rhodamine 123, Rhodamine 5 GLD, Rhodamine 6G, Rhodamine B, Rhodamine B 200, Rhodamine B Extra, Rhodamine BB, Rhodamine BG, Rhodamine WT, Serotonin, Sevron Brilliant Red 2B, Sevron Brilliant Red 4G, Sevron Brilliant Red B, Sevron Orange, Sevron Yellow L, SITS (Primuline), SITS (Stilbene Isothiosulphonic acid), Stilbene, Snarf 1, sulpho Rhodamine B Can C, Sulpho Rhodamine G Extra, Tetracycline, Thiazine Red R, Thioflavin S, Thioflavin TCN, Thioflavin 5, Thiolyte, Thiozol Orange, Tinopol CBS, True Blue, Ultralite, Uranine B, Uvitex SFC, Xylene Orange, and XRITC.

Useful fluorescent labels are fluorescein (5-carboxyfluorescein-N-hydroxysuccinimide ester), rhodamine (5,6-tetramethyl rhodamine), and the cyanine dyes Cy3, Cy3.5, Cy5, Cy5.5 and Cy7. The absorption and emission maxima, respectively, for these fluors are: FITC (490 nm; 520 nm), Cy3 (554 nm; 568 nm), Cy3.5 (581 nm; 588 nm), Cy5 (652 nm: 672 nm), Cy5.5 (682 nm; 703 nm) and Cy7 (755 nm; 778 nm), thus allowing their simultaneous detection. Other examples of fluorescein dyes include 6-carboxyfluorescein (6-FAM), 2′,4′,1,4,-tetrachlorofluorescein (TET), 2′,4′,5′,7′,1,4-hexachlorofluorescein (HEX), 2′,7′-dimethoxy-4′,5′-dichloro-6-carboxyrhodamine (JOE), 2′-chloro-5′-fluoro-7′,8′-fused phenyl-1,4-dichloro-6-carboxyfluorescein (NED), and 2′-chloro-7′-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC). Fluorescent labels can be obtained from a variety of commercial sources, including Amersham Pharmacia Biotech, Piscataway, N.J.; Molecular Probes, Eugene, Oreg.; and Research Organics, Cleveland, Ohio.

Additional labels of interest include those that provide for signal only when the probe with which they are associated is specifically bound to a target molecule, where such labels include: “molecular beacons” as described in Tyagi & Kramer, Nature Biotechnology (1996) 14:303 and EP 0 070 685 B1. Other labels of interest include those described in U.S. Pat. No. 5,563,037; WO 97/17471 and WO 97/17076.

Labeled nucleotides are a useful form of detection label for direct incorporation into expressed nucleic acids during synthesis. Examples of detection labels that can be incorporated into nucleic acids include nucleotide analogs such as BrdUrd (5-bromodeoxyuridine, Hoy and Schimke, Mutation Research 290:217-230 (1993)), aminoallyldeoxyuridine (Henegariu et al., Nature Biotechnology 18:345-348 (2000)), 5-methylcytosine (Sano et al., Biochim. Biophys. Acta 951:157-165 (1988)), bromouridine (Wansick et al., J. Cell Biology 122:283-293 (1993)) and nucleotides modified with biotin (Langer et al., Proc. Natl. Acad. Sci. USA 78:6633 (1981)) or with suitable haptens such as digoxygenin (Kerkhof, Anal. Biochem. 205:359-364 (1992)). Suitable fluorescence-labeled nucleotides are Fluorescein-isothiocyanate-dUTP, Cyanine-3-dUTP and Cyanine-5-dUTP (Yu et al., Nucleic Acids Res., 22:3226-3232 (1994)). A preferred nucleotide analog detection label for DNA is BrdUrd (bromodeoxyuridine, BrdUrd, BrdU, BUdR, Sigma-Aldrich Co). Other useful nucleotide analogs for incorporation of detection label into DNA are AA-dUTP (aminoallyl-deoxyuridine triphosphate, Sigma-Aldrich Co.), and 5-methyl-dCTP (Roche Molecular Biochemicals). A useful nucleotide analog for incorporation of detection label into RNA is biotin-16-UTP (biotin-16-uridine-5′-triphosphate, Roche Molecular Biochemicals). Fluorescein, Cy3, and Cy5 can be linked to dUTP for direct labeling. Cy3.5 and Cy7 are available as avidin or anti-digoxygenin conjugates for secondary detection of biotin- or digoxygenin-labeled probes.

Detection labels that are incorporated into nucleic acid, such as biotin, can be subsequently detected using sensitive methods well-known in the art. For example, biotin can be detected using streptavidin-alkaline phosphatase conjugate (Tropix, Inc.), which is bound to the biotin and subsequently detected by chemiluminescence of suitable substrates (for example, chemiluminescent substrate CSPD: disodium, 3-(4-methoxyspiro-[1,2,-dioxetane-3-2′-(5′-chloro)tricyclo [3.3.1.1^3,7]decane]-4-yl)phenyl phosphate; Tropix, Inc.). Labels can also be enzymes, such as alkaline phosphatase, soybean peroxidase, horseradish peroxidase and polymerases, that can be detected, for example, with chemical signal amplification or by using a substrate to the enzyme which produces light (for example, a chemiluminescent 1,2-dioxetane substrate) or fluorescent signal.

Molecules that combine two or more of these detection labels are also considered detection labels. Any of the known detection labels can be used with the disclosed probes, tags, molecules and methods to label and detect activated or deactivated riboswitches or nucleic acid or protein produced in the disclosed methods. Methods for detecting and measuring signals generated by detection labels are also known to those of skill in the art. For example, radioactive isotopes can be detected by scintillation counting or direct visualization; fluorescent molecules can be detected with fluorescent spectrophotometers; phosphorescent molecules can be detected with a spectrophotometer or directly visualized with a camera; enzymes can be detected by detection or visualization of the product of a reaction catalyzed by the enzyme; antibodies can be detected by detecting a secondary detection label coupled to the antibody. As used herein, detection molecules are molecules which interact with a compound or composition to be detected and to which one or more detection labels are coupled.

I. Sequence Similarities

It is understood that as discussed herein the use of the terms homology and identity mean the same thing as similarity. Thus, for example, if the use of the word homology is used between two sequences (non-natural sequences, for example) it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences. Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not.

In general, it is understood that one way to define any known variants and derivatives or those that might arise, of the disclosed riboswitches, aptamers, expression platforms, genes and proteins herein, is through defining the variants and derivatives in terms of homology to specific known sequences. This identity of particular sequences disclosed herein is also discussed elsewhere herein. In general, variants of riboswitches, aptamers, expression platforms, genes and proteins herein disclosed typically have at least, about 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to a stated sequence or a native sequence. Those of skill in the art readily understand how to determine the homology of two proteins or nucleic acids, such as genes. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison can be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by inspection.

The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol. 183:281-306, 1989 which are herein incorporated by reference for at least material related to nucleic acid alignment. It is understood that any of the methods typically can be used and that in certain instances the results of these various methods can differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity.

For example, as used herein, a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above. For example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods. As another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using both the Zuker calculation method and the Pearson and Lipman calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by the Smith and Waterman calculation method, the Needleman and Wunsch calculation method, the Jaeger calculation methods, or any of the other calculation methods. As yet another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages).

J. Hybridization and Selective Hybridization

The term hybridization typically means a sequence driven interaction between at least two nucleic acid molecules, such as a primer or a probe and a riboswitch or a gene. Sequence driven interaction means an interaction that occurs between two nucleotides or nucleotide analogs or nucleotide derivatives in a nucleotide specific manner. For example, G interacting with C or A interacting with T are sequence driven interactions. Typically sequence driven interactions occur on the Watson-Crick face or Hoogsteen face of the nucleotide. The hybridization of two nucleic acids is affected by a number of conditions and parameters known to those of skill in the art. For example, the salt concentrations, pH, and temperature of the reaction all affect whether two nucleic acid molecules will hybridize.

Parameters for selective hybridization between two nucleic acid molecules are well known to those of skill in the art. For example, in some embodiments selective hybridization conditions can be defined as stringent hybridization conditions. For example, stringency of hybridization is controlled by both temperature and salt concentration of either or both of the hybridization and washing steps. For example, the conditions of hybridization to achieve selective hybridization can involve hybridization in high ionic strength solution (6×SSC or 6×SSPE) at a temperature that is about 12-25° C. below the Tm (the melting temperature at which half of the molecules dissociate from their hybridization partners) followed by washing at a combination of temperature and salt concentration chosen so that the washing temperature is about 5° C. to 20° C. below the Tm. The temperature and salt conditions are readily determined empirically in preliminary experiments in which samples of reference DNA immobilized on filters are hybridized to a labeled nucleic acid of interest and then washed under conditions of different stringencies. Hybridization temperatures are typically higher for DNA-RNA and RNA-RNA hybridizations. The conditions can be used as described above to achieve stringency, or as is known in the art (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989; Kunkel et al. Methods Enzymol. 1987:154:367, 1987 which is herein incorporated by reference for material at least related to hybridization of nucleic acids). A preferable stringent hybridization condition for a DNA:DNA hybridization can be at about 68° C. (in aqueous solution) in 6×SSC or 6×SSPE followed by washing at 68° C. Stringency of hybridization and washing, if desired, can be reduced accordingly as the degree of complementarity desired is decreased, and further, depending upon the G-C or A-T richness of any area wherein variability is searched for. Likewise, stringency of hybridization and washing, if desired, can be increased accordingly as homology desired is increased, and further, depending upon the G-C or A-T richness of any area wherein high homology is desired, all as known in the art.

Another way to define selective hybridization is by looking at the amount (percentage) of one of the nucleic acids bound to the other nucleic acid. For example, in some embodiments selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the limiting nucleic acid is bound to the non-limiting nucleic acid. Typically, the non-limiting nucleic acid is in for example, 10 or 100 or 1000 fold excess. This type of assay can be performed at under conditions where both the limiting and non-limiting nucleic acids are for example, 10 fold or 100 fold or 1000 fold below their k_d, or where only one of the nucleic acid molecules is 10 fold or 100 fold or 1000 fold or where one or both nucleic acid molecules are above their k_d.

Another way to define selective hybridization is by looking at the percentage of nucleic acid that gets enzymatically manipulated under conditions where hybridization is required to promote the desired enzymatic manipulation. For example, in some embodiments selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the nucleic acid is enzymatically manipulated under conditions which promote the enzymatic manipulation, for example if the enzymatic manipulation is DNA extension, then selective hybridization conditions would be when at least about 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the nucleic acid molecules are extended. Preferred conditions also include those suggested by the manufacturer or indicated in the art as being appropriate for the enzyme performing the manipulation.

Just as with homology, it is understood that there are a variety of methods herein disclosed for determining the level of hybridization between two nucleic acid molecules. It is understood that these methods and conditions can provide different percentages of hybridization between two nucleic acid molecules, but unless otherwise indicated meeting the parameters of any of the methods would be sufficient. For example if 80% hybridization was required and as long as hybridization occurs within the required parameters in any one of these methods it is considered disclosed herein.

It is understood that those of skill in the art understand that if a composition or method meets any one of these criteria for determining hybridization either collectively or singly it is a composition or method that is disclosed herein.

K. Nucleic Acids

There are a variety of molecules disclosed herein that are nucleic acid based, including, for example, riboswitches, aptamers, and nucleic acids that encode riboswitches and aptamers. The disclosed nucleic acids can be made up of for example, nucleotides, nucleotide analogs, or nucleotide substitutes. Non-limiting examples of these and other molecules are discussed herein. It is understood that for example, when a vector is expressed in a cell, that the expressed mRNA will typically be made up of A, C, G, and U. Likewise, it is understood that if a nucleic acid molecule is introduced into a cell or cell environment through for example exogenous delivery, it is advantageous that the nucleic acid molecule be made up of nucleotide analogs that reduce the degradation of the nucleic acid molecule in the cellular environment.

So long as their relevant function is maintained, riboswitches, aptamers, expression platforms and any other oligonucleotides and nucleic acids can be made up of or include modified nucleotides (nucleotide analogs). Many modified nucleotides are known and can be used in oligonucleotides and nucleic acids. A nucleotide analog is a nucleotide which contains some type of modification to either the base, sugar, or phosphate moieties. Modifications to the base moiety would include natural and synthetic modifications of A, C, G, and T/U as well as different purine or pyrimidine bases, such as uracil-5-yl, hypoxanthin-9-yl (I), and 2-aminoadenin-9-yl. A modified base includes but is not limited to 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Additional base modifications can be found for example in U.S. Pat. No. 3,687,808, Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B. ed., CRC Press, 1993. Certain nucleotide analogs, such as 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine can increase the stability of duplex formation. Other modified bases are those that function as universal bases. Universal bases include 3-nitropyrrole and 5-nitroindole. Universal bases substitute for the normal bases but have no bias in base pairing. That is, universal bases can base pair with any other base. Base modifications often can be combined with for example a sugar modification, such as 2′-O-methoxyethyl, to achieve unique properties such as increased duplex stability. There are numerous United States patents such as U.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; and 5,681,941, which detail and describe a range of base modifications. Each of these patents is herein incorporated by reference in its entirety, and specifically for their description of base modifications, their synthesis, their use, and their incorporation into oligonucleotides and nucleic acids.

Nucleotide analogs can also include modifications of the sugar moiety. Modifications to the sugar moiety would include natural modifications of the ribose and deoxyribose as well as synthetic modifications. Sugar modifications include but are not limited to the following modifications at the 2′ position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C1 to C10, alkyl or C2 to C10 alkenyl and alkynyl. 2′ sugar modifications also include but are not limited to —O[(CH₂)nO]mCH₃, —(CH₂)nOCH₃, —O(CH₂)nNH₂, —O(CH₂)nCH₃, —O(CH₂)n-ONH₂, and —O(CH₂)nON[(CH₂)nCH₃)]₂, where n and m are from 1 to about 10.

Other modifications at the 2′ position include but are not limited to: C1 to C10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. Similar modifications can also be made at other positions on the sugar, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide. Modified sugars would also include those that contain modifications at the bridging ring oxygen, such as CH₂and S. Nucleotide sugar analogs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. There are numerous United States patents that teach the preparation of such modified sugar structures such as U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, each of which is herein incorporated by reference in its entirety, and specifically for their description of modified sugar structures, their synthesis, their use, and their incorporation into nucleotides, oligonucleotides and nucleic acids.

Nucleotide analogs can also be modified at the phosphate moiety. Modified phosphate moieties include but are not limited to those that can be modified so that the linkage between two nucleotides contains a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonates including 3′-alkylene phosphonate and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates. It is understood that these phosphate or modified phosphate linkages between two nucleotides can be through a 3′-5′ linkage or a 2′-5′ linkage, and the linkage can contain inverted polarity such as 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free acid forms are also included. Numerous United States patents teach how to make and use nucleotides containing modified phosphates and include but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050, each of which is herein incorporated by reference its entirety, and specifically for their description of modified phosphates, their synthesis, their use, and their incorporation into nucleotides, oligonucleotides and nucleic acids.

It is understood that nucleotide analogs need only contain a single modification, but can also contain multiple modifications within one of the moieties or between different moieties.

Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize and hybridize to (base pair to) complementary nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid.

Nucleotide substitutes are nucleotides or nucleotide analogs that have had the phosphate moiety and/or sugar moieties replaced. Nucleotide substitutes do not contain a standard phosphorus atom. Substitutes for the phosphate can be for example, short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts. Numerous United States patents disclose how to make and use these types of phosphate replacements and include but are not limited to U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference its entirety, and specifically for their description of phosphate replacements, their synthesis, their use, and their incorporation into nucleotides, oligonucleotides and nucleic acids.

It is also understood in a nucleotide substitute that both the sugar and the phosphate moieties of the nucleotide can be replaced, by for example an amide type linkage (aminoethylglycine) (PNA). U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262 teach how to make and use PNA molecules, each of which is herein incorporated by reference. (See also Nielsen et al., Science 254:1497-1500 (1991)).

Oligonucleotides and nucleic acids can be comprised of nucleotides and can be made up of different types of nucleotides or the same type of nucleotides. For example, one or more of the nucleotides in an oligonucleotide can be ribonucleotides, 2′-O-methyl ribonucleotides, or a mixture of ribonucleotides and 2′-O-methyl ribonucleotides; about 10% to about 50% of the nucleotides can be ribonucleotides, 2′-O-methyl ribonucleotides, or a mixture of ribonucleotides and 2′-O-methyl ribonucleotides; about 50% or more of the nucleotides can be ribonucleotides, 2′-O-methyl ribonucleotides, or a mixture of ribonucleotides and 2′-O-methyl ribonucleotides; or all of the nucleotides are ribonucleotides, 2′-O-methyl ribonucleotides, or a mixture of ribonucleotides and 2′-O-methyl ribonucleotides. Such oligonucleotides and nucleic acids can be referred to as chimeric oligonucleotides and chimeric nucleic acids.

L. Solid Supports

Solid supports are solid-state substrates or supports with which molecules (such as trigger molecules) and riboswitches (or other components used in, or produced by, the disclosed methods) can be associated. Riboswitches and other molecules can be associated with solid supports directly or indirectly. For example, analytes (e.g., trigger molecules, test compounds) can be bound to the surface of a solid support or associated with capture agents (e.g., compounds or molecules that bind an analyte) immobilized on solid supports. As another example, riboswitches can be bound to the surface of a solid support or associated with probes immobilized on solid supports. An array is a solid support to which multiple riboswitches, probes or other molecules have been associated in an array, grid, or other organized pattern.

Solid-state substrates for use in solid supports can include any solid material with which components can be associated, directly or indirectly. This includes materials such as acrylamide, agarose, cellulose, nitrocellulose, glass, gold, polystyrene, polyethylene vinyl acetate, polypropylene, polymethacrylate, polyethylene, polyethylene oxide, polysilicates, polycarbonates, teflon, fluorocarbons, nylon, silicon rubber, polyanhydrides, polyglycolic acid, polylactic acid, polyorthoesters, functionalized silane, polypropylfumerate, collagen, glycosaminoglycans, and polyamino acids. Solid-state substrates can have any useful form including thin film, membrane, bottles, dishes, fibers, woven fibers, shaped polymers, particles, beads, microparticles, or a combination. Solid-state substrates and solid supports can be porous or non-porous. A chip is a rectangular or square small piece of material. Preferred forms for solid-state substrates are thin films, beads, or chips. A useful form for a solid-state substrate is a microtiter dish. In some embodiments, a multiwell glass slide can be employed.

An array can include a plurality of riboswitches, trigger molecules, other molecules, compounds or probes immobilized at identified or predefined locations on the solid support. Each predefined location on the solid support generally has one type of component (that is, all the components at that location are the same). Alternatively, multiple types of components can be immobilized in the same predefined location on a solid support. Each location will have multiple copies of the given components. The spatial separation of different components on the solid support allows separate detection and identification.

Although useful, it is not required that the solid support be a single unit or structure. A set of riboswitches, trigger molecules, other molecules, compounds and/or probes can be distributed over any number of solid supports. For example, at one extreme, each component can be immobilized in a separate reaction tube or container, or on separate beads or microparticles.

Methods for immobilization of oligonucleotides to solid-state substrates are well established. Oligonucleotides, including address probes and detection probes, can be coupled to substrates using established coupling methods. For example, suitable attachment methods are described by Pease et al., Proc. Natl. Acad. Sci. USA 91(11):5022-5026 (1994), and Khrapko et al., Mol Biol (Mosk) (USSR) 25:718-730 (1991). A method for immobilization of 3′-amine oligonucleotides on casein-coated slides is described by Stimpson et al., Proc. Natl. Acad. Sci. USA 92:6379-6383 (1995). A useful method of attaching oligonucleotides to solid-state substrates is described by Guo et al., Nucleic Acids Res. 22:5456-5465 (1994).

Each of the components (for example, riboswitches, trigger molecules, or other molecules) immobilized on the solid support can be located in a different predefined region of the solid support. The different locations can be different reaction chambers. Each of the different predefined regions can be physically separated from each other of the different regions. The distance between the different predefined regions of the solid support can be either fixed or variable. For example, in an array, each of the components can be arranged at fixed distances from each other, while components associated with beads will not be in a fixed spatial relationship. In particular, the use of multiple solid support units (for example, multiple beads) will result in variable distances.

Components can be associated or immobilized on a solid support at any density. Components can be immobilized to the solid support at a density exceeding 400 different components per cubic centimeter. Arrays of components can have any number of components. For example, an array can have at least 1,000 different components immobilized on the solid support, at least 10,000 different components immobilized on the solid support, at least 100,000 different components immobilized on the solid support, or at least 1,000,000 different components immobilized on the solid support.

M. Kits

The materials described above as well as other materials can be packaged together in any suitable combination as a kit useful for performing, or aiding in the performance of, the disclosed method. It is useful if the kit components in a given kit are designed and adapted for use together in the disclosed method. For example disclosed are kits for detecting compounds, the kit comprising one or more biosensor riboswitches. The kits also can contain reagents and labels for detecting activation of the riboswitches.

N. Mixtures

Disclosed are mixtures formed by performing or preparing to perform the disclosed method. For example, disclosed are mixtures comprising riboswitches and trigger molecules.

Whenever the method involves mixing or bringing into contact compositions or components or reagents, performing the method creates a number of different mixtures. For example, if the method includes 3 mixing steps, after each one of these steps a unique mixture is formed if the steps are performed separately. In addition, a mixture is formed at the completion of all of the steps regardless of how the steps were performed. The present disclosure contemplates these mixtures, obtained by the performance of the disclosed methods as well as mixtures containing any disclosed reagent, composition, or component, for example, disclosed herein.

O. Systems

Disclosed are systems useful for performing, or aiding in the performance of, the disclosed method. Systems generally comprise combinations of articles of manufacture such as structures, machines, devices, and the like, and compositions, compounds, materials, and the like. Such combinations that are disclosed or that are apparent from the disclosure are contemplated. For example, disclosed and contemplated are systems comprising biosensor riboswitches, a solid support and a signal-reading device.

P. Data Structures and Computer Control

Disclosed are data structures used in, generated by, or generated from, the disclosed method. Data structures generally are any form of data, information, and/or objects collected, organized, stored, and/or embodied in a composition or medium. Riboswitch structures and activation measurements stored in electronic form, such as in RAM or on a storage disk, is a type of data structure.

The disclosed method, or any part thereof or preparation therefor, can be controlled, managed, or otherwise assisted by computer control. Such computer control can be accomplished by a computer controlled process or method, can use and/or generate data structures, and can use a computer program. Such computer control, computer controlled processes, data structures, and computer programs are contemplated and should be understood to be disclosed herein.

Methods

Disclosed are methods of identifying compounds that activate, deactivate or block a riboswitch. For example, compounds that activate a riboswitch can be identified by bringing into contact a test compound and a riboswitch and assessing activation of the riboswitch. If the riboswitch is activated, the test compound is identified as a compound that activates the riboswitch. Activation of a riboswitch can be assessed in any suitable manner. For example, the riboswitch can be linked to a reporter RNA and expression, expression level, or change in expression level of the reporter RNA can be measured in the presence and absence of the test compound. As another example, the riboswitch can include a conformation dependent label, the signal from which changes depending on the activation state of the riboswitch. Such a riboswitch preferably uses an aptamer domain from or derived from a naturally occurring riboswitch. As can be seen, assessment of activation of a riboswitch can be performed with the use of a control assay or measurement or without the use of a control assay or measurement. Methods for identifying compounds that deactivate a riboswitch can be performed in analogous ways.

Identification of compounds that block a riboswitch can be accomplished in any suitable manner. For example, an assay can be performed for assessing activation or deactivation of a riboswitch in the presence of a compound known to activate or deactivate the riboswitch and in the presence of a test compound. If activation or deactivation is not observed as would be observed in the absence of the test compound, then the test compound is identified as a compound that blocks activation or deactivation of the riboswitch.

Compounds can also be identified using the atomic crystalline structure of a riboswitch. The atomic coordinates of the atomic structure of the GEMM riboswitch are listed in Table 2. The atomic structure of the active site and binding pocket as depicted in FIG. 1 and the atomic coordinates of the active site and binding pocket depicted in FIG. 1 contained within Table 2 can also be used. Compounds can be identified using the crystalline structure of a riboswitch by, for example, modeling the atomic structure of the riboswitch with a test compound; and determining if the test compound interacts with the riboswitch. This can be done by using a predicted minimum interaction energy, a predicted bind constant, a predicted dissociation constant, or a combination, for the test compound in the model of the riboswitch. Compounds can also be identified by, for example, assessing the fit between the riboswitch and a compound known to bind the riboswitch (such as the trigger molecule), identify sites where the compound can be changed with little or no obvious adverse effects on binding of the compound, and incorporating one or more such alterations to produce a new compound. The method of identifying compounds that interact with a riboswitch can also involve production of the compounds so identified.

Typically the method first utilizes a 3-dimensional structure of the riboswitch with a compound, also referred to as a “known compound” or “known target”. Any of the trigger molecules and compounds disclosed herein can be used as such a known compound. The structure of the riboswitch can be determined using any known means, such as crystallography or solution NMR spectroscopy. That structure can also be obtained through computer molecular modeling simulation programs, such as AutoDock. The methods can involve determining the amount of binding, such as determining the binding energy, between a riboswitch, and a potential compound for that riboswitch. An active compound is a compound that has some activity against a riboswitch, such as inhibiting the riboswitch's activity or enhancing the riboswitch's activity. In addition, the potential compound can be an analog, which has some structural relationship to a known compound for the molecule. Any of the trigger molecules, known compounds, and compounds disclosed herein can be used as the basis of or to derive a potential compound.

The identity or relationship of the structure, properties, interaction or binding parameters, and the like of the known compound and potential compound can be viewed in number of ways. For example, any of the measures or interaction parameters that can be measured or assessed using the structural model, and such measures and parameters obtained for a known compound and a potential compound can be compared. One can look at the identity between the entire known compound and the potential compound. One can also look at the identity between the potential compound, such as an analog, and the know compound only in the domain where the potential compound interacts with the riboswitch. One can also look at the identity between the potential compound and the known compound at the level of a sub-domain, such as only those moieties or atoms in the potential compound which are within 7 Å, 6 Å, 5 Å, 4 Å, 3 Å, or 2 Å of a moiety or atom which is in contact with the riboswitch in the known compound. Generally, the more specific the sub-domain the higher the identity will be between the moieties of the potential compound and the known compound. For example, there can be 30% or greater, 35% or greater, 40% or greater, 45% or greater, 50% or greater, 55% or greater, 60% or greater, 65% or greater, 70% or greater, 75% or greater, 80% or greater, 85% or greater, 90% or greater, 95% or greater identity between the known compound and potential compound as a whole, 50% or greater, 55% or greater, 60% or greater, 65% or greater, 70% or greater, 75% or greater, 80% or greater, 85% or greater, 90% or greater, 95% or greater identity between the binding domain of the known compound and the potential compound, and 70% or greater, 75% or greater, 80% or greater, 85% or greater, 90% or greater, 95% or greater identity between the moieties or atoms of the potential compound that correspond to the moieties or atoms of the known compound which are within 5 Å of a moiety or atom which interacts with the riboswitch. Another sub-domain is a sub-domain of moieties or atoms which actually contact the riboswitch. In this case the identity can be, for example, greater than 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or higher.

Typically, the potential compounds exist in a family of potential compounds, i.e. a set of analogs, all of which have some structural relationship to the known compound for the riboswitch. A family consisting of any number of members can be screened. The maximum number of members in the family is only limited by the amount of computer power available to screen each member in a desired amount of time. The methods can involve at least one template structure of the riboswitch and a target, often this would be with a known target. It is not required that this structure be existent, as it can be generated, in some cases during the disclosed methods, using standard structure determination techniques. It is preferred that a real structure exist at the time the methods are employed.

The methods can also involve modeling the structure of the potential compound, using information from the structure of the known compound. This modeling can be performed in any way, and as described herein.

The conformation and position of the potential compound can be held fixed during the calculations; that is, it can be assumed that the riboswitch binds in exactly the same orientation to the potential compound as it does to a known compound.

Then, a binding energy (or other property or parameter) can be determined between the riboswitch and the potential compound, and if the binding energy (or other property or parameter) meets certain criteria, then the potential compound can be designated as an actual compound, i.e. one that is likely to interact with the riboswitch. Although the following refers to the use of binding energy, it should be understood that any property or parameter involving the interaction or modeling of a compound and a riboswitch can be used. The criterion can be that the computed binding energy of the riboswitch with the potential compound is similar to, or more favorable than, the computed binding energy of the same riboswitch with a known compound. For example, an actual compound can be a compound where the computed binding energy as discussed herein is, for example, at least 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 101%, 102%, 103%, 104%, 105%, 106%, 107%, 108%, 109%, 110%, 120%, 130%, 140%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 600%, 700%, 800%, 900%, 1000%, or greater than that of the known compound binding energy. An actual compound can also be a compound which after ordering all potential compounds in terms of the strength of their binding energies, are the compounds which are in the top 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1% of computed binding strengths, of for example, a set of potential compounds where the set is at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 350, 400, 500, 700, or a 1000 potential compounds.

It is also understood that once a potential compound is identified, as disclosed herein, traditional testing and analysis can be performed, such as performing a biological assay using the riboswitch and the actual compound to further define the ability of the actual compound to interact with and/or modulate the riboswitch. The disclosed methods can include the step of assaying the activity of the riboswitch and compound, as well as performing, for example, combinatorial chemistry studies using libraries based on the riboswitch, for example.

Energy calculations can be based on, for example, molecular or quantum mechanics. Molecular mechanics approximates the energy of a system by summing a series of empirical functions representing components of the total energy like bond stretching, van der Waals forces, or electrostatic interactions. Quantum mechanics methods use various degrees of approximation to solve the Schrödinger equation. These methods deal with electronic structure, allowing for the characterization of chemical reactions.

Potential compounds of the riboswitch can be identified. This can be accomplished by selecting potential compounds with a given similarity to the known compound. For example, compounds in the same family as the known compound can be selected.

To prepare each riboswitch for calculation, atoms can be built in that were unresolved or absent from the crystal structures of the potential compound. This can be done, for example, using the PRODRG webserver davapc1.bioch.dundee.ac.uk./programs/prodrg, or standard molecular modeling programs such as InsightII, Quanta (both at www.accelrys.com), CNS (Brunger et al., Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998)), or any other molecular modeling system capable of preparing the riboswitch structure.

The binding energy (or other property or parameter) of the potential compound and riboswitch can then be calculated. There are numerous means for carrying this out. For example, the sampling of sidechain positions and the computation of the binding thermodynamics can be accomplished using an empirical function that models the energy of the potential compound-molecule as a sum of electrostatic and van der Waals interactions between all pairs of atoms within the model. Any other computational method for scoring the binding energy of the potential compound with the riboswitch can be used (H. Gohlke, & G. Klebe. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed. 41, 2644-4676 (2002)). Examples of such scoring methods include, but are not limited to, those implemented in programs such as AutoDock (G. M. Morris et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639-1662 (1998)), Gold (G. Jones et al. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 245, 43-53 (1995)), Chem-Score (M. D. Eldridge et al. J. Comput.-Aided Mol. Des. 11, 425-445 (1997)) and Drug-Score (H. Gohlke et al. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 295, 337-356 (2000)).

Rotamer libraries are known to those of skill in the art and can be obtained from a variety of sources, including the internet. Rotamers are low energy side-chain conformations. The use of a library of rotamers allows for the modeling of a structure to try the most likely side-chain conformations, saving time and producing a structure that is more likely to be correct. The use of a library of rotamers can be restricted to those residues that are within a given region of the potential compound, for example, at the binding site, or within a specified distance of the compound. The latter distance can be set at any desired length, for example, the potential compound can be 2, 3, 4, 5, 6, 7, 8, or 9 Å from any atom of the molecule.

Electrostatic interactions between every pair of atoms can be calculated, for example, using a Coulombic model with the formula:

E
_elec=332.08q₁q₂/∈r.

where q₁and q₂are partial atomic charges, r is the distance between them, and ∈ is the dielectric constant.

Partial atomic charges can be taken from existing parameter sets that have been developed to describe charge distributions in molecules. Example parameter sets include, but are not limited to, PARSE (D. A. Sitkoff et al. Accurate calculation of hydration free-energies using macroscopic solvent models. J. Phys. Chem. 98, 1978-1988 (1994)), CHARMM (MacKerell et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616, 1998) and AMBER (W. D. Cornell et al. A 2^ndgeneration force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J. Am. Chem. Soc. 117. 5179-5195 (1995)). Partial charges for atoms can be assigned either by analogy with those of similar functional groups, or by empirical assignment methods such as that implemented in the PRODRG server (D. M. F. van Aalten et al. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput.-Aided Mol. Design. 10, 255-262 (1996)), or by the use of standard quantum mechanical calculation methods (for example, C. I. Bayly et al. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges—the RESP model. J. Phys. Chem. 97, 10269-10280, (1993)).

The electrostatic interaction can also be calculated by more elaborate methodologies that incorporate electrostatic desolvation effects. These can include explicit solvent and implicit solvent models: in the former, water molecules are directly included in the calculations, whereas in the latter, the effects of water are described by a dielectric continuum approach. Specific examples of implicit solvent methods for calculating electrostatic interactions include but are not limited to: Poisson-Boltzmann based methods and Generalized Born methods (M. Feig & C. L. Brooks. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14, 217-224 (2004)).

van der Waals and hydrophobic interactions between pairs of atoms (where both atoms are either sulfur or carbon) can be calculated using a simple Lennard-Jones formalism with the following equation:

E
_vdw=∈{σ_att¹²/r¹²−σ_att⁶/r⁶}.

where ∈ is an energy, r is the distance between the two atoms and σ_attis the distance at which the energy of interaction is zero.

van der Waals interactions between pairs of atoms (where one or both atoms are neither sulfur nor carbon) can be calculated using a simple repulsive energy term:

E
_vdw=∈{σ_rep¹²/r¹²}.

where ∈ is an energy, r is the distance between the two atoms and σ_repdetermines the distance at which the repulsive interaction is equal to ∈.

Hydrophobic interactions between atoms can also be calculated using a variety of other methods known to those skilled in the art. For example, the energetic contribution can be calculated as being proportional to the amount of solvent accessible surface area of the ligand and receptor that is buried when the complex is formed. Such contributions can be expressed in terms of interactions between pairs of atoms, such as in the method proposed by Street & Mayo (A. G. Street & S. L. Mayo. Pairwise calculation of protein solvent-accessible surface areas. Folding & Design 3, 253-258 (1998)). Any other implementation of a formalism for describing hydrophobic or van der Waals or other energetic contributions can be included in the calculations.

Binding energies can be calculated for each potential compound-riboswitch interaction. For example, Monte Carlo sampling can be conducted in the presence and absence of the riboswitch, and the average energy in each simulation calculated. A binding energy for the riboswitch with the potential compound can then be calculated as the difference between the two calculated average energies.

The computed binding energy of a potential compound with the riboswitch can be compared with the computed binding energy of a known compound with the riboswitch to determine if the potential compound is likely to be an actual compound. These results can then be confirmed using experimental data, wherein the actual interaction between the riboswitch and compound can be measured. Examples of methods that can be used to determine an actual interaction between the riboswitch and the compound include but are not limited to: equilibrium dialysis measurements (wherein binding of a radioactive form of the compound to the riboswitch is detected), enzyme inhibition assays (wherein the activity of the riboswitch can be monitored in the presence and absence of the compound), and chemical shift perturbation measurements (wherein binding of the riboswitch to the potential compound is monitored by observing changes in NMR chemical shifts of atoms).

Modeling can be performed on or with the aid of a computer, a computer program, or a computer operating program. The computer can be made to display an image of the structure in 3D or represented as 3D. The image can be of any or all of the structure represented by the atomic coordinates of Table 2, for example, the structure represented by the atomic structure of the active site and binding pocket as depicted in FIG. 1 and the atomic coordinates of the active site and binding pocket depicted in FIG. 1 contained within Table 2 can be displayed. Any potion of the structure represented by the atomic coordinates of Table 2 that can be used to model and/or assess the ability of a compound to bind or interact specifically with a GEMM riboswitch can be used for modeling and related methods as described herein.

After the atomic crystalline structure of the riboswitch has been modeled with a potential compound, further testing can be carried out to determine the actual interaction between the riboswitch and the compound. For example, multiple different approaches can be used to detect binding RNAs, including allosteric ribozyme assays using gel-based and chip-based detection methods, and in-line probing assays. High throughput testing can also be accomplished by using, for example, fluorescent detection methods. For example, the natural catalytic activity of a glucosamine-6-phosphate sensing riboswitch that controls gene expression by activating RNA-cleaving ribozyme can be used. This ribozyme can be reconfigured to cleave separate substrate molecules with multiple turnover kinetics. Therefore, a fluorescent group held in proximity to a quenching group can be uncoupled (and therefore become more fluorescent) if a compound triggers ribozyme function. Second, molecular beacon technology can be employed. This creates a system that suppresses fluorescence if a compound prevents the beacon from docking to the riboswitch RNA. Either approach can be applied to any of the riboswitch classes by using RNA engineering strategies described herein.

High-throughput screening can also be used to reveal entirely new chemical scaffolds that also bind to riboswitch RNAs either with standard or non-standard modes of molecular recognition. Since riboswitches are the first major form of natural metabolite-binding RNAs to be discovered, there has been little effort made previously to create binding assays that can be adapted for high-throughput screening. Multiple different approaches can be used to detect metabolite binding RNAs, including allosteric ribozyme assays using gel-based and chip-based detection methods, and in-line probing assays. Also disclosed are compounds made by identifying a compound that activates, deactivates or blocks a riboswitch and manufacturing the identified compound. This can be accomplished by, for example, combining compound identification methods as disclosed elsewhere herein with methods for manufacturing the identified compounds. For example, compounds can be made by bringing into contact a test compound and a riboswitch, assessing activation of the riboswitch, and, if the riboswitch is activated by the test compound, manufacturing the test compound that activates the riboswitch as the compound.

Also disclosed are compounds made by checking activation, deactivation or blocking of a riboswitch by a compound and manufacturing the checked compound. This can be accomplished by, for example, combining compound activation, deactivation or blocking assessment methods as disclosed elsewhere herein with methods for manufacturing the checked compounds. For example, compounds can be made by bringing into contact a test compound and a riboswitch, assessing activation of the riboswitch, and, if the riboswitch is activated by the test compound, manufacturing the test compound that activates the riboswitch as the compound. Checking compounds for their ability to activate, deactivate or block a riboswitch refers to both identification of compounds previously unknown to activate, deactivate or block a riboswitch and to assessing the ability of a compound to activate, deactivate or block a riboswitch where the compound was already known to activate, deactivate or block the riboswitch.

Certain materials, compounds, compositions, and components disclosed herein can be obtained commercially or readily synthesized using techniques generally known to those of skill in the art. For example, the starting materials and reagents used in preparing the disclosed compounds and compositions are either available from commercial suppliers such as Aldrich Chemical Co., (Milwaukee, Wis.), Acros Organics (Morris Plains, N.J.), Fisher Scientific (Pittsburgh, Pa.), or Sigma (St. Louis, Mo.) or are prepared by methods known to those skilled in the art following procedures set forth in references such as Fieser and Fieser's Reagents for Organic Synthesis, Volumes 1-17 (John Wiley and Sons, 1991); Rodd's Chemistry of Carbon Compounds, Volumes 1-5 and Supplementals (Elsevier Science Publishers, 1989); Organic Reactions, Volumes 1-40 (John Wiley and Sons, 1991); March's Advanced Organic Chemistry, (John Wiley and Sons, 4th Edition); and Larock's Comprehensive Organic Transformations (VCH Publishers Inc., 1989).

It should be understood that particular contacts and interactions (such as hydrogen bond donation or acceptance) described herein for compounds interacting with riboswitches are preferred but are not essential for interaction of a compound with a riboswitch. For example, compounds can interact with riboswitches with less affinity and/or specificity than compounds having the disclosed contacts and interactions. Further, different or additional functional groups on the compounds can introduce new, different and/or compensating contacts with the riboswitches. For example, for GEMM riboswitches, large functional groups can be used. Such functional groups can have, and can be designed to have, contacts and interactions with other part of the riboswitch. Such contacts and interactions can compensate for contacts and interactions of the trigger molecules and core structure.

Also disclosed are methods for activating, deactivating or blocking a riboswitch. Such methods can involve, for example, bringing into contact a riboswitch and a compound or trigger molecule that can activate, deactivate or block the riboswitch. Riboswitches function to control gene expression through the binding or removal of a trigger molecule. Compounds can be used to activate, deactivate or block a riboswitch. The trigger molecule for a riboswitch (as well as other activating compounds) can be used to activate a riboswitch. Compounds other than the trigger molecule generally can be used to deactivate or block a riboswitch. Riboswitches can also be deactivated by, for example, removing trigger molecules from the presence of the riboswitch. Thus, the disclosed method of deactivating a riboswitch can involve, for example, removing a trigger molecule (or other activating compound) from the presence or contact with the riboswitch. A riboswitch can be blocked by, for example, binding of an analog of the trigger molecule that does not activate the riboswitch.

Also disclosed are methods for altering expression of an RNA molecule, or of a gene encoding an RNA molecule, where the RNA molecule includes a riboswitch, by bringing a compound into contact with the RNA molecule. Riboswitches function to control gene expression through the binding or removal of a trigger molecule. Thus, subjecting an RNA molecule of interest that includes a riboswitch to conditions that activate, deactivate or block the riboswitch can be used to alter expression of the RNA. Expression can be altered as a result of, for example, termination of transcription or blocking of ribosome binding to the RNA. Binding of a trigger molecule can, depending on the nature of the riboswitch, reduce or prevent expression of the RNA molecule or promote or increase expression of the RNA molecule.

Also disclosed are methods for regulating expression of a naturally occurring gene or RNA that contains a riboswitch by activating, deactivating or blocking the riboswitch. If the gene is essential for survival of a cell or organism that harbors it, activating, deactivating or blocking the riboswitch can result in death, stasis or debilitation of the cell or organism. For example, activating a naturally occurring riboswitch in a naturally occurring gene that is essential to survival of a microorganism can result in death of the microorganism (if activation of the riboswitch turns off or represses expression). This is one basis for the use of the disclosed compounds and methods for antimicrobial and antibiotic effects. The compounds that have these antimicrobial effects are considered to be bacteriostatic or bacteriocidal.

Also disclosed are methods for selecting and identifying compounds that can activate, deactivate or block a riboswitch. Activation of a riboswitch refers to the change in state of the riboswitch upon binding of a trigger molecule. A riboswitch can be activated by compounds other than the trigger molecule and in ways other than binding of a trigger molecule. The term trigger molecule is used herein to refer to molecules and compounds that can activate a riboswitch. This includes the natural or normal trigger molecule for the riboswitch and other compounds that can activate the riboswitch. Natural or normal trigger molecules are the trigger molecule for a given riboswitch in nature or, in the case of some non-natural riboswitches, the trigger molecule for which the riboswitch was designed or with which the riboswitch was selected (as in, for example, in vitro selection or in vitro evolution techniques). Non-natural trigger molecules can be referred to as non-natural trigger molecules.

Also disclosed herein is a method of identifying a compound that interacts with a riboswitch comprising: modeling the atomic structure the riboswitch with a test compound; and determining if the test compound interacts with the riboswitch. Determining if the test compound interacts with the riboswitch can be accomplished by, for example, determining a predicted minimum interaction energy, a predicted bind constant, a predicted dissociation constant, or a combination, for the test compound in the model of the riboswitch, as described elsewhere herein. Determining if the test compound interacts with the riboswitch can be accomplished by, for example, determining one or more predicted bonds, one or more predicted interactions, or a combination, of the test compound with the model of the riboswitch. The predicted interactions can be selected from the group consisting of, for example, van der Waals interactions, hydrogen bonds, electrostatic interactions, hydrophobic interactions, or a combination, as described above. In one example, the riboswitch is a guanine riboswitch.

Atomic contacts can be determined when interaction with the riboswitch is determined, thereby determining the interaction of the test compound with the riboswitch. Analogs of the test compound can be identified, and it can be determined if the analogs of the test compound interact with the riboswitch.

Also disclosed are methods of killing or inhibiting bacteria, comprising contacting the bacteria with a compound disclosed herein or identified by the methods disclosed herein.

Also disclosed are methods of identifying compounds that activate, deactivate or block a riboswitch. For examples, compounds that activate a riboswitch can be identified by bringing into contact a test compound and a riboswitch and assessing activation of the riboswitch. If the riboswitch is activated, the test compound is identified as a compound that activates the riboswitch. Activation of a riboswitch can be assessed in any suitable manner. For example, the riboswitch can be linked to a reporter RNA and expression, expression level, or change in expression level of the reporter RNA can be measured in the presence and absence of the test compound. As another example, the riboswitch can include a conformation dependent label, the signal from which changes depending on the activation state of the riboswitch. Such a riboswitch preferably uses an aptamer domain from or derived from a naturally occurring riboswitch. As can be seen, assessment of activation of a riboswitch can be performed with the use of a control assay or measurement or without the use of a control assay or measurement. Methods for identifying compounds that deactivate a riboswitch can be performed in analogous ways.

In addition to the methods disclosed elsewhere herein, identification of compounds that block a riboswitch can be accomplished in any suitable manner. For example, an assay can be performed for assessing activation or deactivation of a riboswitch in the presence of a compound known to activate or deactivate the riboswitch and in the presence of a test compound. If activation or deactivation is not observed as would be observed in the absence of the test compound, then the test compound is identified as a compound that blocks activation or deactivation of the riboswitch.

Also disclosed are methods of detecting compounds using biosensor riboswitches. The method can include bringing into contact a test sample and a biosensor riboswitch and assessing the activation of the biosensor riboswitch. Activation of the biosensor riboswitch indicates the presence of the trigger molecule for the biosensor riboswitch in the test sample. Biosensor riboswitches are engineered riboswitches that produce a detectable signal in the presence of their cognate trigger molecule. Useful biosensor riboswitches can be triggered at or above threshold levels of the trigger molecules. Biosensor riboswitches can be designed for use in vivo or in vitro. For example, GEMM biosensor riboswitches operably linked to a reporter RNA that encodes a protein that serves as or is involved in producing a signal can be used in vivo by engineering a cell or organism to harbor a nucleic acid construct encoding the riboswitch/reporter RNA. An example of a biosensor riboswitch for use in vitro is a GEMM riboswitch that includes a conformation dependent label, the signal from which changes depending on the activation state of the riboswitch. Such a biosensor riboswitch preferably uses an aptamer domain from or derived from a naturally occurring GEMM riboswitch.

Also disclosed are compounds made by identifying a compound that activates, deactivates or blocks a riboswitch and manufacturing the identified compound. This can be accomplished by, for example, combining compound identification methods as disclosed elsewhere herein with methods for manufacturing the identified compounds. For example, compounds can be made by bringing into contact a test compound and a riboswitch, assessing activation of the riboswitch, and, if the riboswitch is activated by the test compound, manufacturing the test compound that activates the riboswitch as the compound.

Disclosed is a method of detecting a compound of interest, the method comprising bringing into contact a sample and a GEMM riboswitch, wherein the riboswitch is activated by the compound of interest, wherein the riboswitch produces a signal when activated by the compound of interest, wherein the riboswitch produces a signal when the sample contains the compound of interest. The riboswitch can change conformation when activated by the compound of interest, wherein the change in conformation produces a signal via a conformation dependent label. The riboswitch can change conformation when activated by the compound of interest, wherein the change in conformation causes a change in expression of an RNA linked to the riboswitch, wherein the change in expression produces a signal. The signal can be produced by a reporter protein expressed from the RNA linked to the riboswitch.

Disclosed is a method comprising (a) testing a compound for inhibition of gene expression of a gene encoding an RNA comprising a riboswitch, wherein the inhibition is via the riboswitch, and (b) inhibiting gene expression by bringing into contact a cell and a compound that inhibited gene expression in step (a), wherein the cell comprises a gene encoding an RNA comprising a riboswitch, wherein the compound inhibits expression of the gene by binding to the riboswitch.

A. Identification of Antimicrobial Compounds

Riboswitches are a class of structured RNAs that have evolved for the purpose of binding small organic molecules. The natural binding pocket of riboswitches can be targeted with metabolite analogs or by compounds that mimic the shape-space of the natural metabolite. The small molecule ligands of riboswitches provide useful sites for derivitization to produce drug candidates. Distribution of some riboswitches is shown in Table 1 of U.S. Application Publication No. 2005-0053951. Once a class of riboswitch has been identified and its potential as a drug target assessed, such as the GEMM riboswitch, candidate molecules can be identified.

The emergence of drug-resistant stains of bacteria highlights the need for the identification of new classes of antibiotics. Anti-riboswitch drugs represent a mode of anti-bacterial action that is of considerable interest for the following reasons. Riboswitches control the expression of genes that are critical for fundamental metabolic processes. Therefore manipulation of these gene control elements with drugs yields new antibiotics. These antimicrobial agents can be considered to be bacteriostatic, or bacteriocidal. Riboswitches also carry RNA structures that have evolved to selectively bind metabolites, and therefore these RNA receptors make good drug targets as do protein enzymes and receptors. Furthermore, it has been shown that two antimicrobial compounds (discussed above) kill bacteria by deactivating the antibiotics resistance to emerge through mutation of the RNA target.

As disclosed herein, the crystal structure for a GEMM riboswitch has been elucidated, which enables the use of structure-based design methods for creating riboswitch-binding compounds. The successful compounds can be used as a scaffold upon which further chemical variation can be introduced to create non-toxic, bioavailable, high affinity, anti-riboswitch compounds.

B. Methods of Using Antimicrobial Compounds

Disclosed herein are in vivo and in vitro anti-bacterial methods. By “anti-bacterial” is meant inhibiting or preventing bacterial growth, killing bacteria, or reducing the number of bacteria. Thus, disclosed is a method of inhibiting or preventing bacterial growth comprising contacting a bacterium with an effective amount of one or more compounds disclosed herein. Additional structures for the disclosed compounds are provided herein.

Disclosed herein is also a method of inhibiting growth of a cell, such as a bacterial cell, that is in a subject, the method comprising administering an effective amount of a compound as disclosed herein to the subject. This can result in the compound being brought into contact with the cell. The subject can have, for example, a bacterial infection, and the bacterial cells can be inhibited by the compound. The bacteria can be any bacteria, such as bacteria from the genus Bacillus or Staphylococcus, for example. Bacterial growth can also be inhibited in any context in which bacteria are found. For example, bacterial growth in fluids, biofilms, and on surfaces can be inhibited. The compounds disclosed herein can be administered or used in combination with any other compound or composition. For example, the disclosed compounds can be administered or used in combination with another antimicrobial compound.

“Inhibiting bacterial growth” is defined as reducing the ability of a single bacterium to divide into daughter cells, or reducing the ability of a population of bacteria to form daughter cells. The ability of the bacteria to reproduce can be reduced by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or 100% or more.

Also provided is a method of killing a bacterium or population of bacteria comprising contacting the bacterium with one or more of the compounds disclosed and described herein.

“Killing a bacterium” is defined as causing the death of a single bacterium, or reducing the number of a plurality of bacteria, such as those in a colony. When the bacteria are referred to in the plural form, the “killing of bacteria” is defined as cell death of a given population of bacteria at the rate of 10% of the population, 20% of the population, 30% of the population, 40% of the population, 50% of the population, 60% of the population, 70% of the population, 80% of the population, 90% of the population, or less than or equal to 100% of the population.

The compounds and compositions disclosed herein have anti-bacterial activity in vitro or in vivo, and can be used in conjunction with other compounds or compositions, which can be bacteriocidal as well.

By the term “therapeutically effective amount” of a compound as provided herein is meant a nontoxic but sufficient amount of the compound to provide the desired reduction in one or more symptoms. As will be pointed out below, the exact amount of the compound required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the disease that is being treated, the particular compound used, its mode of administration, and the like. Thus, it is not possible to specify an exact “effective amount.” However, an appropriate effective amount may be determined by one of ordinary skill in the art using only routine experimentation.

The compositions and compounds disclosed herein can be administered in vivo in a pharmaceutically acceptable carrier. By “pharmaceutically acceptable” is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.

The compositions or compounds disclosed herein can be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including topical intranasal administration or administration by inhalant. As used herein, “topical intranasal administration” means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the nucleic acid or vector. Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation. The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the allergic disorder being treated, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.

Parenteral administration of the composition or compounds, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No. 3,610,795, which is incorporated by reference herein.

The compositions and compounds disclosed herein can be used therapeutically in combination with a pharmaceutically acceptable carrier. Suitable carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, Mack Publishing Company, Easton, Pa. 1995. Typically, an appropriate amount of a pharmaceutically-acceptable salt is used in the formulation to render the formulation isotonic. Examples of the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution. The pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5. Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.

Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. The compositions can be administered intramuscularly or subcutaneously. Other compounds will be administered according to standard procedures used by those skilled in the art.

Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, antiinflammatory agents, anesthetics, and the like.

The pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration may be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection. The disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.

Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.

Formulations for topical administration may include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.

Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders may be desirable.

Some of the compositions may potentially be administered as a pharmaceutically acceptable acid- or base-addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, trialkyl and aryl amines and substituted ethanolamines.

Therapeutic compositions as disclosed herein may also be delivered by the use of monoclonal antibodies as individual carriers to which the compound molecules are coupled. The therapeutic compositions of the present disclosure may also be coupled with soluble polymers as targetable drug carriers. Such polymers can include, but are not limited to, polyvinyl-pyrrolidone, pyran copolymer, polyhydroxypropylmethacryl-amidephenol, polyhydroxyethylaspartamidephenol, or polyethyl-eneoxidepolylysine substituted with palmitoyl residues. Furthermore, the therapeutic compositions of the present disclosure may be coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydro-pyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.

Preferably at least about 3%, more preferably about 10%, more preferably about 20%, more preferably about 30%, more preferably about 50%, more preferably 75% and even more preferably about 100% of the bacterial infection is reduced due to the administration of the compound. A reduction in the infection is determined by such parameters as reduced white blood cell count, reduced fever, reduced inflammation, reduced number of bacteria, or reduction in other indicators of bacterial infection. To increase the percentage of bacterial infection reduction, the dosage can increase to the most effective level that remains non-toxic to the subject.

As used throughout, “subject” refers to an individual. Preferably, the subject is a mammal such as a non-human mammal or a primate, and, more preferably, a human. “Subjects” can include domesticated animals (such as cats, dogs, etc.), livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), laboratory animals (e.g., mouse, rabbit, rat, guinea pig, etc.) and fish.

A “bacterial infection” is defined as the presence of bacteria in a subject or sample. Such bacteria can be an outgrowth of naturally occurring bacteria in or on the subject or sample, or can be due to the invasion of a foreign organism.

The compounds disclosed herein can be used in the same manner as antibiotics. Uses of antibiotics are well established in the art. One example of their use includes treatment of animals. When needed, the disclosed compounds can be administered to the animal via injection or through feed or water, usually with the professional guidance of a veterinarian or nutritionist. They are delivered to animals either individually or in groups, depending on the circumstances such as disease severity and animal species. Treatment and care of the entire herd or flock may be necessary if all animals are of similar immune status and all are exposed to the same disease-causing microorganism.

Another example of a use for the compounds includes reducing a microbial infection of an aquatic animal, comprising the steps of selecting an aquatic animal having a microbial infection, providing an antimicrobial solution comprising a compound as disclosed, chelating agents such as EDTA, TRIENE, adding a pH buffering agent to the solution and adjusting the pH thereof to a value of between about 7.0 and about 9.0, immersing the aquatic animal in the solution and leaving the aquatic animal therein for a period that is effective to reduce the microbial burden of the animal, removing the aquatic animal from the solution and returning the animal to water not containing the solution. The immersion of the aquatic animal in the solution containing the EDTA, a compound as disclosed, and TRIENE and pH buffering agent may be repeated until the microbial burden of the animal is eliminated. (U.S. Pat. No. 6,518,252).

Other uses of the compounds disclosed herein include, but are not limited to, dental treatments and purification of water (this can include municipal water, sewage treatment systems, potable and non-potable water supplies, and hatcheries, for example).

EXAMPLES
A. RNA Crystallization and Structure Determination

Riboswitch sequences were cloned from genomic DNA and transcribed and purified as previously described (Cochrane, J. C., Lipchock, S. V. & Strobel, S. Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor. Chem Biol 14, 97-105 (2007)). c-di-GMP was chemically synthesized following previously published procedures with minor modifications (Hyodo, M. & Hayakawa, Y. An Improved Method for Synthesizing Cyclic Bis(3′-5′)diguanylic Acid (c-di-GMP). Bull. Chem. Soc. Jpn. 77, 2089-2093 (2004)). The primary difference was modifications to the final deprotections where N-methylamine and aqueous ammonia were used in place of only aqueous ammonia. A solution containing 100 μM GEMM riboswitch RNA and 215 μM c-di-GMP was heated to 70° C. and slow cooled in folding buffer containing 10 mM MgCl₂, 10 mM KCl, and 10 mM Na cacodylate. The co-crystallization protein U1A was added at a final concentration of 140 μM and the complex was allowed to equilibrate for 1 hour. This solution was then mixed in a one to one ratio with well solution: 22% PEG550 mme, 5 mM MgSO₄, 50 mM MES, pH 6.0, and 0.3 M NaCl. Crystal were grown at 25° C. using hanging drop vapor diffusion. Crystals appeared within two days and grew in large clusters which could be broken apart to produce single crystals with a maximum size of 400 μm×50 μm×5 μm. Crystals were stabilized in mother liquor with 30% PEG550 mme and flash frozen in liquid nitrogen. For phasing, crystals were soaked in stabilization solution with the addition of 1 mM iridium hexamine for approximately 3 hours before flash freezing. Three-wavelength MAD data were collected at beamline X29 at NSLS. Iridium hexamine was synthesized as described previously. Data were processed using HKL2000. Initial phase information was obtained by locating the U1A protein by molecular replacement using Phaser. Initial sites were located by difference Fourier methods and used in Solve to generate initial maps. Solvent flattening was performed using Resolve. Model building was done in Coot, and Refmac was used for refinement. Figures were made in PyMol.

B. K_dMeasurements of Wild-Type and Mutant RNAs

Point mutants were cloned using the Quik Change protocol. Radiolabeled c-di-GMP was obtained enzymatically according to published procedures and purified by polyacrylamide gel electrophoresis (PAGE) (Paul, R. et al. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes & Development 18, 715-27 (2004); Christen, M., Christen, B., Folcher, M., Schauerte, A. & Jenal, U. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J Biol Chem 280, 30829-37 (2005)). A constitutively active DGC, PleD* was expressed and purified as described and the reaction was initiated using [α-³²P]GTP as the substrate (Paul, R. et al. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes & Development 18, 715-27 (2004)). A single band appeared as the reaction proceeded that ran slower than the starting material when purified by PAGE. Radiolabeled c-diAMP was obtained similarly, using the protein DisA and [α-³²P]ATP as the substrate. Riboswitch RNAs were folded in the presence of radiolabeled c-di-GMP or c-diAMP and folding buffer. The complex was allowed to equilibrate for 1 hour and bound and free c-di-GMP were separated by native (100 mM Tris/HEPES pH 7.5, 10 mM MgCl₂, 0.1 mM EDTA) PAGE at 4° C. A STORM phosphorimager was used to scan gels and the bands were quantitated using ImageQuant. Fraction bound was graphed versus RNA concentration and fit using KaleidaGraph to obtain K_ds according to the equation:

F=(F_∞*C)/(C+K_d)

F=fraction bound; F_∞=fraction bound at saturation; C=riboswitch concentration

C. Structure Determination of the GEMM Riboswitch

The 2.7 Å crystal structure of a GEMM riboswitch from V. cholerae bound to c-di-GMP was determined (FIG. 1; Table 2). The crystallized RNA corresponds to a sequence upstream of the COG3070 (tfoX-like) gene from V. cholerae, referred to as Vc2 (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)). A binding site for the RNA binding domain of the human U1A protein was incorporated into the hairpin loop at the top of the P3 helix for use in RNA co-crystallization (Ferré-D'Amaré, A. R. & Doudna, J. A. Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. J Mol Biol 295, 541-56 (2000)). The 5′ and 3′ ends of the RNA were chosen to correspond to the minimal RNA aptamer that was still able to bind c-di-GMP with high affinity (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008)) with one additional nucleotide on the 5′ end. The first nucleotide on the 5′ end corresponds to nucleotide number 10 of the Vc2 sequence reported in Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3 (2008), which corresponds to nucleotide number 3 in SEQ ID NO:1. The last nucleotide on the 3′ end corresponds to nucleotide 98 in that sequence, which corresponds to nucleotide number 91 in SEQ ID NO:1. This numbering from Sudarsan, N. et al. is used throughout this application. The structure was solved using MAD with a single crystal soaked with iridium hexamine.

D. Biochemical Characterization of Wild-Type and Mutant Riboswitches

A gel-shift assay, which directly measures c-di-GMP binding to the GEMM RNA (FIG. 3A, B), was developed in order to test biochemical predictions resulting from the GEMM riboswitch structure. Specifically, radiolabeled c-di-GMP was incubated with the riboswitch and the RNA bound ligand was separated from the free on a native polyacrylamide gel. A distinct shift to a slower mobility band was seen for c-di-GMP bound to the riboswitch (FIG. 3). When labeled RNA was incubated with unlabeled c-di-GMP, no shift was observed, indicating that this method is not sensitive enough to detect conformational changes in the RNA or the slight additional change in mass resulting from c-di-GMP binding.

This assay was used to measure a binding constant for the crystallized RNA and also to verify that this method gave the K_dmeasurements similar to what had been fond using in-line probing. To validate the method, Vc2 110 was used and found to have a K_dof ˜7 nM. This value agrees well with affinities obtained previously by in-line probing for this same sequence (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3). A RNA corresponding to the crystallization construct with no U1A binding loop (Vc2 91) was then tested. This sequence also binds c-di-GMP with an affinity of <10 nM, agreeing well with what was seen with in-line probing (Table 1). The RNA used in the crystallographic studies (Vc2 91 with a U1A binding loop) bound with a K_dslightly weaker than wild-type, but is within 9-fold of the original value.

The three nucleotides directly involved in ligand recognition (G20, A47 and C92) were mutated and affinity for c-di-GMP was measured by gel shift analysis in the context of the WT-110 nucleotide background (Table 1) (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3). Mutational analysis supports the crystallographically observed base pair between a conserved cytidine, C92, and c-di-GMP. Mutation of C92 to an A or a G reduces affinity for c-di-GMP substantially, while mutation of C92 to a U results in only a 6-fold loss in affinity. By mutating it to an A or G, this ability to base pair with the ligand is lost. The large effect that these mutations have on ligand binding confirms that C92 is making an important contact with G_β. The minor affect seen upon mutation to a U is in a reasonable range given the potential to form a wobble pair with G_β. A natural GEMM sequence has been identified that lacks a C at position 92, but instead has a C at position 93. This RNA can bind c-di-GMP with an affinity of approximately 1 uM. When this C is mutated to an A, all affinity for c-di-GMP is lost, indicating that a C at one of these two positions is essential for ligand binding.

When G20 is mutated to a U, an approximately 45-fold loss in affinity is observed while mutation to either A or C maintains approximately wild-type affinity. G20 forms two hydrogen bonds to the Hoogsteen face of G_α. When these mutations were modeled into the crystal structure, the U mutation was not able to form either hydrogen bond. However both the A and C were both able to maintain one hydrogen bond to G_α. Because C is not as large as a purine, it is possible that it cannot make as tight of an interaction and this difference may lead to the small, 2-fold reduction in affinity seen in the G20C case. The nucleotide at position 20 is conserved as either a G or an A, so the result with A is consistent with phylogenetic covariation at this position.

To explore the role of base stacking in c-di-GMP binding, A47 was mutated to the other three bases. All mutations resulted in an approximately 1000-fold decrease in binding affinity. Strict conservation of A47 is seen in GEMM riboswitch sequences and would be predicted from the structure: if it was a pyrimidine, stacking interactions would not be as strong, and if it was a guanosine, the O6 would potentially clash with one of the non-bridging oxygens of c-di-GMP. With an adenosine, stacking interactions are maximized and a hydrogen bond is present between the exocyclic amine of A47 and the ligand. The role of A47 thus appears to be multifaceted, as it interacts by both hydrogen bonding and stacking, but the large reduction in affinity upon mutation of this nucleotide suggests that base stacking plays a critical role c-di-GMP binding.

The affinity of the breakdown product of c-di-GMP and pGpG was also measured using the gel-shift assay. This linear dinucleotide is produced when PDE enzymes degrade c-di-GMP and has also been reported to bind to the GEMM riboswitch (Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411-3). In the wild-type sequence, an affinity approximately 66-fold lower than that of the cyclic ligand was measured. The only mutant that was able to bind pGpG was A47G, which binds the linear form 3-fold better than c-di-GMP. Perhaps the additional conformational freedom available to pGpG allows it to adopt a position that enables binding to this mutant that maintains stacking interactions but avoids the steric clash with 06 of the guanosine at position 47 and the non-bridging oxygen of c-di-GMP.

E. Specificity Switch of the GEMM Riboswitch

A specificity switch to a chimeric ligand with both a guanine and an adenine base was attempted to further investigate the role of nucleotides important in c-di-GMP recognition. In this regard, mutant RNAs with the chimeric ligands pGpA and pApG were tested. The C92U RNA does not bind to pGpG, but binding was observed for pGpA, which binds with an affinity approximately 27-fold lower than that of the wild-type RNA for pGpG. Interestingly, it does not bind to pApG, suggesting that the free 5′ phosphate corresponds to the one that is hydrogen bonded to A47. The wild-type sequence binds pGpG but not pGpA, but with a single nucleotide substitution, the C92U mutant RNA now binds only pGpA and not pGpG.

After the above-described attempt to switch the specificity from a ligand with two guanine bases to one with both a guanine and an adenine succeeded, a mutant riboswitch that would selectively recognize a ligand with two adenine bases was sought. Prokaryotes encode proteins with diadenylate cyclase activity, synthesizing cyclic diadenosine monophosphate (c-di-AMP) from ATP (Witte, G., Hartung, S., Biittner, K. & Hopfner, K. P. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol Cell 30, 167-78 (2008)). Radiolabeled c-di-AMP was obtained and a gel-shift assay was performed to test if any mutants were able to bind this alternative ligand. It was found that the C92U/G20A double mutant bound c-di-AMP approximately 6-fold better than c-di-GMP, showing that with the mutation of only two nucleotides, the specificity of the GEMM riboswitch could be switched from c-di-GMP to c-diAMP.

The C92U mutation presumably allows a Watson-Crick pair to be formed between A_βand U92. To identify a mutation that would be productive for A_αbinding at G20, all combinations were tested. G20A was the only one that produced a switch in specificity. It is possible that A20 forms two hydrogen bonds to A_α, one between the N6 of A_αand the N1 of A20 and another between the A_αN7 and the N6 of A20.

TABLE 1

c-di-GMP
pGpG
pGpA
pApG
c-di-AMP

K_d(nM)
K_d(nM)
K_d(nM)
K_d(nM)
K_d(nM)

WT-91
6.4 ± 2.8
—

WT-U1A
55 ± 14
—

WT-110
7.4 ± 2.4
490 ± 150
—
—
—

C92U
43 ± 19
—
16000 ± 5200
—
—

C92U, G20A
3200 ± 600
—
—
—
540 ± 29

C92U, G20C
*
—
—
—
—

C92U, G20U
—
—
—
—
—

G20A
4.7 ± 1.3
—
—
—
—

G20C
13 ± 1.2
—
—
—
—

G20U
330 ± 150
—
—
—
—

A47C
8500 ± 3000
—
—
—
—

A47G
4200 ± 1700
1400 ± 120
—
—
—

A47U
3500 ± 520
—
—
—
—

* This mutant does bind a little with a little smear at 100 uM, but there is no way to get K_destimate.

F. Significance of Understanding the Crystal Structure of GEMM Riboswitch

The discovery of the GEMM riboswitch was a major advance in understanding the mechanism of action of the second messenger c-di-GMP. Understanding how this RNA effector interacts with c-di-GMP is necessary to establish a full molecular view of this signaling pathway. Structural characterization of the GEMM riboswitch bound to c-di-GMP contributes to a broader understanding of the intracellular mechanisms of signaling and how RNA provides a critical link in the c-di-GMP pathway.

The GEMM riboswitch recognizes the ligand c-di-GMP asymmetrically, contacting the Watson-Crick face of one guanine and the Hoogsteen face of the other. Riboswitches that sense other purine ligands also use Watson-Crick base pairing as a primary means of recognition (Kim, J. & Breaker, R. Purine sensing by riboswitches. Biol. Cell 100, 1-11 (2008)). Contacts to the Hoogsteen face have also been seen in the SAM riboswitches (Gilbert, S., Rambo, R., Van Tyne, D. & Batey, R. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 15, 177-182 (2008); Montange, R. & Batey, R. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441, 1172-5 (2006)) and the group I intron (Adams, P., Stahley, M., Kosek, A., Wang, J. & Strobel, S. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50 (2004)).

Several structures of proteins bound to c-di-GMP have also been solved, including those of DGCs, PDEAs, and the PilZ domain proteins. These structures reveal the major ways in which c-di-GMP is recognized by proteins. Proteins do not contain residues capable of forming Watson-Crick type interactions with nucleobases and so must use different strategies when recognizing c-di-GMP.

In both the inhibitory site (I-site) of DGCs and the PilZ domain, arginine side chains contact O6 and N7, fulfilling a similar role to G20 in the GEMM riboswitch (Chan, C. et al. Structural basis of activity and allosteric control of diguanylate cyclase. Proc Natl Acad Sci USA 101, 17084-9 (2004); Wassmann, P. et al. Structure of BeF3-modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure 15, 915-27 (2007); De, N. et al. Phosphorylation-independent regulation of the diguanylate cyclase WspR. Plos Biol 6, e67 (2008)). Stacking interactions are critical to c-di-GMP binding in the GEMM riboswitch, and very similar stacked structures have been observed in the crystal structures of c-di-GMP itself as well as c-di-GMP binding in the I-site of DGCs. In these cases, two c-di-GMP molecules are intercalated with each other to form a stack of four guanosines. The conformation of c-di-GMP bound to the GEMM riboswitch is essentially identical to that of crystallized c-di-GMP (Egli, M. et al. Atomic-resolution structure of the cellulose synthase regulator cyclic diguanylic acid. Proc Natl Acad Sci USA 87, 3235-9 (1990); Liaw, Y. C. et al. Cyclic diguanylic acid behaves as a host molecule for planar intercalators. FEBS Lett 264, 223-7 (1990)) and c-di-GMP bound to the inhibitory site of DGCs (Chan, C. et al. Structural basis of activity and allosteric control of diguanylate cyclase. Proc Natl Acad Sci USA 101, 17084-9 (2004); Wassmann, P. et al. Structure of BeF3-modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure 15, 915-27 (2007); De, N. et al. Phosphorylation-independent regulation of the diguanylate cyclase WspR. Plos Biol 6, e67 (2008)) as well as the PilZ domain (Benach, J. et al. The structural basis of cyclic diguanylate signal transduction by PilZ domains. EMBO J. 26, 5153-66 (2007)). The only difference is that in the GEMM riboswitch the guanine bases are vertically aligned with respect to one another, presumably to form optimal stacking interactions with A47. In DGCs and PilZ proteins, the bases are off-set from each other. In the EAL domain, the sugar phosphate ring conformation is very similar, but the guanine bases are not parallel but are instead oriented away from one another (Minasov, G. et al. Crystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodiester bond cleavage by EAL domains. J Biol Chem (2009)). Stacking interactions are provided by aromatic residues in the PDEA protein structure, and with arginine guanidino groups in the DGCs I-sites and PilZ domain proteins. The unique configuration of the guanine bases in the GEMM riboswitch is most likely due to the fact that it is the only structure of c-di-GMP binding to a nucleic acid. Because A47 can stack directly between the two guanines, this arrangement of the two bases in presumably more favorable.

Despite the ways that proteins have evolved to bind c-di-GMP, RNA is well equipped to bind to this second messenger, which is itself a small RNA. The riboswitch is able to form tight, base-pairing and stacking interactions with other purines, unlike protein receptors. This is reflected in the binding affinity of this RNA, around 1 nM, versus those of the known c-di-GMP binding proteins, which range from 50 nM to several micromolar (Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro 7, 263-73 (2009)).

Due to the presence of GEMM riboswitches in many pathogenic organisms, this class of riboswitches may be an attractive antibiotic target. Because c-di-GMP is used widely in the bacterial kingdom and many effector proteins are also present in the cell, it would be very useful to design an inhibitor that would be specific for the riboswitch. This structure allows the targeted design of molecules that may be used as potential therapeutics.

The ability to make a mutant GEMM riboswitch with affinity for c-di-AMP suggests the possibility of naturally occurring c-di-AMP riboswitches. This small molecule was only recently discovered and little is known about is biological function (Witte, G., Hartung, S., Büttner, K. & Hopfner, K. P. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol Cell 30, 167-78 (2008)). If a riboswitch could be found that recognizes this molecule, it may reveal important information concerning its physiological role, depending upon which genes it regulates. Initial inspection of known GEMM riboswitch sequences does not reveal any examples of naturally occurring RNAs containing both point mutations which produced c-di-AMP specificity in this study, but this remains an interesting possibility.

The structure of the GEMM riboswitch bound to c-di-GMP not only reveals the interactions important for ligand binding and recognition in this system, but also provides a detailed view of c-di-GMP interacting with a downstream target and gives insight into how this second messenger regulates gene expression on the molecular level. It reveals that formation of the P1 helix, which was previously overlooked in the secondary structure of this riboswitch, accompanies ligand binding. P1 is formed from the 5′ and 3′ ends of the RNA, and by in-line probing, these ends appear to be less structured in the ligand-free form of the riboswitch. This information combined with the crystal structure led to the realization that when c-di-GMP binds to the GEMM riboswitch, it locks the 3′ end of the RNA into a specific conformation through base pairing with C92, initiating the formation of the P1 helix. P1 helix formation is the molecular switch that adjusts gene expression levels in response to c-di-GMP levels.

TABLE 2

Atomic Coordinates of GEMM Riboswitch

HEADER

RNA

TITLE

STRUCTURE OF A C-DI-GMP RIBOSWITCH FROM V.CHOLERAE
3IRW

COMPND

MOL_ID: 1;

COMPND
2
MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A;

COMPND
3
CHAIN: P;

COMPND
4
FRAGMENT: RNA BINDING DOMAIN;

COMPND
5
SYNONYM: U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A;

COMPND
6
ENGINEERED: YES;

COMPND
7
MUTATION: YES;

COMPND
8
MOL_ID: 2;

COMPND
9
MOLECULE: C-DI-GMP RIBOSWITCH;

COMPND
10
CHAIN: R;

COMPND
11
ENGINEERED: YES

SOURCE

MOL_ID: 1;

SOURCE
2
ORGANISM_SCIENTIFIC: HOMOSAPIENS;

SOURCE
3
ORGANISM_COMMON: HUMAN;

SOURCE
4
ORGANISM_TAXID: 9606;

SOURCE
5
GENE: SNRPA;

SOURCE
6
EXPRESSION_SYSTEM: ESCHERICHIACOLI;

SOURCE
7
EXPRESSION_SYSTEM_TAXID: 562;

SOURCE
8
EXPRESSION_SYSTEM_STRAIN: BL21;

SOURCE
9
EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;

SOURCE
10
EXPRESSION_SYSTEM_PLASMID: PET11;

SOURCE
11
MOL_ID: 2;

SOURCE
12
SYNTHETIC: YES;

SOURCE
13
ORGANISM_SCIENTIFIC: VIBRIOCHOLERAE;

SOURCE
14
ORGANISM_TAXID: 666;

SOURCE
15
OTHER_DETAILS: IN VITRO SYNTHESIS FROM A PLASMID DNA

SOURCE
16
TEMPLATE OF NATURAL SEQUENCE FROM VIBRIOCHOLERAE

KEYWDS

RIBOSWITCH, C-DI-GMP

EXPDTA

X-RAY DIFFRACTION

AUTHOR

K. D. SMITH

REVDAT
1
3IRW 0

JRNL

AUTH
K. D. SMITH, S. V. LIPCHOCK, T. D. AMES, J. WANG, R. R. BREAKER,

JRNL

AUTH 2
S. A. STROBEL

JRNL

TITL
STRUCTURAL BASIS OF LIGAND BINDING BY A C-DI-GMP

JRNL

TITL 2
RIBOSWITCH

JRNL

REF
NAT. STRUCT. MOL. BIOL.

JRNL

REFN
ESSN 1545-9985

REMARK
1

REMARK
2

REMARK
2
RESOLUTION. 2.70 ANGSTROMS.

REMARK
3

REMARK
3
REFINEMENT.

REMARK
3
PROGRAM
REFMAC 5.4.0077

REMARK
3
AUTHORS
MURSHUDOV, VAGIN, DODSON

REMARK
3

REMARK
3
REFINEMENT TARGET
MAXIMUM LIKELIHOOD WITH PHASES

REMARK
3

REMARK
3
DATA USED IN REFINEMENT.

REMARK
3
RESOLUTION RANGE HIGH (ANGSTROMS)
2.70

REMARK
3
RESOLUTION RANGE LOW (ANGSTROMS)
43.69

REMARK
3
DATA CUTOFF (SIGMA (F))
NULL

REMARK
3
COMPLETENESS FOR RANGE (%)
94.8

REMARK
3
NUMBER OF REFLECTIONS
8497

REMARK
3

REMARK
3
FIT TO DATA USED IN REFINEMENT.

REMARK
3
CROSS-VALIDATION METHOD
THROUGHOUT

REMARK
3
FREE R VALUE TEST SET SELECTION
RANDOM

REMARK
3
R VALUE (WORKING + TEST SET)
0.199

REMARK
3
R VALUE (WORKING SET)
0.196

REMARK
3
FREE R VALUE
0.251

REMARK
3
FREE R VALUE TEST SET SIZE (%)
4.900

REMARK
3
FREE R VALUE TEST SET COUNT
439

REMARK
3

REMARK
3
FIT IN THE HIGHEST RESOLUTION BIN.

REMARK
3
TOTAL NUMBER OF BINS USED
20

REMARK
3
BIN RESOLUTION RANGE HIGH
(A)
2.70

REMARK
3
BIN RESOLUTION RANGE LOW
(A)
2.77

REMARK
3
REFLECTION IN BIN
(WORKING SET)
477

REMARK
3
BIN COMPLETENESS
(WORKING + TEST) (%)
72.51

REMARK
3
BIN R VALUE
(WORKING SET)
0.3110

REMARK
3
BIN FREE R VALUE SET COUNT
19

REMARK
3
BIN FREE R VALUE
0.4130

REMARK
3

REMARK
3
NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.

REMARK
3
PROTEIN ATOMS
734

REMARK
3
NUCLEIC ACID ATOMS
1961

REMARK
3
HETEROGEN ATOMS
111

REMARK
3
SOLVENT ATOMS
92

REMARK
3

REMARK
3
B VALUES.

REMARK
3
FROM WILSON PLOT (A**2)
NULL

REMARK
3
MEAN B VALUE (OVERALL, A**2)
50.65

REMARK
3
OVERALL ANISOTROPIC B VALUE.

REMARK
3
B11
(A**2)
0.83000

REMARK
3
B22
(A**2)
−4.89000

REMARK
3
B33
(A**2)
4.40000

REMARK
3
B12
(A**2)
0.00000

REMARK
3
B13
(A**2)
1.44000

REMARK
3
B23
(A**2)
0.00000

REMARK
3

REMARK
3
ESTIMATED OVERALL COORDINATE ERROR.

REMARK
3
ESU BASED ON R VALUE
(A)
NULL

REMARK
3
ESU BASED ON FREE R VALUE
(A)
0.411

REMARK
3
ESU BASED ON MAXIMUM
(A)
0.320

LIKELIHOOD

REMARK
3
ESU FOR B VALUES BASED ON
(A**2)
NULL

MAXIMUM LIKELIHOOD

REMARK
3

REMARK
3
CORRELATION COEFFICIENTS.

REMARK
3
CORRELATION COEFFICIENT FO—FC
0.952

REMARK
3
CORRELATION COEFFICIENT FO—FC FREE
0.923

REMARK
3

REMARK
3
RMS DEVIATIONS FROM IDEAL VALUES

COUNT
RMS
WEIGHT

REMARK
3
BOND LENGTHS REFINED ATOMS
(A)
3045;
0.006;
0.021

REMARK
3
BOND LENGTHS OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
BOND ANGLES REFINED ATOMS
(DEGREES)
4631;
0.953;
2.776

REMARK
3
BOND ANGLES OTHERS
(DEGREES)
NULL;
NULL;
NULL

REMARK
3
TORSION ANGLES, PERIOD 1
(DEGREES)
89;
5.686;
5.000

REMARK
3
TORSION ANGLES, PERIOD 2
(DEGREES)
34;
27.392;
23.235

REMARK
3
TORSION ANGLES, PERIOD 3
(DEGREES)
150;
14.327;
15.000

REMARK
3
TORSION ANGLES, PERIOD 4
(DEGREES)
6;
16.926;
15.000

REMARK
3
CHIRAL-CENTER RESTRAINTS
(A**3)
NULL;
NULL;
NULL

REMARK
3
GENERAL PLANES REFINED ATOMS
(A)
1519;
0.004;
0.020

REMARK
3
GENERAL PLANES OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
NON-BONDED CONTACTS REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
NON-BONDED CONTACTS OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
NON-BONDED TORSION REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
NON-BONDED TORSION OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
H-BOND (X . . . Y) REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
H-BOND (X . . . Y) OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
POTENTIAL METAL-ION REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
POTENTIAL METAL-ION OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
SYMMETRY VDW REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
SYMMETRY VDW OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
SYMMETRY H-BOND REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
SYMMETRY H-BOND OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
SYMMETRY METAL-ION REFINED ATOMS
(A)
NULL;
NULL;
NULL

REMARK
3
SYMMETRY METAL-ION OTHERS
(A)
NULL;
NULL;
NULL

REMARK
3
ISOTROPIC THERMAL FACTOR RESTRAINTS.

COUNT
RMS
WEIGHT

REMARK
3
MAIN-CHAIN BOND REFINED ATOMS
(A**2)
449;
2.120;
5.000

REMARK
3
MAIN-CHAIN BOND OTHERS ATOMS
(A**2)
NULL;
NULL;
NULL

REMARK
3
MAIN-CHAIN ANGLE REFINED ATOMS
(A**2)
727;
3.848;
10.000

REMARK
3
SIDE-CHAIN BOND REFINED ATOMS
(A**2)
2596;
1.901;
5.000

REMARK
3
SIDE-CHAIN ANGLE REFINED ATOMS
(A**2)
3904;
3.102;
10.00

REMARK
3

REMARK
3
ANISOTROPIC THERMAL FACTOR RESTRAINTS.

COUNT
RMS
WEIGHT

REMARK
3
RIGID-BOND RESTRAINTS
(A**2)
NULL;
NULL;
NULL

REMARK
3
SPHERICITY; FREE ATOMS
(A**2)
NULL;
NULL;
NULL

REMARK
3
SPHERICITY; BONDED ATOMS
(A**2)
NULL;
NULL;
NULL

REMARK
3

REMARK
3
NCS RESTRAINTS STATISTICS

REMARK
3
NUMBER OF DIFFERENT NCS GROUPS
NULL

REMARK
3

REMARK
3
TLS DETAILS

REMARK
3
NUMBER OF TLS GROUPS
4

REMARK
3

REMARK
3
TLS GROUP
1

REMARK
3
NUMBER OF COMPONENT GROUP
2

REMARK
3
COMPONENTS
C
SSSEQI
TO
C
SSSEQI

REMARK
3
RESIDUE RANGE
R
8

R
14

REMARK
3
RESIDUE RANGE
R
92

R
97

REMARK
3
ORIGIN FOR THE GROUP (A)
18.4220
−30.6540
−11.9340

REMARK
3
T TENSOR

REMARK
3
T11
0.2563
T22
0.3514

REMARK
3
T33
0.0532
T12
0.1455

REMARK
3
T13
0.1124
T23
0.0379

REMARK
3
L TENSOR

REMARK
3
L11
9.2098
L22
3.5636

REMARK
3
L33
0.7918
L12
−0.4908

REMARK
3
L13
−0.8068
L23
1.6402

REMARK
3
S TENSOR

REMARK
3
S11
0.0919
S12
−0.7027
S13
−0.1654

REMARK
3
S21
−0.0115
S22
0.0286
S23
−0.1136

REMARK
3
S31
0.3680
S32
0.2970
S33
−0.1205

REMARK
3

REMARK
3
TLS GROUP
2

REMARK
3
NUMBER OF COMPONENT GROUP
1

REMARK
3
COMPONENTS
C
SSSEQI
TO
C
SSSEQI

REMARK
3
RESIDUE RANGE
R
15

R
47

REMARK
3
ORIGIN FOR THE GROUP (A)
4.5290
−25.8600
−6.5500

REMARK
3
T TENSOR

REMARK
3
T11
0.2047
T22
0.1259

REMARK
3
T33
0.0709
T12
0.0236

REMARK
3
T13
−0.0194
T23
−0.0047

REMARK
3
L TENSOR

REMARK
3
L11
1.1305
L22
2.0594

REMARK
3
L33
1.9843
L12
−0.9168

REMARK
3
L13
−0.9429
L23
0.0234

REMARK
3
S TENSOR

REMARK
3
S11
0.2826
S12
0.0211
S13
0.0458

REMARK
3
S21
−0.2669
S22
−0.2328
S23
−0.0999

REMARK
3
S31
0.0656
S32
0.1520
S33
−0.0498

REMARK
3

REMARK
3
TLS GROUP
3

REMARK
3
NUMBER OF COMPONENTS GROUP
2

REMARK
3
COMPONENTS
C
SSSEQI
TO
C
SSSEQI

REMARK
3
RESIDUE RANGE
R
48

R
91

REMARK
3
RESIDUE RANGE
R
660

R
669

REMARK
3
ORIGIN FOR THE GROUP (A)
10.5870
−22.0700
12.3180

REMARK
3
T TENSOR

REMARK
3
T11
0.2272
T22
0.2474

REMARK
3
T33
0.1882
T12
−0.0777

REMARK
3
T13
0.0168
T23
−0.0087

REMARK
3
L TENSOR

REMARK
3
L11
0.1830
L22
0.6966

REMARK
3
L33
1.2797
L12
−0.3101

REMARK
3
L13
−0.2750
L23
0.8510

REMARK
3
S TENSOR

REMARK
3
S11
0.0584
S12
−0.0168
S13
0.1455

REMARK
3
S21
−0.0360
S22
0.0024
S23
−0.1003

REMARK
3
S31
0.0043
S32
0.0515
S33
−0.0607

REMARK
3

REMARK
3
TLS GROUP
4

REMARK
3
NUMBER OF COMPONENT GROUP
1

REMARK
3
COMPONENTS
C
SSSEQI
TO
C
SSSEQI

REMARK
3
RESIDUE RANGE
P
7

P
96

REMARK
3
ORIGIN FOR THE GROUP (A)
5.2040
−4.4590
37.5330

REMARK
3
T TENSOR

REMARK
3
T11
0.1906
T22
0.1906

REMARK
3
T33
0.1906
T12
0.0000

REMARK
3
T13
0.0000
T23
0.0000

REMARK
3
L TENSOR

REMARK
3
L11
0.0000
L22
0.0000

REMARK
3
L33
0.0000
L12
0.0000

REMARK
3
L13
0.0000
L23
0.0000

REMARK
3
S TENSOR

REMARK
3
S11
0.0000
S12
0.0000
S13
0.0000

REMARK
3
S21
0.0000
S22
0.0000
S23
0.0000

REMARK
3
S31
0.0000
S32
0.0000
S33
0.0000

REMARK
3

REMARK
3
BULK SOLVENT MODELLING.

REMARK
3
METHOD USED MASK

REMARK
3
PARAMETERS FOR MASK CALCULATION

REMARK
3
VDW PROBE RADIUS
1.20

REMARK
3
ION PROBE RADIUS
0.80

REMARK
3
SHRINKAGE RADIUS
0.80

REMARK
3

REMARK
3
OTHER REFINEMENT REMARKS
HYDROGENS HAVE BEEN ADDED IN THE

REMARK
3
RIDING POSITIONS

REMARK
4

REMARK
4
3IRW COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK
100

REMARK
100
THIS ENTRY HAS BEEN PROCESSED BY RCSB.

REMARK
200
THE RCSB ID CODE IS RCSB054788.

REMARK
200
EXPERIMENTAL DETAILS

REMARK
200
EXPERIMENT TYPE
X-RAY DIFFRACTION

REMARK
200

REMARK
200
TEMPERATURE (KELVIN)
100

REMARK
200
PH
6.0

REMARK
200
NUMBER OF CRYSTALS USED
1

REMARK
200

REMARK
200
SYNCHROTRON (Y/N)
Y

REMARK
200
RADIATION SOURCE
NSLS

REMARK
200
BEAMLINE
X29A

REMARK
200
X-RAY GENERATOR MODEL
NULL

REMARK
200
MONOCHROMATIC OR LAUE (M/L)
M

REMARK
200
WAVELENGTH OR RANGE (A)
1.1050, 1.1054, 1.0762

REMARK
200
MONOCHROMATOR
DOUBLE CRYSTAL MONOCHROMETER

REMARK
200

WITH HORIZONTAL FOCUSING

REMARK
200

SAGITTAL BEND SECOND MONO

REMARK
200

CRYSTAL WITH 4:1 MAGNIFICATION

REMARK
200

RATIO AND VERTICALLY FOCUSING

REMARK
200

MIRROR.

REMARK
200
OPTICS
CRYOGENICALLY COOLED DOUBLE

REMARK
200

CRYSTAL MONOCHROMETER WITH

REMARK
200

HORIZONTAL FOCUSING SAGITTAL

REMARK
200

BEND SECOND MONO CRYSTAL WITH

REMARK
200

4:1 MAGNIFICATION RATIO AND

REMARK
200

VERTICALLY FOCUSING MIRROR.

REMARK
200

REMARK
200
DETECTOR TYPE
CCD

REMARK
200
DETECTOR MANUFACTURER
ADSC QUANTUM 315

REMARK
200
INTENSITY-INTEGRATION SOFTWARE
HKL-2000

REMARK
200
DATA SCALING SOFTWARE
HKL-2000

REMARK
200

REMARK
200
NUMBER OF UNIQUE REFLECTIONS
8935

REMARK
200
RESOLUTION RANGE HIGH (A)
2.700

REMARK
200
RESOLUTION RANGE LOW (A)
50.000

REMARK
200
REJECTION CRITERIA (SIGMA (I))
1.900

REMARK
200

REMARK
200
OVERALL.

REMARK
200
COMPLETENESS FOR RANGE (%)
94.8

REMARK
200
DATA REDUNDANCY
2.700

REMARK
200
R MERGE (I)
0.07200

REMARK
200
R SYM (I)
NULL

REMARK
200
<I/SIGMA (I) > FOR THE DATA SET
12.5000

REMARK
200

REMARK
200
IN THE HIGHEST RESOLUTION SHELL.

REMARK
200
HIGHEST RESOLUTION SHELL, RANGE HIGH (A)
2.70

REMARK
200
HIGHEST RESOLUTION SHELL, RANGE LOW (A)
2.80

REMARK
200
COMPLETENESS FOR SHELL (%)
82.4

REMARK
200
DATA REDUNDANCY IN SHELL
2.00

REMARK
200
R MERGE FOR SHELL (I)
0.38200

REMARK
200
R SYM FOR SHELL (I)
NULL

REMARK
200
<I/SIGMA (I) > FOR SHELL
1.900

REMARK
200

REMARK
200
DIFFRACTION PROTOCOL
MAD

REMARK
200
METHOD USED TO DETERMINE THE STRUCTURE
MAD

REMARK
200
SOFTWARE USED
SOLVE

REMARK
200
STARTING MODEL
NULL

REMARK
200

REMARK
200
REMARK
NULL

REMARK
280

REMARK
280
CRYSTAL

REMARK
280
SOLVENT CONTENT, VS (%)
40.15

REMARK
280
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA)
2.06

REMARK
280

REMARK
280
CRYSTALLIZATION CONDITIONS
22% PEG550MME, 50 MM MES, PH 6.0, 5

REMARK
280

MM MGSO4, 300 MM NACL, VAPOR DIFFUSION, HANGING DROP,

REMARK
280

TEMPERATURE 298K

REMARK
290

REMARK
290
CRYSTALLOGRAPHIC SYMMETRY

REMARK
290
SYMMETRY OPERATORS FOR SPACE GROUP
P 1 21 1

REMARK
290

REMARK
290
SYMOP
SYMMETRY

REMARK
290
NNNMMM
OPERATOR

REMARK
290
1555
X, Y, Z

REMARK
290
2555
−X, Y + 1/2, −Z

REMARK
290

REMARK
290
WHERE NNN → OPERATOR NUMBER

REMARK
290
MMM → TRANSLATION VECTOR

REMARK
290

REMARK
290
CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS

REMARK
290
THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM

REMARK
290
RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY

REMARK
290
RELATED MOLECULES.

REMARK
290
SMTRY1
1
1.000000
0.000000
0.000000
0.00000

REMARK
290
SMTRY2
1
0.000000
1.000000
0.000000
0.00000

REMARK
290
SMTRY3
1
0.000000
0.000000
1.000000
0.00000

REMARK
290
SMTRY1
2
−1.000000
0.000000
0.000000
0.00000

REMARK
290
SMTRY2
2
0.000000
1.000000
0.000000
22.56150

REMARK
290
SMTRY3
2
0.000000
0.000000
−1.000000
0.00000

REMARK
290

REMARK
290
REMARK
NULL

REMARK
300

REMARK
300
BIOMOLECULE
1

REMARK
300
SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM

REMARK
300
GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN

REMARK
300
THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON

REMARK
300
BURIED SURFACE AREA.

REMARK
350

REMARK
350
COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN

REMARK
350
BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE

REMARK
350
MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS

REMARK
350
GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND

REMARK
350
CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.

REMARK
350

REMARK
350
BIOMOLECULE
1

REMARK
350
AUTHOR DETERMINED BIOLOGICAL UNIT:
DIMERIC

REMARK
350
SOFTWARE DETERMINED QUATERNARY STRUCTURE
DIMERIC

REMARK
350
SOFTWARE USED
PISA

REMARK
350
TOTAL BURIED SURFACE AREA
6430 ANGSTROM**2

REMARK
350
SURFACE AREA OF THE COMPLEX
18100 ANGSTROM**2

REMARK
350
CHANGE IN SOLVENT FREE ENERGY
−34.0 KCAL/MOL

REMARK
350
APPLY THE FOLLOWING TO CHAINS
P, R

REMARK
350
BIOMT1
1
1.000000
0.000000
0.000000
0.00000

REMARK
350
BIOMT2
1
0.000000
1.000000
0.000000
0.00000

REMARK
350
BIOMT3
1
0.000000
0.000000
1.000000
0.00000

REMARK
465

REMARK
465
MISSING RESIDUES

REMARK
465
THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE

REMARK
465
EXPERIMENT. (M = MODEL NUMBER; RES = RESIDUE NAME; C = CHAIN

REMARK
465
IDENTIFIER; SSSEQ = SEQUENCE NUMBER; I = INSERTION CODE.)

REMARK
465

REMARK
465
M
RES
C
SSSEQI

REMARK
465

MET
P
1

REMARK
465

ALA
P
2

REMARK
465

VAL
P
3

REMARK
465

PRO
P
4

REMARK
465

GLU
P
5

REMARK
465

THR
P
6

REMARK
465

MET
P
97

REMARK
465

LYS
P
98

REMARK
465

G
R
98

REMARK
500

REMARK
500
GEOMETRY AND STEREOCHEMISTRY

REMARK
500
SUBTOPIC

REMARK
500

REMARK
500
TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS

REMARK
500
(M = MODEL NUMBER; RES = RESIDUE NAME; C = CHAIN IDENTIFIER;

REMARK
500
SSEQ = SEQUENCE NUMBER; I = INSERTION CODE).

REMARK
500

REMARK
500
STANDARD TABLE

REMARK
500
FORMAT (10X, I3, 1X, A3, 1X, A1, I4, A1,4X, F7.2, 3X, F7.2)

REMARK
500

REMARK
500
EXPECTED VALUES G. J. KLEYWEGT AND T. A. JONES (1996)

REMARK
500
PHI/PSI-CHOLOGY RAMACHANDRAN REVISITED. STRUCTURE 4, 1395-1400

REMARK
500

REMARK
500
M
CSSEQI
PSI
PHI

REMARK
500
PRO
P 8
141.69
−36.40

REMARK
500

REMARK
500
REMARK
NULL

REMARK
800

REMARK
800
SITE

REMARK
800
SITE_IDENTIFIER
AC1

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE C2E R 1

REMARK
800
SITE_IDENTIFIER
AC2

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 670

REMARK
800
SITE_IDENTIFIER
AC3

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 2

REMARK
800
SITE_IDENTIFIER
AC4

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 3

REMARK
800
SITE_IDENTIFIER
AC5

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 4

REMARK
800
SITE_IDENTIFIER
AC6

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 5

REMARK
800
SITE_IDENTIFIER
AC7

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 6

REMARK
800
SITE_IDENTIFIER
AC8

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 7

REMARK
800
SITE_IDENTIFIER
AC9

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 671

REMARK
800
SITE_IDENTIFIER
BC1

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE IRI R 672

REMARK
800
SITE_IDENTIFIER
BC2

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE MG R 673

REMARK
800
SITE_IDENTIFIER
BC3

REMARK
800
EVIDENCE_CODE
SOFTWARE

REMARK
800
SITE_DESCRIPTION
BINDING SITE FOR RESIDUE MG R 674

DBREF
3IRW
P
1
98
UNP
P09012
SNRPA_HUMAN
1
98

DBREF
3IRW
R
8
98
PDB
3IRW
3IRW
8
98

SEQADV
3IRW
HIS
P
31
UNP
P09012
TYR
31
ENGINEERED

SEQADV
3IRW
ARG
P
36
UNP
P09012
GLN
36
ENGINEERED

SEQRES
1
P
98
MET
ALA
VAL
PRO
GLU
THR
ARG
PRO
ASN
HIS
THR
ILE
TYR

SEQRES
2
P
98
ILE
ASN
ASN
LEU
ASN
GLU
LYS
ILE
LYS
LYS
ASP
GLU
LEU

SEQRES
3
P
98
LYS
LYS
SER
LEU
HIS
ALA
ILE
PHE
SER
ARG
PHE
GLY
GLN

SEQRES
4
P
98
ILE
LEU
ASP
ILE
LEU
VAL
SER
ARG
SER
LEU
LYS
MET
ARG

SEQRES
5
P
98
GLY
GLN
ALA
PHE
VAL
ILE
PHE
LYS
GLU
VAL
SER
SER
ALA

SEQRES
6
P
98
THR
ASN
ALA
LEU
ARG
SER
MET
GLN
GLY
PHE
PRO
PHE
TYR

SEQRES
7
P
98
ASP
LYS
PRO
MET
ARG
ILE
GLN
TYR
ALA
LYS
THR
ASP
SER

SEQRES
8
P
98
ASP
ILE
ILE
ALA
LYS
MET
LYS

SEQRES
1
R
92
GTP
G
U
C
A
C
G
C
A
C
A
G
G

SEQRES
2
R
92
G
C
A
A
A
C
C
A
U
U
C
G
A

SEQRES
3
R
92
A
A
G
A
G
U
G
G
G
A
C
G
C

SEQRES
4
R
92
A
A
A
G
C
C
U
C
C
G
G
C
C

SEQRES
5
R
92
U
A
A
A
C
C
A
U
U
G
C
A
C

SEQRES
6
R
92
U
C
C
G
G
U
A
G
G
U
A
G
C

SEQRES
7
R
92
G
G
G
G
U
U
A
C
C
G
A
U
G

SEQRES
8
R
92
G

MODRES
3IRW
GTP R 8
G
GUANOSINE-5′-TRIPHOSPHATE

HET
GTP
R
8
32

HET
C2E
R
1
46

HET
IRI
R
670
7

HET
IRI
R
2
7

HET
IRI
R
3
7

HET
IRI
R
4
7

HET
IRI
R
5
7

HET
IRI
R
6
7

HET
IRI
R
7
7

HET
IRI
R
671
7

HET
IRI
R
672
7

HET
MG
R
673
1

HET
MG
R
674
1

HETNAM

GTP
GUANOSINE-5′-TRIPHOSPHATE

HETNAM

C2E
9,9′-[(2R, 3R, 3AS, 5S, 7AR, 9R, 10R, 10AS, 12S, 14AR)-3, 5, 10,

HETNAM
2
C2E
12-TETRAHYDROXY-5, 12-DIOXIDOOCTAHYDRO-2H, 7H-DIFURO [3,

HETNAM
3
C2E
2-D
3′, 2′-J] [1, 3, 7, 9, 2,

HETNAM
4
C2E
8] TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS (2-AMINO-

HETNAM
5
C2E
1, 9-DIHYDRO-6H-PURIN-6-ONE)

HETNAM

IRI
IRIDIUM HEXAMMINE ION

HETNAM

MG
MAGNESIUM ION

HETSYN

C2E
C-DI-GMP, CYCLIC DIGUANOSINE MONOPHOSPHATE

FORMUL
2
GTP
C10
H16
N5
O14
P3

FORMUL
3
C2E
C20
H24
N10
O14
P2

FORMUL
4
IRI

9 (H18 IR N6 3+)

FORMUL
13
MG

2 (MG 2+)

FORMUL
15
HOH

*92 (H2 O)

HELIX
1
1
LYS
P
22
SER
P
35
1
14

HELIX
2
2
GLU
P
61
GLN
P
13
1
13

HELIX
3
3
SER
P
91
LYS
P
96
1
6

SHEET
1
A
4 ILE
P
40
LEU
P
44
0

SHEET
2
A
4 GLN
P
54
PHE
P
59
−1
O
PHE
P
56
N
LEU
P
44

SHEET
3
A
4 THR
P
11
ASN
P
15
−1
N
ILE
P
14
O
ALA
P
55

SHEET
4
A
4 ARG
P
83
TYR
P
86
−1
O
GLN
P
85
N
TYR
P
13

SHEET
1
B
2 PRO
P
76
PHE
P
77
0

SHEET
2
B
2 LYS
P
80
PRO
P
81
−1
O
LYS
P
80
N
PHE
P
77

LINK

O3′ GTP
R 8

P

G R 9
1555
1555
1.66

SITE
1
AC1
17
IRI
R
3
G
R
14
A
R
16
C
R
17

SITE
2
AC1
17
A
R
18
G
R
19
G
R
20
G
R
21

SITE
3
AC1
17
C
R
46
A
R
47
A
R
48
A
R
49

SITE
4
AC1
17
C
R
92
C
R
93
HOH
R
111
HOH
R
124

SITE
5
AC1
17
MG
R
674

SITE
1
AC2
6
C
R
46
A
R
47
A
R
48
A
R
49

SITE
2
AC2
6
G
R
85
HOH
R
182

SITE
1
AC3
9
U
R
53
G
R
56
G
R
57
C
R
58

SITE
2
AC3
9
G
R
80
U
R
81
HOH
R
102
HOH
R
104

SITE
3
AC3
9
IRI
R
672

SITE
1
AC4
4
C2E
R
1
C
R
17
G
R
19
G
R
20

SITE
1
AC5
6
IRI
R
7
A
R
82
G
R
85
G
R
86

SITE
2
AC5
6
G
R
87
HOH
R
172

SITE
1
AC6
5
GTP
R
8
G
R
9
U
R
10
U
R
96

SITE
2
AC6
5
G
R
97

SITE
1
AC7
3
G
R
32
A
R
34
HOH
R
180

SITE
1
AC8
5
IRI
R
4
G
R
87
G
R
88
U
R
89

SITE
2
AC8
5
HOH
R
114

SITE
1
AC9
4
A
R
24
A
R
25
G
R
83
C
R
84

SITE
1
BC1
5
IRI
R
2
A
R
78
G
R
79
G
R
80

SITE
2
BC1
5
HOH
R
104

SITE
1
BC2
4
C
R
22
A
R
23
G
R
45
A
R
49

SITE
1
BC3
3
C2E
R
1
C
R
15
HOH
R
111

CRYST1
49.461
45.123
76.573
90.00
96.79
90.00
P
1
21
1
2

ORIGX1

1.000000
0.000000
0.000000
0.00000

ORIGX2

0.000000
1.000000
0.000000
0.00000

ORIGX3

0.000000
0.000000
1.000000
0.00000

SCALE1

0.020218
0.000000
0.002407
0.00000

SCALE2

0.000000
0.022162
0.000000
0.00000

SCALE3

0.000000
0.000000
0.013152
0.00000

ATOM
1
N
ARG
P
7
16.117
5.580
45.389
1.00
65.85
N

ATOM
2
CA
ARG
P
7
15.276
4.383
45.100
1.00
65.87
C

ATOM
3
C
ARG
P
7
14.014
4.757
44.314
1.00
63.07
C

ATOM
4
O
ARG
P
7
13.846
4.342
43.165
1.00
64.31
O

ATOM
5
CB
ARG
P
7
14.910
3.660
46.400
1.00
68.45
C

ATOM
6
CG
ARG
P
7
15.967
3.800
47.475
1.00
71.49
C

ATOM
7
CD
ARG
P
7
17.323
4.079
46.841
1.00
74.93
C

ATOM
8
NE
ARG
P
7
18.218
4.814
47.734
1.00
77.44
N

ATOM
9
CZ
ARG
P
7
19.306
4.296
48.299
1.00
78.46
C

ATOM
10
NH1
ARG
P
7
19.640
3.033
48.066
1.00
78.97
N

ATOM
11
NH2
ARG
P
7
20.063
5.042
49.094
1.00
77.88
N

ATOM
12
N
PRO
P
8
13.136
5.569
44.921
1.00
58.80
N

ATOM
13
CA
PRO
P
8
11.886
5.877
44.245
1.00
55.18
C

ATOM
14
C
PRO
P
8
12.127
5.995
42.756
1.00
50.26
C

ATOM
15
O
PRO
P
8
13.158
6.509
42.346
1.00
49.42
O

ATOM
16
CB
PRO
P
8
11.496
7.244
44.828
1.00
55.70
C

ATOM
17
CG
PRO
P
8
12.724
7.743
45.526
1.00
56.88
C

ATOM
18
CD
PRO
P
8
13.428
6.529
45.991
1.00
57.73
C

ATOM
19
N
ASN
P
9
12.724
7.743
45.526
1.00
56.88
C

ATOM
20
CA
ASN
P
9
13.428
6.529
45.991
1.00
57.73
C

ATOM
21
C
ASN
P
9
11.190
5.09
41.952
1.00
46.63
N

ATOM
22
O
ASN
P
9
11.342
5.570
40.507
1.00
44.41
C

ATOM
23
CB
ASN
P
9
10.020
5.482
39.770
1.00
43.65
C

ATOM
24
CG
ASN
P
9
9.068
4.881
40.258
1.00
43.24
O

ATOM
25
OD1
ASN
P
9
12.268
4.466
40.016
1.00
44.08
C

ATOM
26
ND2
ASN
P
9
12.312
4.384
38.513
1.00
45.66
C

ATOM
27
N
HIS
P
10
9.967
6.081
38.586
1.00
43.82
N

ATOM
28
CA
HIS
P
10
8.783
5.983
37.752
1.00
44.80
C

ATOM
29
C
HIS
P
10
8.355
4.536
37.649
1.00
44.05
C

ATOM
30
O
HIS
P
10
7.167
4.225
37.666
1.00
46.50
O

ATOM
31
CB
HIS
P
10
9.053
6.542
36.356
1.00
47.55
C

ATOM
32
CG
HIS
P
10
8.996
8.033
36.285
1.00
50.24
C

ATOM
33
ND1
HIS
P
10
10.103
8.808
36.019
1.00
52.83
N

ATOM
34
CD2
HIS
P
10
7.965
8.894
36.456
1.00
51.71
C

ATOM
35
CE1
HIS
P
10
9.757
10.082
36.024
1.00
53.30
C

ATOM
36
NE2
HIS
P
10
8.465
10.162
36.289
1.00
52.72
N

ATOM
37
N
THR
P
11
9.337
3.649
37.559
1.00
42.19
N

ATOM
38
CA
THR
P
11
9.073
2.237
37.324
1.00
40.97
C

ATOM
39
C
THR
P
11
9.097
1.441
38.617
1.00
40.31
C

ATOM
40
O
THR
P
11
9.946
1.671
39.474
1.00
43.31
O

ATOM
41
CB
THR
P
11
10.114
1.632
36.378
1.00
41.38
C

ATOM
42
OG1
THR
P
11
10.080
2.315
35.118
1.00
40.77
O

ATOM
43
CG2
THR
P
11
9.832
0.156
36.162
1.00
43.47
C

ATOM
44
N
ILE
P
12
8.161
0.505
38.758
1.00
37.43
N

ATOM
45
CA
ILE
P
12
8.250
−0.495
39.812
1.00
34.40
C

ATOM
46
C
ILE
P
12
8.654
−1.825
39.213
1.00
33.85
C

ATOM
47
O
ILE
P
12
8.250
−2.162
38.099
1.00
35.37
O

ATOM
48
CB
ILE
P
12
6.927
−0.681
40.548
1.00
34.25
C

ATOM
49
CG1
ILE
P
12
5.829
−1.099
39.567
1.00
34.65
C

ATOM
50
CG2
ILE
P
12
6.557
0.584
41.307
1.00
33.71
C

ATOM
51
CD1
ILE
P
12
4.592
−1.649
40.246
1.00
35.76
C

ATOM
52
N
TYR
P
13
9.454
−2.580
39.957
1.00
31.59
N

ATOM
53
CA
TYR
P
13
9.951
−3.867
39.489
1.00
28.21
C

ATOM
54
C
TYR
P
13
9.316
−5.011
40.256
1.00
27.42
C

ATOM
55
O
TYR
P
13
9.510
−5.142
41.463
1.00
27.59
O

ATOM
56
CB
TYR
P
13
11.465
−3.933
39.633
1.00
26.24
C

ATOM
57
CG
TYR
P
13
12.045
−5.291
39.320
1.00
24.76
C

ATOM
58
CD1
TYR
P
13
12.380
−5.638
38.017
1.00
24.10
C

ATOM
59
CD2
TYR
P
13
12.264
−6.224
40.324
1.00
22.94
C

ATOM
60
CE1
TYR
P
13
12.912
−6.875
37.722
1.00
22.60
C

ATOM
61
CE2
TYR
P
13
12.795
−7.461
40.039
1.00
23.14
C

ATOM
62
CZ
TYR
P
13
13.120
−7.782
38.736
1.00
23.81
C

ATOM
63
OH
TYR
P
13
13.650
−9.016
38.445
1.00
26.97
O

ATOM
64
N
ILE
P
14
8.565
−5.843
39.540
1.00
28.92
N

ATOM
65
CA
ILE
P
14
7.842
−6.963
40.142
1.00
29.31
C

ATOM
66
C
ILE
P
14
8.450
−8.300
39.719
1.00
31.30
C

ATOM
67
O
ILE
P
14
8.883
−8.464
38.581
1.00
34.17
O

ATOM
68
CB
ILE
P
14
6.353
−6.956
39.723
1.00
25.69
C

ATOM
69
CG1
ILE
P
14
5.728
−5.587
39.992
1.00
27.39
C

ATOM
70
CG2
ILE
P
14
5.592
−8.046
40.450
1.00
23.46
C

ATOM
71
CD1
ILE
P
14
4.579
−5.244
39.058
1.00
28.67
C

ATOM
72
N
ASN
P
15
8.482
−9.254
40.639
1.00
30.49
N

ATOM
73
CA
ASN
P
15
8.834
−10.619
40.285
1.00
31.52
C

ATOM
74
C
ASN
P
15
8.252
−11.628
41.264
1.00
32.95
C

ATOM
75
O
ASN
P
15
7.461
−11.274
42.135
1.00
33.96
O

ATOM
76
CB
ASN
P
15
10.350
−10.785
40.129
1.00
29.88
C

ATOM
77
CG
ASN
P
15
11.093
−10.652
41.443
1.00
28.72
C

ATOM
78
OD1
ASN
P
15
10.502
−10.745
42.520
1.00
28.18
O

ATOM
79
ND2
ASN
P
15
12.399
−10.438
41.360
1.00
25.52
N

ATOM
80
N
ASN
P
16
8.631
−12.886
41.114
1.00
34.03
N

ATOM
81
CA
ASN
P
16
7.872
−13.957
41.719
1.00
38.58
C

ATOM
82
C
ASN
P
16
6.524
−14.042
41.020
1.00
38.19
C

ATOM
83
O
ASN
P
16
5.491
−14.273
41.649
1.00
34.49
O

ATOM
84
CB
ASN
P
16
7.673
−13.704
43.212
1.00
43.79
C

ATOM
85
CG
ASN
P
16
7.189
−14.941
43.954
1.00
48.13
C

ATOM
86
OD1
ASN
P
16
7.729
−16.037
43.776
1.00
49.26
O

ATOM
87
ND2
ASN
P
16
6.167
−14.771
44.796
1.00
49.89
N

ATOM
88
N
LEU
P
17
6.543
−13.827
39.711
1.00
38.85
N

ATOM
89
CA
LEU
P
17
5.335
−13.867
38.915
1.00
40.98
C

ATOM
90
C
LEU
P
17
5.104
−15.259
38.351
1.00
44.64
C

ATOM
91
O
LEU
P
17
5.966
−15.815
37.671
1.00
47.86
O

ATOM
92
CB
LEU
P
17
5.417
−12.853
37.774
1.00
39.61
C

ATOM
93
CG
LEU
P
17
5.183
−11.396
38.169
1.00
40.25
C

ATOM
94
CD1
LEU
P
17
5.301
−10.480
36.957
1.00
39.19
C

ATOM
95
CD2
LEU
P
17
3.825
−11.245
38.831
1.00
39.76
C

ATOM
96
N
ASN
P
18
3.938
−15.822
38.639
1.00
45.55
N

ATOM
97
CA
ASN
P
18
3.537
−17.080
38.039
1.00
47.33
C

ATOM
98
C
ASN
P
18
3.933
−17.118
36.568
1.00
48.21
C

ATOM
99
O
ASN
P
18
3.406
−16.367
35.756
1.00
48.00
O

ATOM
100
CB
ASN
P
18
2.029
−17.277
38.196
1.00
49.62
C

ATOM
101
CG
ASN
P
18
1.575
−18.662
37.789
1.00
51.13
C

ATOM
102
OD1
ASN
P
18
2.082
−19.235
36.827
1.00
52.54
O

ATOM
103
ND2
ASN
P
18
0.603
−19.204
38.516
1.00
50.93
N

ATOM
104
N
GLU
P
19
4.881
−17.984
36.235
1.00
51.19
N

ATOM
105
CA
GLU
P
19
5.425
−18.041
34.885
1.00
53.14
C

ATOM
106
C
GLU
P
19
4.460
−18.699
33.903
1.00
52.91
C

ATOM
107
O
GLU
P
19
4.646
−18.609
32.691
1.00
52.48
O

ATOM
108
CB
GLU
P
19
6.765
−18.777
34.884
1.00
56.11
C

ATOM
109
CG
GLU
P
19
7.772
−18.228
35.890
1.00
60.92
C

ATOM
110
CD
GLU
P
19
8.996
−19.122
36.050
1.00
64.18
C

ATOM
111
OE1
GLU
P
19
9.110
−20.121
35.304
1.00
66.27
O

ATOM
112
OE2
GLU
P
19
9.843
−18.824
36.920
1.00
64.11
O

ATOM
113
N
LYS
P
20
3.435
−19.361
34.431
1.00
53.78
N

ATOM
114
CA
LYS
P
20
2.452
−20.052
33.602
1.00
56.29
C

ATOM
115
C
LYS
P
20
1.589
−1.069
32.824
1.00
57.25
C

ATOM
116
O
LYS
P
20
1.039
−19.408
31.783
1.00
57.10
O

ATOM
117
CB
LYS
P
20
1.559
−20.934
34.468
1.00
59.72
C

ATOM
118
CG
LYS
P
20
2.307
−21.957
35.306
1.00
63.26
C

ATOM
119
CD
LYS
P
20
2.408
−23.291
34.584
1.00
66.82
C

ATOM
120
CE
LYS
P
20
2.641
−24.433
35.564
1.00
68.54
C

ATOM
121
NZ
LYS
P
20
2.374
−25.763
34.944
1.00
69.09
N

ATOM
122
N
ILE
P
21
1.465
−17.853
33.347
1.00
60.41
N

ATOM
123
CA
ILE
P
21
0.668
−16.804
32.711
1.00
62.91
C

ATOM
124
C
ILE
P
21
1.354
−16.295
31.448
1.00
64.83
C

ATOM
125
O
ILE
P
21
2.578
−16.295
31.362
1.00
65.70
O

ATOM
126
CB
ILE
P
21
0.454
−15.605
33.666
1.00
63.76
C

ATOM
127
CG1
ILE
P
21
0.200
−16.088
35.097
1.00
63.92
C

ATOM
128
CG2
ILE
P
21
−0.680
−14.714
33.175
1.00
64.23
C

ATOM
129
CD1
ILE
P
21
−0.940
−17.061
35.224
1.00
64.18
C

ATOM
130
N
LYS
P
22
0.563
−15.851
30.477
1.00
68.28
N

ATOM
131
CA
LYS
P
22
1.103
−15.394
29.194
1.00
71.67
C

ATOM
132
C
LYS
P
22
1.271
−13.874
29.132
1.00
71.30
C

ATOM
133
O
LYS
P
22
0.536
−13.130
29.783
1.00
71.93
O

ATOM
134
CB
LYS
P
22
0.220
−15.879
28.040
1.00
75.07
C

ATOM
135
CG
LYS
P
22
0.193
−17.392
27.881
1.00
77.61
C

ATOM
136
CD
LYS
P
22
−1.092
−17.862
27.224
1.00
79.09
C

ATOM
137
CE
LYS
P
22
1.205
−19.375
27.281
1.00
80.18
C

ATOM
138
NZ
LYS
P
22
2.531
−19.854
26.809
1.00
80.59
N

ATOM
139
N
LYS
P
23
2.243
−13.421
28.347
1.00
70.76
N

ATOM
140
CA
LYS
P
23
2.499
−11.995
28.204
1.00
70.18
C

ATOM
141
C
LYS
P
23
1.191
−11.217
28.078
1.00
70.61
C

ATOM
142
O
LYS
P
23
0.960
−10.245
28.797
1.00
71.09
O

ATOM
143
CB
LYS
P
23
3.388
−11.724
26.990
1.00
68.82
C

ATOM
144
CG
LYS
P
23
3.681
−10.257
26.779
1.00
69.40
C

ATOM
145
CD
LYS
P
23
4.128
−9.972
25.366
1.00
70.66
C

ATOM
146
CE
LYS
P
23
4.207
−8.473
25.122
1.00
71.73
C

ATOM
147
NZ
LYS
P
23
4.627
−8.151
23.732
1.00
72.61
N

ATOM
148
N
ASP
P
24
0.338
−11.655
27.160
1.00
70.93
N

ATOM
149
CA
ASP
P
24
−0.923
−10.976
26.898
1.00
71.75
C

ATOM
150
C
ASP
P
24
−1.731
−10.760
28.171
1.00
70.49
C

ATOM
151
O
ASP
P
24
−2.027
−9.625
28.544
1.00
70.20
O

ATOM
152
CB
ASP
P
24
−1.749
−11.773
25.894
1.00
75.00
C

ATOM
153
CG
ASP
P
24
−0.957
−12.150
24.661
1.00
78.87
C

ATOM
154
OD1
ASP
P
24
−0.173
−11.306
24.172
1.00
80.64
O

ATOM
155
OD2
ASP
P
24
−1.122
−13.290
24.175
1.00
80.62
O

ATOM
156
N
GLU
P
25
−2.093
−11.858
28.827
1.00
68.88
N

ATOM
157
CA
GLU
P
25
−2.966
−11.816
29.999
1.00
67.17
C

ATOM
158
C
GLU
P
25
−2.268
−11.206
31.219
1.00
62.68
C

ATOM
159
O
GLU
P
25
−2.844
−10.373
31.930
1.00
59.88
O

ATOM
160
CB
GLU
P
25
−3.474
−13.223
30.323
1.00
71.37
C

ATOM
161
CG
GLU
P
25
−4.607
−13.265
31.335
1.00
76.85
C

ATOM
162
CD
GLU
P
25
−5.133
−14.671
31.563
1.00
80.24
C

ATOM
163
OE1
GLU
P
25
−4.626
−15.613
30.913
1.00
81.74
O

ATOM
164
OE2
GLU
P
25
−6.056
−14.835
32.392
1.00
81.75
O

ATOM
165
N
LEU
P
26
−1.032
−11.629
31.460
1.00
59.23
N

ATOM
166
CA
LEU
P
26
−0.228
−11.053
32.526
1.00
56.27
C

ATOM
167
C
LEU
P
26
−0.312
−9.534
32.466
1.00
54.01
C

ATOM
168
O
LEU
P
26
−0.619
−8.883
33.462
1.00
54.32
O

ATOM
169
CB
LEU
P
26
1.228
−11.511
32.412
1.00
56.46
C

ATOM
170
CG
LEU
P
26
2.199
−11.008
33.487
1.00
56.26
C

ATOM
171
CD1
LEU
P
26
1.671
−11.313
34.878
1.00
56.09
C

ATOM
172
CD2
LEU
P
26
3.580
−11.618
33.291
1.00
56.41
C

ATOM
173
N
LYS
P
27
−0.044
−8.974
31.291
1.00
52.19
N

ATOM
174
CA
LYS
P
27
−0.194
−7.536
31.088
1.00
52.38
C

ATOM
175
C
LYS
P
27
−1.594
−7.068
31.508
1.00
52.14
C

ATOM
176
O
LYS
P
27
−1.747
−6.328
32.482
1.00
51.14
O

ATOM
177
CB
LYS
P
27
0.070
−7.160
29.626
1.00
53.07
C

ATOM
178
CG
LYS
P
27
1.527
−7.253
29.191
1.00
54.90
C

ATOM
179
CD
LYS
P
27
1.774
−6.405
27.946
1.00
56.94
C

ATOM
180
CE
LYS
P
27
2.960
−6.914
27.134
1.00
59.34
C

ATOM
181
NZ
LYS
P
27
3.152
−6.110
25.888
1.00
59.48
N

ATOM
182
N
LYS
P
28
−2.609
−7.513
30.772
1.00
50.89
C

ATOM
183
CA
LYS
P
28
−3.988
−7.119
31.041
1.00
48.47
C

ATOM
184
C
LYS
P
28
−4.289
−7.078
32.531
1.00
44.28
C

ATOM
185
O
LYS
P
28
−4.828
−6.096
33.031
1.00
44.61
O

ATOM
186
CB
LYS
P
28
−4.968
−8.062
30.341
1.00
51.22
C

ATOM
187
CG
LYS
P
28
−4.948
−7.965
28.826
1.00
54.17
C

ATOM
188
CD
LYS
P
28
−6.107
−8.738
28.200
1.00
57.22
C

ATOM
189
CE
LYS
P
28
−7.453
−8.128
28.580
1.00
58.23
C

ATOM
190
NZ
LYS
P
28
−8.576
−8.743
27.816
1.00
58.78
N

ATOM
191
N
SER
P
29
−3.947
−8.151
33.235
1.00
40.58
N

ATOM
192
CA
SER
P
29
−4.279
−8.266
34.654
1.00
40.33
C

ATOM
193
C
SER
P
29
−3.473
−7.296
35.512
1.00
40.48
C

ATOM
194
O
SER
P
29
−4.029
−6.573
36.337
1.00
40.54
O

ATOM
195
CB
SER
P
29
−4.058
−9.694
35.130
1.00
41.38
C

ATOM
196
OG
SER
P
29
−4.360
−10.612
34.095
1.00
45.40
O

ATOM
197
N
LEU
P
30
−2.159
−7.287
35.313
1.00
40.33
N

ATOM
198
CA
LEU
P
30
−1.293
−6.318
35.966
1.00
41.65
C

ATOM
199
C
LEU
P
30
−1.811
−4.912
35.734
1.00
41.49
C

ATOM
200
O
LEU
P
30
−1.870
−4.099
36.656
1.00
40.17
O

ATOM
201
CB
LEU
P
30
0.130
−6.429
35.423
1.00
42.72
C

ATOM
202
CG
LEU
P
30
0.940
−7.633
35.894
1.00
42.81
C

ATOM
203
CD1
LEU
P
30
2.185
−7.798
35.042
1.00
42.32
C

ATOM
204
CD2
LEU
P
30
1.301
−7.479
37.365
1.00
42.47
C

ATOM
205
N
HIS
P
31
−2.174
−4.630
34.487
1.00
42.08
N

ATOM
206
CA
HIS
P
31
−2.697
−3.327
34.111
1.00
43.91
C

ATOM
207
C
HIS
P
31
−4.009
−3.071
34.819
1.00
44.94
C

ATOM
208
O
HIS
P
31
−4.330
−1.932
35.164
1.00
43.98
O

ATOM
209
CB
HIS
P
31
−2.914
−3.254
32.601
1.00
46.73
C

ATOM
210
CG
HIS
P
31
−3.088
−1.860
32.086
1.00
49.37
C

ATOM
211
ND1
HIS
P
31
−2.261
−1.313
31.127
1.00
50.36
N

ATOM
212
CD2
HIS
P
31
−3.979
−0.893
32.411
1.00
50.81
C

ATOM
213
CE1
HIS
P
31
−2.643
−0.074
30.875
1.00
51.61
C

ATOM
214
NE2
HIS
P
31
−3.682
0.206
31.642
1.00
51.85
N

ATOM
215
N
ALA
P
32
−4.775
−4.139
35.021
1.00
45.32
N

ATOM
216
CA
ALA
P
32
−6.021
−4.059
35.761
1.00
45.72
C

ATOM
217
C
ALA
P
32
−5.745
−3.641
37.202
1.00
47.02
C

ATOM
218
O
ALA
P
32
−6.109
−2.543
37.626
1.00
49.01
O

ATOM
219
CB
ALA
P
32
−6.748
−5.396
35.720
1.00
45.07
C

ATOM
220
N
ILE
P
33
−5.082
−4.516
37.945
1.00
46.31
N

ATOM
221
CA
ILE
P
33
−4.754
−4.238
39.329
1.00
46.66
C

ATOM
222
C
ILE
P
33
−4.100
−2.872
39.518
1.00
46.79
C

ATOM
223
O
ILE
P
33
−4.594
−2.046
40.283
1.00
48.82
O

ATOM
224
CB
ILE
P
33
−3.832
−5.309
39.902
1.00
48.53
C

ATOM
225
CG1
ILE
P
33
−4.589
−6.631
40.042
1.00
50.96
C

ATOM
226
CG2
ILE
P
33
−3.278
−4.863
41.238
1.00
49.59
C

ATOM
227
CD1
ILE
P
33
−3.909
−7.635
40.953
1.00
52.51
C

ATOM
228
N
PHE
P
34
−2.997
−2.635
38.812
1.00
45.81
N

ATOM
229
CA
PHE
P
34
−2.132
−1.482
39.101
1.00
45.34
C

ATOM
230
C
PHE
P
34
−2.617
−0.155
38.528
1.00
48.47
C

ATOM
231
O
PHE
P
34
−2.269
−0.905
39.042
1.00
51.35
O

ATOM
232
CB
PHE
P
34
−0.697
−1.742
38.635
1.00
41.84
C

ATOM
233
CG
PHE
P
34
0.130
−2.517
39.616
1.00
39.60
C

ATOM
234
CD1
PHE
P
34
0.368
−2.021
40.881
1.00
39.86
C

ATOM
235
CD2
PHE
P
34
0.685
−3.733
39.266
1.00
39.00
C

ATOM
236
CE1
PHE
P
34
1.133
−2.732
41.784
1.00
39.92
C

ATOM
237
CE2
PHE
P
34
1.450
−4.444
40.163
1.00
38.04
C

ATOM
238
CZ
PHE
P
34
1.674
−3.944
41.421
1.00
38.72
C

ATOM
239
N
SER
P
35
−3.390
−0.200
37.450
1.00
49.94
N

ATOM
240
CA
SER
P
35
−3.870
1.036
36.843
1.00
50.21
C

ATOM
241
C
SER
P
35
−4.704
1.810
37.855
1.00
50.91
C

ATOM
242
O
SER
P
35
−5.112
2.943
37.611
1.00
51.51
O

ATOM
243
CB
SER
P
35
−4.677
0.749
35.576
1.00
49.75
C

ATOM
244
OG
SER
P
35
−5.826
−0.019
35.866
1.00
50.59
O

ATOM
245
N
ARG
P
36
−4.925
1.191
39.007
1.00
52.38
N

ATOM
246
CA
ARG
P
36
−5.704
1.796
40.078
1.00
54.48
C

ATOM
247
C
ARG
P
36
−4.952
2.919
40.795
1.00
53.85
C

ATOM
248
O
ARG
P
36
−5.551
3.703
41.526
1.00
56.03
O

ATOM
249
CB
ARG
P
36
−6.125
0.719
41.086
1.00
58.05
C

ATOM
250
CG
ARG
P
36
−6.422
1.243
42.481
1.00
62.15
C

ATOM
251
CD
ARG
P
36
−7.031
0.158
43.359
1.00
66.94
C

ATOM
252
NE
ARG
P
36
−7.168
0.588
44.750
1.00
71.00
N

ATOM
253
CZ
ARG
P
36
−6.362
0.203
45.737
1.00
73.33
C

ATOM
254
NH1
ARG
P
36
−6.561
0.646
46.971
1.00
74.17
N

ATOM
255
NH2
ARG
P
36
−5.360
−0.630
45.494
1.00
74.24
N

ATOM
256
N
PHE
P
37
−3.643
2.999
40.581
1.00
52.70
N

ATOM
257
CA
PHE
P
37
−2.797
3.889
41.382
1.00
51.39
C

ATOM
258
C
PHE
P
37
−2.303
5.107
40.600
1.00
49.12
C

ATOM
259
O
PHE
P
37
−1.761
6.044
41.179
1.00
47.92
O

ATOM
260
CB
PHE
P
37
−1.608
3.114
41.971
1.00
54.27
C

ATOM
261
CG
PHE
P
37
−2.008
1.900
42.782
1.00
56.34
C

ATOM
262
CD1
PHE
P
37
−2.372
2.027
44.116
1.00
56.49
C

ATOM
263
CD2
PHE
P
37
−2.019
0.631
42.206
1.00
56.47
C

ATOM
264
CE1
PHE
P
37
−2.746
0.915
44.861
1.00
56.52
C

ATOM
265
CE2
PHE
P
37
−2.391
−0.486
42.947
1.00
56.54
C

ATOM
266
CZ
PHE
P
37
−2.752
−0.343
44.275
1.00
56.88
C

ATOM
267
N
GLY
P
38
−2.496
5.087
39.286
1.00
48.43
N

ATOM
268
CA
GLY
P
38
−2.051
6.173
38.421
1.00
47.18
C

ATOM
269
C
GLY
P
38
−2.114
5.776
36.957
1.00
49.08
C

ATOM
270
O
GLY
P
38
−2.815
4.833
36.591
1.00
50.08
O

ATOM
271
N
GLN
P
39
−1.382
6.499
36.118
1.00
50.85
N

ATOM
272
CA
GLN
P
39
−1.308
6.192
34.689
1.00
51.77
C

ATOM
273
C
GLN
P
39
−0.079
5.344
34.365
1.00
48.32
C

ATOM
274
O
GLN
P
39
−1.032
5.665
34.778
1.00
48.45
O

ATOM
275
CB
GLN
P
39
−1.268
7.486
33.868
1.00
56.73
C

ATOM
276
CG
GLN
P
39
−2.633
8.056
33.512
1.00
61.87
C

ATOM
277
CD
GLN
P
39
−3.203
7.461
32.235
1.00
65.23
C

ATOM
278
OE1
GLN
P
39
−2.460
6.999
31.365
1.00
65.65
O

ATOM
279
NE2
GLN
P
39
−4.529
7.478
32.112
1.00
66.82
N

ATOM
280
N
ILE
P
40
−0.278
4.269
33.614
1.00
45.22
N

ATOM
281
CA
ILE
P
40
0.834
3.416
33.219
1.00
42.32
C

ATOM
282
C
ILE
P
40
1.336
3.767
31.831
1.00
41.09
C

ATOM
283
O
ILE
P
40
0.667
3.506
30.836
1.00
39.48
O

ATOM
284
CB
ILE
P
40
0.445
1.942
33.234
1.00
40.55
C

ATOM
285
CG1
ILE
P
40
−0.040
1.538
34.627
1.00
39.66
C

ATOM
286
CG2
ILE
P
40
1.624
1.085
32.785
1.00
39.94
C

ATOM
287
CD1
ILE
P
40
−1.003
0.367
34.620
1.00
39.85
C

ATOM
288
N
LEU
P
41
2.519
4.360
31.764
1.00
41.96
N

ATOM
289
CA
LEU
P
41
3.128
4.654
30.482
1.00
42.21
C

ATOM
290
C
LEU
P
41
3.272
3.367
29.683
1.00
43.30
C

ATOM
291
O
LEU
P
41
3.191
3.371
28.458
1.00
43.86
O

ATOM
292
CB
LEU
P
41
4.495
5.311
30.667
1.00
41.19
C

ATOM
293
CG
LEU
P
41
4.520
6.701
31.298
1.00
40.15
C

ATOM
294
CD1
LEU
P
41
5.910
7.311
31.165
1.00
40.82
C

ATOM
295
CD2
LEU
P
41
3.476
7.600
30.658
1.00
39.61
C

ATOM
296
N
ASP
P
42
3.486
2.256
30.377
1.00
44.29
N

ATOM
297
CA
ASP
P
42
3.627
0.976
29.696
1.00
45.28
C

ATOM
298
C
ASP
P
42
3.782
0.150
30.710
1.00
44.67
C

ATOM
299
O
ASP
P
42
3.901
0.089
31.912
1.00
43.93
O

ATOM
300
CB
ASP
P
42
4.648
1.087
28.561
1.00
47.47
C

ATOM
301
CG
ASP
P
42
4.617
−0.110
27.630
1.00
50.45
C

ATOM
302
OD1
ASP
P
42
3.719
−0.964
27.787
1.00
53.08
O

ATOM
303
OD2
ASP
P
42
5.491
−0.196
26.741
1.00
49.90
O

ATOM
304
N
ILE
P
43
3.782
−1.379
30.207
1.00
43.66
N

ATOM
305
CA
ILE
P
43
3.967
−2.557
31.039
1.00
44.64
C

ATOM
306
C
ILE
P
43
4.848
−3.470
30.200
1.00
48.36
C

ATOM
307
O
ILE
P
43
4.480
−3.845
29.088
1.00
51.07
O

ATOM
308
CB
ILE
P
43
2.713
−3.333
31.470
1.00
43.21
C

ATOM
309
CG1
ILE
P
43
1.867
−2.495
32.425
1.00
42.61
C

ATOM
310
CG2
ILE
P
43
3.101
−4.634
32.138
1.00
42.25
C

ATOM
311
CD1
ILE
P
43
0.636
−3.203
32.906
1.00
41.22
C

ATOM
312
N
LEU
P
44
6.012
−3.825
30.734
1.00
50.85
N

ATOM
313
CA
LEU
P
44
6.969
−4.648
29.999
1.00
52.91
C

ATOM
314
C
LEU
P
44
7.065
−6.056
30.572
1.00
53.68
C

ATOM
315
O
LEU
P
44
7.469
−6.246
31.716
1.00
53.24
O

ATOM
316
CB
LEU
P
44
8.350
−3.987
29.975
1.00
53.86
C

ATOM
317
CG
LEU
P
44
8.463
−2.722
29.121
1.00
55.23
C

ATOM
318
CD1
LEU
P
44
9.917
−2.431
28.779
1.00
55.69
C

ATOM
319
CD2
LEU
P
44
7.629
−2.861
27.853
1.00
55.40
C

ATOM
320
N
VAL
P
45
6.700
−7.040
29.761
1.00
55.92
N

ATOM
321
CA
VAL
P
45
6.709
−8.427
30.184
1.00
58.43
C

ATOM
322
C
VAL
P
45
7.323
−9.308
29.104
1.00
61.53
C

ATOM
323
O
VAL
P
45
6.777
−9.431
28.008
1.00
63.62
O

ATOM
324
CB
VAL
P
45
5.278
−8.930
30.477
1.00
59.09
C

ATOM
325
CG1
VAL
P
45
5.304
−10.382
30.936
1.00
58.85
C

ATOM
326
CG2
VAL
P
45
4.606
−8.048
31.517
1.00
58.90
C

ATOM
327
N
SER
P
46
8.463
−9.914
29.415
1.00
63.98
N

ATOM
328
CA
SER
P
46
9.080
−10.897
28.525
1.00
66.75
C

ATOM
329
C
SER
P
46
9.228
−12.250
29.227
1.00
66.16
C

ATOM
330
O
SER
P
46
9.376
−12.315
30.447
1.00
66.61
O

ATOM
331
CB
SER
P
46
10.440
−10.397
28.017
1.00
69.65
C

ATOM
332
OG
SER
P
46
11.244
−9.910
29.081
1.00
72.33
O

ATOM
333
N
ARG
P
47
9.178
−13.328
28.454
1.00
64.93
N

ATOM
334
CA
ARG
P
47
9.194
−14.665
29.028
1.00
64.38
C

ATOM
335
C
ARG
P
47
10.467
−15.426
28.681
1.00
63.72
C

ATOM
336
O
ARG
P
47
10.507
−16.653
28.755
1.00
65.02
O

ATOM
337
CB
ARG
P
47
7.958
−15.445
28.587
1.00
65.29
C

ATOM
338
CG
ARG
P
47
6.658
−14.740
28.931
1.00
67.94
C

ATOM
339
CD
ARG
P
47
5.467
−15.418
28.291
1.00
70.60
C

ATOM
340
NE
ARG
P
47
5.205
−16.730
28.874
1.00
72.42
N

ATOM
341
CZ
ARG
P
47
4.159
−17.489
28.561
1.00
73.22
C

ATOM
342
NH1
ARG
P
47
3.269
−17.065
27.670
1.00
74.07
N

ATOM
343
NH2
ARG
P
47
3.998
−18.672
29.141
1.00
72.68
N

ATOM
344
N
SER
P
48
11.510
−14.690
28.313
1.00
61.48
N

ATOM
345
CA
SER
P
48
12.798
−15.296
28.023
1.00
59.38
C

ATOM
346
C
SER
P
48
13.409
−15.870
29.294
1.00
58.59
C

ATOM
347
O
SER
P
48
12.975
−15.560
30.401
1.00
56.07
O

ATOM
348
CB
SER
P
48
13.747
−14.275
27.397
1.00
59.80
C

ATOM
349
OG
SER
P
48
14.267
−13.397
28.378
1.00
61.08
O

ATOM
350
N
LEU
P
49
14.426
−16.702
29.127
1.00
60.15
N

ATOM
351
CA
LEU
P
49
15.028
−17.406
30.247
1.00
61.91
C

ATOM
352
C
LEU
P
49
15.094
−16.572
31.516
1.00
60.16
C

ATOM
353
O
LEU
P
49
14.679
−17.016
32.584
1.00
57.78
O

ATOM
354
CB
LEU
P
49
16.428
−17.886
29.886
1.00
65.03
C

ATOM
355
CG
LEU
P
49
17.207
−18.480
31.059
1.00
67.24
C

ATOM
356
CD1
LEU
P
49
16.489
−19.709
31.616
1.00
66.68
C

ATOM
357
CD2
LEU
P
49
18.635
−18.819
30.642
1.00
68.26
C

ATOM
358
N
LYS
P
50
15.637
−15.370
31.403
1.00
61.56
N

ATOM
359
CA
LYS
P
50
15.950
−14.589
32.588
1.00
65.05
C

ATOM
360
C
LYS
P
50
15.207
−13.257
32.669
1.00
65.67
C

ATOM
361
O
LYS
P
50
15.556
−12.391
33.474
1.00
68.13
O

ATOM
362
CB
LYS
P
50
17.464
−14.398
32.724
1.00
67.23
C

ATOM
363
CG
LYS
P
50
18.158
−15.588
33.373
1.00
69.34
C

ATOM
364
CD
LYS
P
50
19.643
−15.630
33.059
1.00
71.12
C

ATOM
365
CE
LYS
P
50
20.273
−16.911
33.600
1.00
72.28
C

ATOM
366
NZ
LYS
P
50
21.687
−17.084
33.160
1.00
72.63
N

ATOM
367
N
MET
P
51
14.174
−13.102
31.850
1.00
63.36
N

ATOM
368
CA
MET
P
51
13.242
−11.988
32.014
1.00
61.92
C

ATOM
369
C
MET
P
51
11.885
−12.486
32.502
1.00
58.67
C

ATOM
370
O
MET
P
51
10.905
−11.744
32.523
1.00
57.56
O

ATOM
371
CB
MET
P
51
13.085
−11.212
30.708
1.00
63.86
C

ATOM
372
CG
MET
P
51
14.190
−10.207
30.467
1.00
65.21
C

ATOM
373
SD
MET
P
51
14.732
−9.442
32.005
1.00
67.41
S

ATOM
374
CE
MET
P
51
13.254
−8.560
32.508
1.00
66.92
C

ATOM
375
N
ARG
P
52
11.853
−13.744
32.919
1.00
55.77
N

ATOM
376
CA
ARG
P
52
10.611
−14.435
33.207
1.00
53.00
C

ATOM
377
C
ARG
P
52
10.301
−14.443
34.701
1.00
49.79
C

ATOM
378
O
ARG
P
52
11.206
−14.466
35.534
1.00
50.96
O

ATOM
379
CB
ARG
P
52
10.688
−15.861
32.664
1.00
56.41
C

ATOM
380
CG
ARG
P
52
9.721
−16.831
33.289
1.00
61.70
C

ATOM
381
CD
ARG
P
52
9.814
−18.199
32.624
1.00
66.08
C

ATOM
382
NE
ARG
P
52
11.195
−18.662
32.486
1.00
69.08
N

ATOM
383
CZ
ARG
P
52
11.774
−18.964
31.325
1.00
71.34
C

ATOM
384
NH1
ARG
P
52
11.094
−18.858
30.190
1.00
71.49
N

ATOM
385
NH2
ARG
P
52
13.032
−19.382
31.300
1.00
73.22
N

ATOM
386
N
GLY
P
53
9.015
−14.421
35.034
1.00
45.88
N

ATOM
387
CA
GLY
P
53
8.586
−14.354
36.425
1.00
40.45
C

ATOM
388
C
GLY
P
53
8.729
−12.950
36.968
1.00
35.94
C

ATOM
389
O
GLY
P
53
8.723
−12.734
38.175
1.00
35.59
O

ATOM
390
N
GLN
P
54
8.854
−11.991
36.067
1.00
34.14
N

ATOM
391
CA
GLN
P
54
9.032
−10.609
36.458
1.00
35.98
C

ATOM
392
C
GLN
P
54
8.381
−9.680
35.451
1.00
36.24
C

ATOM
393
O
GLN
P
54
8.112
−10.072
34.313
1.00
37.88
O

ATOM
394
CB
GLN
P
54
10.521
−10.284
36.601
1.00
37.48
C

ATOM
395
CG
GLN
P
54
11.378
−10.783
35.445
1.00
38.49
C

ATOM
396
CD
GLN
P
54
12.769
−11.205
35.889
1.00
37.89
C

ATOM
397
OE1
GLN
P
54
13.467
−10.459
36.571
1.00
38.70
O

ATOM
398
NE2
GLN
P
54
13.175
−12.410
35.501
1.00
36.17
N

ATOM
399
N
ALA
P
55
8.121
−8.451
35.876
1.00
33.70
N

ATOM
400
CA
ALA
P
55
7.499
−7.467
35.013
1.00
32.99
C

ATOM
401
C
ALA
P
55
7.790
−6.070
35.510
1.00
34.50
C

ATOM
402
O
ALA
P
55
7.893
−5.839
36.712
1.00
36.40
O

ATOM
403
CB
ALA
P
55
6.007
−7.699
34.942
1.00
32.86
C

ATOM
404
N
PHE
P
56
7.926
−5.135
34.578
1.00
35.98
N

ATOM
405
CA
PHE
P
56
8.159
−3.742
34.928
1.00
37.78
C

ATOM
406
C
PHE
P
56
6.893
−2.938
34.703
1.00
36.55
C

ATOM
407
O
PHE
P
56
6.269
−3.039
33.654
1.00
38.42
O

ATOM
408
CB
PHE
P
56
9.300
−3.164
34.089
1.00
39.36
C

ATOM
409
CG
PHE
P
56
10.620
−3.842
34.314
1.00
41.17
C

ATOM
410
CD1
PHE
P
56
11.003
−4.920
33.534
1.00
41.97
C

ATOM
411
CD2
PHE
P
56
11.479
−3.404
35.312
1.00
41.86
C

ATOM
412
CE1
PHE
P
56
12.218
−5.549
33.745
1.00
43.09
C

ATOM
413
CE2
PHE
P
56
12.695
−4.026
35.525
1.00
40.82
C

ATOM
414
CZ
PHE
P
56
13.064
−5.099
34.742
1.00
41.93
C

ATOM
415
N
VAL
P
57
6.508
−2.145
35.690
1.00
35.05
N

ATOM
416
CA
VAL
P
57
5.346
−1.293
35.542
1.00
34.82
C

ATOM
417
C
VAL
P
57
5.731
0.172
35.654
1.00
37.17
C

ATOM
418
O
VAL
P
57
6.046
0.660
36.743
1.00
37.39
O

ATOM
419
CB
VAL
P
57
4.269
−1.622
36.572
1.00
35.14
C

ATOM
420
CG1
VAL
P
57
3.122
−0.639
36.457
1.00
34.80
C

ATOM
421
CG2
VAL
P
57
3.774
−3.046
36.371
1.00
35.15
C

ATOM
422
N
ILE
P
58
5.707
0.865
34.517
1.00
38.97
N

ATOM
423
CA
ILE
P
58
6.123
2.265
34.441
1.00
39.66
C

ATOM
424
C
ILE
P
58
4.951
3.207
34.620
1.00
39.56
C

ATOM
425
O
ILE
P
58
3.987
3.169
33.852
1.00
37.62
O

ATOM
426
CB
ILE
P
58
6.756
2.585
33.088
1.00
41.77
C

ATOM
427
CG1
ILE
P
58
7.719
1.474
32.671
1.00
42.71
C

ATOM
428
CG2
ILE
P
58
7.459
3.930
33.139
1.00
42.81
C

ATOM
429
CD1
ILE
P
58
8.249
1.633
31.264
1.00
44.14
C

ATOM
430
N
PHE
P
59
5.053
4.078
35.615
1.00
41.12
N

ATOM
431
CA
PHE
P
59
3.981
5.010
35.920
1.00
44.12
C

ATOM
432
C
PHE
P
59
4.265
6.412
35.385
1.00
47.76
C

ATOM
433
O
PHE
P
59
5.414
6.773
35.133
1.00
49.60
O

ATOM
434
CB
PHE
P
59
3.738
5.063
37.426
1.00
43.49
C

ATOM
435
CG
PHE
P
59
3.186
3.793
37.994
1.00
43.98
C

ATOM
436
CD1
PHE
P
59
1.820
3.553
37.992
1.00
44.02
C

ATOM
437
CD2
PHE
P
59
4.029
2.835
38.532
1.00
44.47
C

ATOM
438
CE1
PHE
P
59
1.306
2.384
38.516
1.00
44.97
C

ATOM
439
CE2
PHE
P
59
3.522
1.665
39.060
1.00
45.06
C

ATOM
440
CZ
PHE
P
59
2.158
1.438
39.052
1.00
45.71
C

ATOM
441
N
LYS
P
60
3.204
7.195
35.214
1.00
49.77
N

ATOM
442
CA
LYS
P
60
3.321
8.580
34.785
1.00
49.97
C

ATOM
443
C
LYS
P
60
3.954
9.416
35.890
1.00
48.89
C

ATOM
444
O
LYS
P
60
4.867
10.199
35.640
1.00
49.28
O

ATOM
445
CB
LYS
P
60
1.939
9.132
34.422
1.00
52.79
C

ATOM
446
CG
LYS
P
60
1.917
10.598
34.020
1.00
55.76
C

ATOM
447
CD
LYS
P
60
0.486
11.137
33.997
1.00
58.02
C

ATOM
448
CE
LYS
P
60
0.458
12.648
33.777
1.00
59.17
C

ATOM
449
NZ
LYS
P
60
−0.887
13.238
34.048
1.00
60.24
N

ATOM
450
N
GLU
P
61
3.468
9.234
37.114
1.00
48.84
N

ATOM
451
CA
GLU
P
61
3.987
9.955
38.268
1.00
49.18
C

ATOM
452
C
GLU
P
61
4.799
9.036
39.158
1.00
47.49
C

ATOM
453
O
GLU
P
61
4.338
7.965
39.531
1.00
47.52
O

ATOM
454
CB
GLU
P
61
2.340
10.543
39.077
1.00
53.68
C

ATOM
455
CG
GLU
P
61
1.336
11.294
38.245
1.00
59.67
C

ATOM
456
CD
GLU
P
61
2.463
12.442
37.493
1.00
64.43
C

ATOM
457
OE1
GLU
P
61
3.314
13.145
38.080
1.00
66.11
O

ATOM
458
OE2
GLU
P
61
2.105
12.644
36.315
1.00
67.05
O

ATOM
459
N
VAL
P
62
6.004
9.466
39.512
1.00
47.43
N

ATOM
460
CA
VAL
P
62
6.346
8.702
40.427
1.00
48.20
C

ATOM
461
C
VAL
P
62
6.120
8.411
41.732
1.00
49.03
C

ATOM
462
O
VAL
P
62
6.464
7.473
42.442
1.00
51.69
O

ATOM
463
CB
VAL
P
62
8.160
9.439
40.754
1.00
48.25
C

ATOM
464
CG1
VAL
P
62
8.796
8.856
42.007
1.00
46.94
C

ATOM
465
CG2
VAL
P
62
9.119
9.370
39.577
1.00
48.65
C

ATOM
466
N
SER
P
63
5.124
9.226
42.054
1.00
48.87
N

ATOM
467
CA
SER
P
63
4.362
9.032
43.277
1.00
49.41
C

ATOM
468
C
SER
P
63
3.351
7.896
43.130
1.00
49.56
C

ATOM
469
O
SER
P
63
2.949
7.285
44.118
1.00
51.30
O

ATOM
470
CB
SER
P
63
3.669
10.331
43.700
1.00
50.75
C

ATOM
471
OG
SER
P
63
3.191
11.046
42.574
1.00
52.21
O

ATOM
472
N
SER
P
64
2.947
7.613
41.894
1.00
49.01
N

ATOM
473
CA
SER
P
64
2.085
6.460
41.613
1.00
46.53
C

ATOM
474
C
SER
P
64
2.794
5.154
41.981
1.00
44.69
C

ATOM
475
O
SER
P
64
2.218
4.280
42.629
1.00
43.75
O

ATOM
476
CB
SER
P
64
1.682
6.434
40.133
1.00
45.88
C

ATOM
477
OG
SER
P
64
0.757
7.462
39.823
1.00
45.38
O

ATOM
478
N
ALA
P
65
4.047
5.034
41.558
1.00
43.58
N

ATOM
479
CA
ALA
P
65
4.842
3.844
41.817
1.00
43.45
C

ATOM
480
C
ALA
P
65
4.909
3.538
43.304
1.00
44.31
C

ATOM
481
O
ALA
P
65
4.659
2.410
43.726
1.00
45.47
O

ATOM
482
CB
ALA
P
65
6.242
4.014
41.252
1.00
42.97
C

ATOM
483
N
THR
P
66
5.255
4.548
44.095
1.00
43.94
N

ATOM
484
CA
THR
P
66
5.429
4.372
45.530
1.00
43.84
C

ATOM
485
C
THR
P
66
4.188
3.768
46.157
1.00
43.46
C

ATOM
486
O
THR
P
66
4.275
2.855
46.976
1.00
43.98
O

ATOM
487
CB
THR
P
66
5.740
5.703
46.230
1.00
45.10
C

ATOM
488
OG1
THR
P
66
6.804
6.372
45.542
1.00
46.63
O

ATOM
489
CG2
THR
P
66
6.145
5.461
47.681
1.00
45.29
C

ATOM
490
N
ASN
P
67
3.030
4.283
45.776
1.00
44.83
N

ATOM
491
CA
ASN
P
67
1.780
3.743
46.265
1.00
48.89
C

ATOM
492
C
ASN
P
67
1.661
2.277
45.900
1.00
48.26
C

ATOM
493
O
ASN
P
67
1.520
1.419
46.770
1.00
48.84
O

ATOM
494
CB
ASN
P
67
0.601
4.531
45.704
1.00
53.87
C

ATOM
495
CG
ASN
P
67
0.594
5.975
46.174
1.00
57.09
C

ATOM
496
OD1
ASN
P
67
1.432
6.381
46.985
1.00
57.15
O

ATOM
497
ND2
ASN
P
67
−0.351
6.759
45.665
1.00
59.20
N

ATOM
498
N
ALA
P
68
1.734
1.994
44.605
1.00
47.17
N

ATOM
499
CA
ALA
P
68
1.791
0.624
44.124
1.00
46.08
C

ATOM
500
C
ALA
P
68
2.641
−0.230
45.058
1.00
44.72
C

ATOM
501
O
ALA
P
68
2.140
−1.137
45.710
1.00
42.30
O

ATOM
502
CB
ALA
P
68
2.348
0.585
42.703
1.00
47.06
C

ATOM
503
N
LEU
P
69
3.933
0.072
45.124
1.00
47.77
N

ATOM
504
CA
LEU
P
69
4.836
−0.656
45.999
1.00
49.77
C

ATOM
505
C
LEU
P
69
4.209
−0.832
47.364
1.00
50.65
C

ATOM
506
O
LEU
P
69
3.945
−1.950
47.796
1.00
51.58
O

ATOM
507
CB
LEU
P
69
6.165
0.083
46.140
1.00
50.43
C

ATOM
508
CG
LEU
P
69
7.244
−0.637
46.958
1.00
51.92
C

ATOM
509
CD1
LEU
P
69
8.591
0.049
46.802
1.00
51.65
C

ATOM
510
CD2
LEU
P
69
6.857
−0.738
48.432
1.00
52.82
C

ATOM
511
N
ARG
P
70
3.973
0.283
48.041
1.00
52.95
N

ATOM
512
CA
ARG
P
70
3.445
0.256
49.392
1.00
57.54
C

ATOM
513
C
ARG
P
70
2.137
−0.507
49.462
1.00
59.64
C

ATOM
514
O
ARG
P
70
1.954
−1.361
50.325
1.00
61.66
O

ATOM
515
CB
ARG
P
70
3.235
1.673
49.909
1.00
60.56
C

ATOM
516
CG
ARG
P
70
4.517
2.449
50.125
1.00
65.01
C

ATOM
517
CD
ARG
P
70
4.225
3.812
50.725
1.00
68.74
C

ATOM
518
NE
ARG
P
70
5.445
4.566
50.994
1.00
71.53
N

ATOM
519
CZ
ARG
P
70
5.484
5.698
51.690
1.00
73.20
C

ATOM
520
NH1
ARG
P
70
4.366
6.209
52.192
1.00
73.88
N

ATOM
521
NH2
ARG
P
70
6.640
6.318
51.887
1.00
73.86
N

ATOM
522
N
SER
P
71
1.227
−0.197
48.547
1.00
60.99
N

ATOM
523
CA
SER
P
71
−0.128
−0.737
48.610
1.00
61.57
C

ATOM
524
C
SER
P
71
−0.193
−2.249
48.429
1.00
63.43
C

ATOM
525
O
SER
P
71
−0.827
−2.942
49.222
1.00
65.97
O

ATOM
526
CB
SER
P
71
−1.037
−0.050
47.590
1.00
60.56
C

ATOM
527
OG
SER
P
71
−1.375
−1.258
48.009
1.00
60.71
O

ATOM
528
N
MET
P
72
0.454
−2.761
47.386
1.00
63.89
N

ATOM
529
CA
MET
P
72
0.224
−4.148
46.971
1.00
64.36
C

ATOM
530
C
MET
P
72
1.438
−5.075
47.088
1.00
61.19
C

ATOM
531
O
MET
P
72
1.574
−6.029
46.321
1.00
59.13
O

ATOM
532
CB
MET
P
72
−0.355
−4.196
45.555
1.00
68.13
C

ATOM
533
CG
MET
P
72
−1.723
−3.542
45.435
1.00
72.60
C

ATOM
534
SD
MET
P
72
−2.553
−3.897
43.876
1.00
77.84
S

ATOM
535
CE
MET
P
72
−3.941
−2.768
43.966
1.00
78.13
C

ATOM
536
N
GLN
P
73
2.304
−4.807
48.058
1.00
59.86
N

ATOM
537
CA
GLN
P
73
3.397
−5.717
48.353
1.00
58.79
C

ATOM
538
C
GLN
P
73
2.836
−7.078
48.739
1.00
60.03
C

ATOM
539
O
GLN
P
73
1.809
−7.166
49.405
1.00
61.20
O

ATOM
540
CB
GLN
P
73
4.263
−5.171
49.484
1.00
57.19
C

ATOM
541
CG
GLN
P
73
5.641
−5.790
49.538
1.00
57.15
C

ATOM
542
CD
GLN
P
73
6.498
−5.383
48.359
1.00
58.10
C

ATOM
543
OE1
GLN
P
73
7.020
−6.228
47.629
1.00
58.31
O

ATOM
544
NE2
GLN
P
73
6.635
−4.079
48.155
1.00
59.06
N

ATOM
545
N
GLY
P
74
3.503
−8.139
48.304
1.00
61.62
N

ATOM
546
CA
GLY
P
74
3.098
−9.496
48.657
1.00
64.04
C

ATOM
547
C
GLY
P
74
1.662
−9.852
48.298
1.00
65.83
C

ATOM
548
O
GLY
P
74
1.186
−10.938
48.627
1.00
67.36
O

ATOM
549
N
PHE
P
75
0.968
−8.942
47.623
1.00
66.24
N

ATOM
550
CA
PHE
P
75
−0.403
−9.206
47.196
1.00
67.45
C

ATOM
551
C
PHE
P
75
−0.497
−10.500
46.384
1.00
66.32
C

ATOM
552
O
PHE
P
75
0.238
−10.688
45.415
1.00
63.98
O

ATOM
553
CB
PHE
P
75
−0.949
−8.033
46.382
1.00
70.95
C

ATOM
554
CG
PHE
P
75
−2.412
−8.154
46.048
1.00
74.57
C

ATOM
555
CD1
PHE
P
75
−3.381
−7.841
46.991
1.00
75.64
C

ATOM
556
CD2
PHE
P
75
−2.820
−8.572
44.788
1.00
75.91
C

ATOM
557
CE1
PHE
P
75
−4.730
−7.949
46.686
1.00
76.50
C

ATOM
558
CE2
PHE
P
75
−4.169
−8.681
44.477
1.00
77.00
C

ATOM
559
CZ
PHE
P
75
−5.124
−8.369
45.428
1.00
76.90
C

ATOM
560
N
PRO
P
76
−1.416
−11.396
46.781
1.00
66.67
N

ATOM
561
CA
PRO
P
76
−1.627
−12.686
46.120
1.00
65.09
C

ATOM
562
C
PRO
P
76
−2.080
−12.519
44.676
1.00
62.59
C

ATOM
563
O
PRO
P
76
−3.129
−11.935
44.417
1.00
63.51
O

ATOM
564
CB
PRO
P
76
−2.745
−13.329
46.953
1.00
66.39
C

ATOM
565
CG
PRO
P
76
−2.689
−12.632
48.275
1.00
67.08
C

ATOM
566
CD
PRO
P
76
−2.283
−11.230
47.960
1.00
67.32
C

ATOM
567
N
PHE
P
77
−1.294
−13.045
43.746
1.00
60.35
N

ATOM
568
CA
PHE
P
77
−1.546
−12.842
42.329
1.00
58.19
C

ATOM
569
C
PHE
P
77
−1.346
−14.140
41.557
1.00
57.16
C

ATOM
570
O
PHE
P
77
−0.216
−14.550
41.301
1.00
56.82
O

ATOM
571
CB
PHE
P
77
−0.610
−11.768
41.791
1.00
57.94
C

ATOM
572
CG
PHE
P
77
−0.997
−11.249
40.448
1.00
57.65
C

ATOM
573
CD1
PHE
P
77
−2.227
−10.647
40.255
1.00
58.25
C

ATOM
574
CD2
PHE
P
77
−0.125
−11.345
39.378
1.00
57.10
C

ATOM
575
CE1
PHE
P
77
−2.586
−10.159
39.016
1.00
58.72
C

ATOM
576
CE2
PHE
P
77
−0.476
−10.857
38.138
1.00
58.01
C

ATOM
577
CZ
PHE
P
77
−1.709
−10.262
37.955
1.00
59.00
C

ATOM
578
N
TYR
P
78
−2.445
−14.780
41.181
1.00
56.26
N

ATOM
579
CA
TYR
P
78
−2.374
−16.114
40.614
1.00
55.19
C

ATOM
580
C
TYR
P
78
−1.776
−17.067
41.627
1.00
57.46
C

ATOM
581
O
TYR
P
78
−0.896
−17.862
41.303
1.00
57.02
O

ATOM
582
CB
TYR
P
78
−1.540
−16.111
39.342
1.00
52.77
C

ATOM
583
CG
TYR
P
78
−2.228
−15.430
38.196
1.00
52.54
C

ATOM
584
CD1
TYR
P
78
−2.992
−16.152
37.297
1.00
53.24
C

ATOM
585
CD2
TYR
P
78
−2.140
−14.059
38.028
1.00
53.68
C

ATOM
586
CE1
TYR
P
78
−3.640
−15.530
36.251
1.00
54.38
C

ATOM
587
CE2
TYR
P
78
−2.781
−13.425
36.983
1.00
53.96
C

ATOM
588
CZ
TYR
P
78
−3.531
−14.166
36.096
1.00
54.82
C

ATOM
589
OH
TYR
P
78
−4.172
−13.544
35.049
1.00
55.53
O

ATOM
590
N
ASP
P
79
−2.251
−16.963
42.865
1.00
60.19
N

ATOM
591
CA
ASP
P
79
−1.846
−17.872
43.932
1.00
63.25
C

ATOM
592
C
ASP
P
79
−0.395
−17.675
44.353
1.00
64.39
C

ATOM
593
O
ASP
P
79
0.120
−18.407
45.197
1.00
65.96
O

ATOM
594
CB
ASP
P
79
−2.098
−19.325
43.527
1.00
65.21
C

ATOM
595
CG
ASP
P
79
−3.506
−19.778
43.848
1.00
66.02
C

ATOM
596
OD1
ASP
P
79
−3.742
−20.206
44.996
1.00
64.93
O

ATOM
597
OD2
ASP
P
79
−4.378
−19.702
42.956
1.00
66.81
O

ATOM
598
N
LYS
P
80
0.258
−16.682
43.765
1.00
64.23
N

ATOM
599
CA
LYS
P
80
1.583
−16.280
44.213
1.00
64.01
C

ATOM
600
C
LYS
P
80
1.546
−14.884
44.827
1.00
63.30
C

ATOM
601
O
LYS
P
80
0.592
−14.129
44.620
1.00
63.54
O

ATOM
602
CB
LYS
P
80
2.583
−16.325
43.057
1.00
64.16
C

ATOM
603
CG
LYS
P
80
2.665
−17.675
42.368
1.00
64.60
C

ATOM
604
CD
LYS
P
80
4.030
−17.884
41.739
1.00
63.89
C

ATOM
605
CE
LYS
P
80
5.133
−17.730
42.771
1.00
63.72
C

ATOM
606
NZ
LYS
P
80
6.468
−18.070
42.210
1.00
64.45
N

ATOM
607
N
PRO
P
81
2.582
−14.542
45.597
1.00
62.04
N

ATOM
608
CA
PRO
P
81
2.711
−13.237
46.202
1.00
61.82
C

ATOM
609
C
PRO
P
81
3.655
−12.383
45.372
1.00
60.76
C

ATOM
610
O
PRO
P
81
4.593
−12.910
44.771
1.00
62.45
O

ATOM
611
CB
PRO
P
81
3.350
−13.557
47.551
1.00
61.97
C

ATOM
612
CG
PRO
P
81
4.164
−14.844
47.290
1.00
62.62
C

ATOM
613
CD
PRO
P
81
3.705
−15.417
45.963
1.00
61.62
C

ATOM
614
N
MET
P
82
3.413
−11.077
45.338
1.00
56.46
N

ATOM
615
CA
MET
P
82
4.211
−10.182
44.514
1.00
51.79
C

ATOM
616
C
MET
P
82
5.400
−9.605
45.259
1.00
49.90
C

ATOM
617
O
MET
P
82
5.239
−8.921
46.263
1.00
49.80
O

ATOM
618
CB
MET
P
82
3.345
−9.055
43.971
1.00
50.15
C

ATOM
619
CG
MET
P
82
2.349
−9.507
42.932
1.00
48.87
C

ATOM
620
SD
MET
P
82
1.356
−8.145
42.313
1.00
46.98
S

ATOM
621
CE
MET
P
82
2.633
−7.000
41.816
1.00
50.00
C

ATOM
622
N
ARG
P
83
6.597
−9.895
44.767
1.00
50.21
N

ATOM
623
CA
ARG
P
83
7.783
−9.189
45.212
1.00
52.56
C

ATOM
624
C
ARG
P
83
7.843
−7.885
44.446
1.00
49.90
C

ATOM
625
O
ARG
P
83
8.114
−7.884
43.247
1.00
50.77
O

ATOM
626
CB
ARG
P
83
9.045
−10.005
44.913
1.00
58.16
C

ATOM
627
CG
ARG
P
83
9.108
−11.369
45.589
1.00
64.64
C

ATOM
628
CD
ARG
P
83
9.622
−11.262
47.022
1.00
70.15
C

ATOM
629
NE
ARG
P
83
9.820
−12.577
47.634
1.00
74.49
N

ATOM
630
CZ
ARG
P
83
10.353
−12.775
48.839
1.00
76.69
C

ATOM
631
NH1
ARG
P
83
10.748
−11.741
49.575
1.00
77.41
N

ATOM
632
NH2
ARG
P
83
10.493
−14.009
49.309
1.00
76.75
N

ATOM
633
N
ILE
P
84
7.571
−6.774
45.117
1.00
45.73
N

ATOM
634
CA
ILE
P
84
7.687
−5.483
44.462
1.00
42.90
C

ATOM
635
C
ILE
P
84
8.906
−4.729
44.952
1.00
41.39
C

ATOM
636
O
ILE
P
84
9.362
−4.926
46.074
1.00
41.05
O

ATOM
637
CB
ILE
P
84
6.438
−4.608
44.654
1.00
42.63
C

ATOM
638
CG1
ILE
P
84
5.167
−5.436
44.485
1.00
42.43
C

ATOM
639
CG2
ILE
P
84
6.452
−3.444
43.665
1.00
41.71
C

ATOM
640
CD1
ILE
P
84
3.897
−4.614
44.545
1.00
41.88
C

ATOM
641
N
GLN
P
85
9.434
−3.869
44.095
1.00
39.84
N

ATOM
642
CA
GLN
P
85
10.538
−3.010
44.460
1.00
40.93
C

ATOM
643
C
GLN
P
85
10.858
−2.113
43.283
1.00
41.93
C

ATOM
644
O
GLN
P
85
10.345
−2.319
42.187
1.00
42.31
O

ATOM
645
CB
GLN
P
85
11.757
−3.837
44.844
1.00
41.45
C

ATOM
646
CG
GLN
P
85
12.533
−4.373
43.661
1.00
44.64
C

ATOM
647
CD
GLN
P
85
13.592
−5.382
44.067
1.00
46.10
C

ATOM
648
OE1
GLN
P
85
14.385
−5.837
43.240
1.00
45.76
O

ATOM
649
NE2
GLN
P
85
13.606
−5.741
45.344
1.00
46.32
N

ATOM
650
N
TYR
P
86
11.696
−1.110
43.511
1.00
42.58
N

ATOM
651
CA
TYR
P
86
12.015
−0.143
42.473
1.00
44.00
C

ATOM
652
C
TYR
P
86
12.988
−0.712
41.459
1.00
43.69
C

ATOM
653
O
TYR
P
86
13.757
−1.617
41.764
1.00
45.29
O

ATOM
654
CB
TYR
P
86
12.597
1.129
43.085
1.00
48.19
C

ATOM
655
CG
TYR
P
86
11.610
1.927
43.906
1.00
50.63
C

ATOM
656
CD1
TYR
P
86
10.613
2.677
43.294
1.00
51.60
C

ATOM
657
CD2
TYR
P
86
11.679
1.935
45.292
1.00
52.18
C

ATOM
658
CE1
TYR
P
86
9.711
3.410
44.039
1.00
53.36
C

ATOM
659
CE2
TYR
P
86
10.782
2.665
46.049
1.00
53.85
C

ATOM
660
CZ
TYR
P
86
9.798
3.399
45.419
1.00
54.96
O

ATOM
661
OH
TYR
P
86
8.901
4.128
46.172
1.00
56.49
O

ATOM
662
N
ALA
P
87
12.940
−0.184
40.245
1.00
42.84
N

ATOM
663
CA
ALA
P
87
13.932
−0.515
39.245
1.00
42.39
C

ATOM
664
C
ALA
P
87
15.212
0.235
39.566
1.00
43.92
C

ATOM
665
O
ALA
P
87
15.191
1.446
39.764
1.00
44.49
O

ATOM
666
CB
ALA
P
87
13.433
−0.143
37.866
1.00
41.05
C

ATOM
667
N
LYS
P
88
16.320
−0.489
39.646
1.00
45.70
N

ATOM
668
CA
LYS
P
88
17.612
0.136
39.877
1.00
48.69
C

ATOM
669
C
LYS
P
88
17.808
1.297
38.901
1.00
49.44
C

ATOM
670
O
LYS
P
88
18.418
2.315
39.234
1.00
48.61
O

ATOM
671
CB
LYS
P
88
18.738
−0.884
39.699
1.00
50.05
C

ATOM
672
CG
LYS
P
88
18.493
−2.220
40.370
1.00
50.67
C

ATOM
673
CD
LYS
P
88
19.483
−3.251
39.865
1.00
52.59
C

ATOM
674
CE
LYS
P
88
19.208
−4.626
40.438
1.00
53.47
C

ATOM
675
NZ
LYS
P
88
20.103
−5.651
39.825
1.00
54.36
N

ATOM
676
N
THR
P
89
17.281
1.132
37.694
1.00
49.41
N

ATOM
677
CA
THR
P
89
17.418
2.136
36.656
1.00
50.84
C

ATOM
678
C
THR
P
89
16.050
2.570
36.163
1.00
52.18
C

ATOM
679
O
THR
P
89
15.036
1.985
36.538
1.00
51.94
O

ATOM
680
CB
THR
P
89
18.228
1.593
35.468
1.00
50.90
C

ATOM
681
OG1
THR
P
89
19.622
1.619
35.789
1.00
50.79
O

ATOM
682
CG2
THR
P
89
17.985
2.432
34.225
1.00
51.25
C

ATOM
683
N
ASP
P
90
16.023
3.600
35.325
1.00
54.93
N

ATOM
684
CA
ASP
P
90
14.784
4.038
34.703
1.00
60.12
C

ATOM
685
C
ASP
P
90
14.522
3.261
33.429
1.00
63.56
C

ATOM
686
O
ASP
P
90
15.312
2.400
33.046
1.00
64.62
O

ATOM
687
CB
ASP
P
90
14.838
5.528
34.398
1.00
60.84
C

ATOM
688
CG
ASP
P
90
15.216
6.340
35.598
1.00
62.67
C

ATOM
689
OD1
ASP
P
90
15.399
5.733
36.674
1.00
63.84
O

ATOM
690
OD2
ASP
P
90
15.336
7.577
35.473
1.00
63.59
O

ATOM
691
N
SER
P
91
13.407
3.567
32.777
1.00
66.94
N

ATOM
692
CA
SER
P
91
13.056
2.922
31.522
1.00
70.93
C

ATOM
693
C
SER
P
91
13.316
3.865
30.358
1.00
74.74
C

ATOM
694
O
SER
P
91
13.153
5.080
30.486
1.00
75.34
O

ATOM
695
CB
SER
P
91
11.592
2.486
31.537
1.00
70.85
C

ATOM
696
OG
SER
P
91
11.334
1.618
32.628
1.00
71.07
O

ATOM
697
N
ASP
P
92
13.722
3.303
29.223
1.00
78.12
N

ATOM
698
CA
ASP
P
92
14.129
4.105
28.069
1.00
80.98
C

ATOM
699
C
ASP
P
92
13.172
5.268
27.792
1.00
80.34
C

ATOM
700
O
ASP
P
92
13.606
6.360
27.416
1.00
81.81
O

ATOM
701
CB
ASP
P
92
14.302
3.226
26.824
1.00
84.59
C

ATOM
702
CG
ASP
P
92
15.635
2.481
26.810
1.00
87.33
C

ATOM
703
OD1
ASP
P
92
16.264
2.351
27.884
1.00
88.24
O

ATOM
704
OD2
ASP
P
92
16.052
2.027
25.723
1.00
88.58
O

ATOM
705
N
ILE
P
93
11.876
5.034
27.977
1.00
77.81
N

ATOM
706
CA
ILE
P
93
10.899
6.113
27.906
1.00
75.55
C

ATOM
707
C
ILE
P
93
11.263
7.214
28.903
1.00
72.71
C

ATOM
708
O
ILE
P
93
11.550
8.347
28.516
1.00
71.92
O

ATOM
709
CB
ILE
P
93
9.456
5.604
28.163
1.00
76.01
C

ATOM
710
CG1
ILE
P
93
8.877
4.990
26.886
1.00
76.03
C

ATOM
711
CG2
ILE
P
93
8.556
6.734
28.666
1.00
76.50
C

ATOM
712
CD1
ILE
P
93
7.392
4.696
26.963
1.00
76.54
C

ATOM
713
N
ILE
P
94
11.279
6.864
30.184
1.00
70.30
N

ATOM
714
CA
ILE
P
94
11.583
7.825
31.236
1.00
68.57
C

ATOM
715
C
ILE
P
94
13.021
8.345
31.148
1.00
67.92
C

ATOM
716
O
ILE
P
94
13.301
9.483
31.526
1.00
68.54
O

ATOM
717
CB
ILE
P
94
11.326
7.229
32.630
1.00
67.76
C

ATOM
718
CG1
ILE
P
94
9.832
6.947
32.813
1.00
67.71
C

ATOM
719
CG2
ILE
P
94
11.835
8.169
33.714
1.00
67.38
C

ATOM
720
CD1
ILE
P
94
9.494
6.180
34.078
1.00
68.30
C

ATOM
721
N
ALA
P
95
13.926
7.514
30.642
1.00
65.88
N

ATOM
722
CA
ALA
P
95
15.323
7.914
30.488
1.00
64.36
C

ATOM
723
C
ALA
P
95
15.485
8.958
29.386
1.00
63.01
C

ATOM
724
O
ALA
P
95
15.929
10.075
29.640
1.00
64.31
O

ATOM
725
CB
ALA
P
95
16.198
6.703
30.207
1.00
64.37
C

ATOM
726
N
LYS
P
96
15.123
8.584
28.164
1.00
60.72
N

ATOM
727
CA
LYS
P
96
15.181
9.499
27.032
1.00
59.56
C

ATOM
728
C
LYS
P
96
14.127
10.598
27.144
1.00
58.82
C

ATOM
729
O
LYS
P
96
14.265
11.532
27.935
1.00
57.81
O

ATOM
730
CB
LYS
P
96
14.992
8.732
25.727
1.00
59.73
C

ATOM
731
CG
LYS
P
96
14.356
9.551
24.621
1.00
61.19
C

ATOM
732
CD
LYS
P
96
14.057
8.693
23.400
1.00
62.88
C

ATOM
733
CE
LYS
P
96
15.341
8.207
22.733
1.00
64.64
C

ATOM
734
NZ
LYS
P
96
15.077
7.216
21.650
1.00
65.07
N

TER
735

LYS
P
96

HETATM
736
PG
GTP
R
8
21.015
−31.209
−29.555
1.00
99.65
P

HETATM
737
O1G
GTP
R
8
22.207
−32.131
−29.663
1.00
99.66
O

HETATM
738
O2G
GTP
R
8
21.435
−29.799
−29.899
1.00
100.19
O

HETATM
739
O3G
GTP
R
8
19.921
−31.656
−30.498
1.00
99.38
O

HETATM
740
O3B
GTP
R
8
20.489
−31.261
−28.035
1.00
98.13
O

HETATM
741
PB
GTP
R
8
21.193
−32.278
−27.007
1.00
97.15
P

HETATM
742
O1B
GTP
R
8
20.656
−32.075
−25.608
1.00
96.88
O

HETATM
743
O2B
GTP
R
8
22.692
−32.113
−27.061
1.00
97.36
O

HETATM
744
O3A
GTP
R
8
20.780
−33.735
−27.540
1.00
93.30
O

HETATM
745
PA
GTP
R
8
19.540
−33.985
−28.535
1.00
88.94
P

HETATM
746
O1A
GTP
R
8
20.049
−34.379
−29.902
1.00
88.66
O

HETATM
747
O2A
GTP
R
8
18.583
−32.815
−28.608
1.00
89.22
O

HETATM
748
O5′
GTP
R
8
18.870
−35.233
−27.796
1.00
84.94
O

HETATM
749
C5′
GTP
R
8
19.412
−35.578
−26.545
1.00
79.45
C

HETATM
750
C4′
GTP
R
8
19.322
−37.072
−26.324
1.00
75.30
C

HETATM
751
O4′
GTP
R
8
20.084
−37.749
−27.309
1.00
73.67
O

HETATM
752
C3′
GTP
R
8
19.951
−37.388
−24.992
1.00
73.11
C

HETATM
753
O3′
GTP
R
8
18.985
−37.884
−24.099
1.00
71.28
O

HETATM
754
C2′
GTP
R
8
21.013
−38.421
−25.271
1.00
71.98
C

HETATM
755
O2′
GTP
R
8
20.509
−39.705
−24.996
1.00
71.66
O

HETATM
756
C1′
GTP
R
8
21.270
−38.282
−26.747
1.00
70.24
C

HETATM
757
N9
GTP
R
8
22.372
−37.317
−26.883
1.00
65.79
N

HETATM
758
C8
GTP
R
8
22.325
−36.078
−27.469
1.00
64.85
C

HETATM
759
N7
GTP
R
8
23.552
−35.512
−27.379
1.00
62.55
N

HETATM
760
C5
GTP
R
8
24.372
−36.370
−26.732
1.00
60.49
C

HETATM
761
C6
GTP
R
8
25.708
−36.292
−26.371
1.00
57.99
C

HETATM
762
O6
GTP
R
8
26.362
−35.292
−26.651
1.00
56.83
O

HETATM
763
N1
GTP
R
8
26.298
−37.342
−25.702
1.00
57.04
N

HETATM
764
C2
GTP
R
8
25.555
−38.461
−25.394
1.00
57.49
C

HETATM
765
N2
GTP
R
8
26.123
−39.475
−24.749
1.00
56.61
N

HETATM
766
N3
GTP
R
8
24.224
−38.531
−25.755
1.00
59.20
N

HETATM
767
C4
GTP
R
8
23.642
−37.503
−26.414
1.00
61.59
C

ATOM
768
P
G
R
9
19.515
−37.664
−22.542
1.00
67.68
P

ATOM
769
OP1
G
R
9
18.264
−37.968
−21.808
1.00
69.60
O

ATOM
770
OP2
G
R
9
20.157
−36.335
−22.408
1.00
67.66
O

ATOM
771
O5′
G
R
9
20.606
−38.783
−22.206
1.00
64.68
O

ATOM
772
C5′
G
R
9
20.537
−39.537
−21.024
1.00
63.35
C

ATOM
773
C4′
G
R
9
21.950
−39.761
−20.562
1.00
62.76
C

ATOM
774
O4′
G
R
9
22.814
−39.701
−21.722
1.00
62.89
O

ATOM
775
C3′
G
R
9
22.461
−38.651
−19.676
1.00
62.54
C

ATOM
776
O3′
G
R
9
22.107
−38.908
−18.349
1.00
63.03
O

ATOM
777
C2′
G
R
9
23.963
−38.737
−19.902
1.00
61.92
C

ATOM
778
O2′
G
R
9
24.552
−39.829
−19.225
1.00
62.19
O

ATOM
779
C1′
G
R
9
23.995
−38.977
−21.405
1.00
61.29
C

ATOM
780
N9
G
R
9
24.067
−37.731
−22.177
1.00
58.26
N

ATOM
781
C8
G
R
9
23.122
−37.178
−23.013
1.00
57.12
C

ATOM
782
N7
G
R
9
23.505
−36.047
−23.550
1.00
55.36
N

ATOM
783
C5
G
R
9
24.783
−35.837
−23.037
1.00
54.09
C

ATOM
784
C6
G
R
9
25.708
−34.778
−23.250
1.00
51.74
C

ATOM
785
O6
G
R
9
25.585
−33.773
−23.958
1.00
50.52
O

ATOM
786
N1
G
R
9
26.883
−34.964
−22.528
1.00
51.64
N

ATOM
787
C2
G
R
9
27.134
−36.039
−21.704
1.00
53.27
C

ATOM
788
N2
G
R
9
28.321
−36.058
−21.084
1.00
52.89
N

ATOM
789
N3
G
R
9
26.282
−37.032
−21.497
1.00
54.52
N

ATOM
790
C4
G
R
9
25.134
−36.865
−22.192
1.00
55.52
C

ATOM
791
P
U
R
10
21.847
−37.652
−17.417
1.00
64.46
P

ATOM
792
OP1
U
R
10
21.448
−38.142
−16.080
1.00
66.39
O

ATOM
793
OP2
U
R
10
20.997
−36.705
−18.172
1.00
65.08
O

ATOM
794
O5′
U
R
10
23.299
−37.022
−17.293
1.00
62.11
O

ATOM
795
C5′
U
R
10
24.241
−37.712
−16.515
1.00
59.23
C

ATOM
796
C4′
U
R
10
25.551
−36.976
−16.577
1.00
57.32
C

ATOM
797
O4′
U
R
10
25.880
−36.697
−17.954
1.00
55.97
O

ATOM
798
C3′
U
R
10
25.491
−35.603
−15.955
1.00
56.57
C

ATOM
799
O3′
U
R
10
25.603
−35.731
−14.563
1.00
57.03
O

ATOM
800
C2′
U
R
10
26.698
−34.928
−16.595
1.00
55.46
C

ATOM
801
O2′
U
R
10
27.915
−35.252
−15.954
1.00
54.74
O

ATOM
802
C1′
U
R
10
26.648
−35.509
−18.010
1.00
55.13
C

ATOM
803
N1
U
R
10
25.982
−34.595
−18.956
1.00
54.29
N

ATOM
804
C2
U
R
10
26.664
−33.488
−19.414
1.00
54.11
C

ATOM
805
O2
U
R
10
27.808
−33.228
−19.085
1.00
54.20
O

ATOM
806
N3
U
R
10
25.958
−32.693
−20.281
1.00
54.22
N

ATOM
807
C4
U
R
10
24.661
−32.894
−20.718
1.00
55.08
C

ATOM
808
O4
U
R
10
24.153
−32.096
−21.502
1.00
55.76
O

ATOM
809
C5
U
R
10
24.014
−34.068
−20.187
1.00
54.65
C

ATOM
810
C6
U
R
10
24.685
−34.858
−19.342
1.00
54.03
C

ATOM
811
P
C
R
11
24.523
−34.999
−13.656
1.00
56.86
P

ATOM
812
OP1
C
R
11
24.506
−35.668
−12.339
1.00
57.32
O

ATOM
813
OP2
C
R
11
23.281
−34.873
−14.450
1.00
56.76
O

ATOM
814
O5′
C
R
11
25.174
−33.549
−13.490
1.00
57.62
O

ATOM
815
C5′
C
R
11
26.492
−33.465
−12.962
1.00
60.02
C

ATOM
816
C4′
C
R
11
27.194
−32.179
−13.361
1.00
61.31
C

ATOM
817
O4′
C
R
11
27.535
−32.200
−14.770
1.00
62.63
O

ATOM
818
C3′
C
R
11
26.377
−30.910
−13.231
1.00
63.10
C

ATOM
819
O3′
C
R
11
26.280
−30.493
−11.875
1.00
64.78
O

ATOM
820
C2′
C
R
11
27.234
−29.967
−14.061
1.00
63.78
C

ATOM
821
O2′
C
R
11
28.426
−29.596
−13.398
1.00
64.89
O

ATOM
822
C1′
C
R
11
27.542
−30.865
−15.256
1.00
63.38
C

ATOM
823
N1
C
R
11
26.527
−30.727
−16.342
1.00
63.73
N

ATOM
824
C2
C
R
11
26.641
−29.673
−17.256
1.00
64.21
C

ATOM
825
O2
C
R
11
27.587
−28.882
−17.150
1.00
65.77
O

ATOM
826
N3
C
R
11
25.712
−29.551
−18.238
1.00
62.92
N

ATOM
827
C4
C
R
11
24.708
−30.424
−18.320
1.00
62.62
C

ATOM
828
N4
C
R
11
23.820
−30.261
−19.306
1.00
62.19
N

ATOM
829
C5
C
R
11
24.570
−31.503
−17.395
1.00
63.08
C

ATOM
830
C6
C
R
11
25.492
−31.614
−16.430
1.00
63.70
C

ATOM
831
P
A
R
12
25.008
−29.636
−11.402
1.00
66.37
P

ATOM
832
OP1
A
R
12
24.725
−29.966
−9.985
1.00
67.09
O

ATOM
833
OP2
A
R
12
23.936
−29.787
−12.417
1.00
66.02
O

ATOM
834
O5′
A
R
12
25.562
−28.138
−11.493
1.00
63.65
O

ATOM
835
C5′
A
R
12
24.673
−27.090
−11.818
1.00
59.49
C

ATOM
836
C4′
A
R
12
25.312
−26.140
−12.805
1.00
55.65
C

ATOM
837
O4′
A
R
12
25.714
−26.841
−14.008
1.00
52.93
O

ATOM
838
C3′
A
R
12
24.370
−25.074
−13.310
1.00
54.79
C

ATOM
839
O3′
A
R
12
24.250
−24.049
−12.346
1.00
55.83
O

ATOM
840
C2′
A
R
12
25.082
−24.636
−14.586
1.00
53.50
C

ATOM
841
O2′
A
R
12
26.221
−23.837
−14.338
1.00
54.70
O

ATOM
842
C1′
A
R
12
25.518
−25.991
−15.129
1.00
50.63
C

ATOM
843
N9
A
R
12
24.522
−26.595
−16.006
1.00
46.52
N

ATOM
844
C8
A
R
12
23.848
−27.770
−15.811
1.00
45.58
C

ATOM
845
N7
A
R
12
23.002
−28.065
−16.777
1.00
43.11
N

ATOM
846
C5
A
R
12
23.127
−27.006
−17.664
1.00
40.55
C

ATOM
847
C6
A
R
12
22.502
−26.716
−18.895
1.00
36.94
C

ATOM
848
N6
A
R
12
21.587
−27.504
−19.468
1.00
35.74
N

ATOM
849
N1
A
R
12
22.862
−25.582
−19.524
1.00
36.09
N

ATOM
850
C2
A
R
12
23.775
−24.791
−18.949
1.00
39.53
C

ATOM
851
N3
A
R
12
24.430
−24.952
−17.798
1.00
41.95
N

ATOM
852
C4
A
R
12
24.058
−26.091
−17.200
1.00
43.00
C

ATOM
853
P
C
R
13
22.797
−23.447
−12.078
1.00
58.77
P

ATOM
854
OP1
C
R
13
22.859
−22.513
−10.927
1.00
59.06
O

ATOM
855
OP2
C
R
13
21.840
−24.575
−12.061
1.00
60.81
O

ATOM
856
O5′
C
R
13
22.565
−22.615
−13.420
1.00
55.63
O

ATOM
857
C5′
C
R
13
23.684
−22.028
−14.044
1.00
51.30
C

ATOM
858
C4′
C
R
13
23.244
−21.356
−15.313
1.00
50.50
C

ATOM
859
O4′
C
R
13
23.325
−22.314
−16.384
1.00
50.46
O

ATOM
860
C3′
C
R
13
21.796
−20.915
−15.294
1.00
50.58
C

ATOM
861
O3′
C
R
13
21.724
−19.596
−14.835
1.00
51.37
O

ATOM
862
C2′
C
R
13
21.409
−20.984
−16.759
1.00
50.57
C

ATOM
863
O2′
C
R
13
21.837
−19.844
−17.477
1.00
52.12
O

ATOM
864
C1′
C
R
13
22.196
−22.195
−17.215
1.00
48.97
C

ATOM
865
N1
C
R
13
21.458
−23.423
−17.074
1.00
46.88
N

ATOM
866
C2
C
R
13
20.418
−23.687
−17.955
1.00
47.18
C

ATOM
867
O2
C
R
13
20.152
−22.851
−18.826
1.00
46.56
O

ATOM
868
N3
C
R
13
19.740
−24.854
−17.830
1.00
49.17
N

ATOM
869
C4
C
R
13
20.079
−25.720
−16.866
1.00
50.24
C

ATOM
870
N4
C
R
13
19.378
−26.857
−16.772
1.00
49.66
N

ATOM
871
C5
C
R
13
21.150
−25.456
−15.954
1.00
50.22
C

ATOM
872
C6
C
R
13
21.809
−24.302
−16.096
1.00
48.58
C

ATOM
873
P
G
R
14
20.323
−19.060
−14.324
1.00
51.80
P

ATOM
874
OP1
G
R
14
20.515
−17.664
−13.876
1.00
52.71
O

ATOM
875
OP2
G
R
14
19.775
−20.076
−13.401
1.00
54.13
O

ATOM
876
O5′
G
R
14
19.422
−19.078
−15.641
1.00
50.45
O

ATOM
877
C5′
G
R
14
19.307
−17.912
−16.430
1.00
50.43
C

ATOM
878
C4′
G
R
14
18.234
−18.132
−17.467
1.00
50.62
C

ATOM
879
O4′
G
R
14
18.237
−19.533
−17.827
1.00
49.88
O

ATOM
880
C3′
G
R
14
16.828
−17.805
−16.981
1.00
52.52
C

ATOM
881
O3′
G
R
14
16.187
−16.952
−17.924
1.00
56.89
O

ATOM
882
C2′
G
R
14
16.130
−19.159
−16.843
1.00
50.16
C

ATOM
883
O2′
G
R
14
14.771
−19.115
−17.237
1.00
50.54
O

ATOM
884
C1′
G
R
14
16.924
−20.048
−17.793
1.00
48.62
C

ATOM
885
N9
G
R
14
16.995
−21.452
−17.373
1.00
44.41
N

ATOM
886
C8
G
R
14
17.745
−21.971
−16.342
1.00
42.18
C

ATOM
887
N7
G
R
14
17.608
−23.260
−16.201
1.00
39.54
N

ATOM
888
C5
G
R
14
16.714
−23.620
−17.203
1.00
38.97
C

ATOM
889
C6
G
R
14
16.191
−24.890
−17.547
1.00
39.04
C

ATOM
890
O6
G
R
14
16.417
−25.985
−17.013
1.00
39.94
O

ATOM
891
N1
G
R
14
15.320
−24.819
−18.631
1.00
38.63
N

ATOM
892
C2
G
R
14
14.992
−23.664
−19.300
1.00
37.72
C

ATOM
893
N2
G
R
14
14.129
−23.794
−20.323
1.00
35.46
N

ATOM
894
N3
G
R
14
15.476
−22.468
−18.986
1.00
37.73
N

ATOM
895
C4
G
R
14
16.330
−22.522
−17.935
1.00
39.55
C

ATOM
896
P
C
R
15
16.322
−15.364
−17.787
1.00
45.38
P

ATOM
897
OP1
C
R
15
17.746
−15.047
−17.536
1.00
43.81
O

ATOM
898
OP2
C
R
15
15.284
−14.898
−16.840
1.00
45.84
O

ATOM
899
O5′
C
R
15
15.925
−14.843
−19.247
1.00
47.52
O

ATOM
900
C5′
C
R
15
14.576
−14.496
−19.536
1.00
49.59
C

ATOM
901
C4′
C
R
15
14.398
−14.209
−21.016
1.00
50.25
C

ATOM
902
O4′
C
R
15
15.678
−13.843
−21.593
1.00
52.52
O

ATOM
903
C3′
C
R
15
13.901
−15.388
−21.842
1.00
49.02
C

ATOM
904
O3′
C
R
15
12.480
−15.374
−21.903
1.00
43.41
O

ATOM
905
C2′
C
R
15
14.522
−15.113
−23.207
1.00
51.92
C

ATOM
906
O2′
C
R
15
13.784
−14.166
−23.954
1.00
53.47
O

ATOM
907
C1′
C
R
15
15.876
−14.532
−22.812
1.00
55.13
C

ATOM
908
N1
C
R
15
16.927
−15.567
−22.601
1.00
60.39
N

ATOM
909
C2
C
R
15
17.828
−15.859
−23.631
1.00
62.90
C

ATOM
910
O2
C
R
15
17.736
−15.250
−24.704
1.00
63.68
O

ATOM
911
N3
C
R
15
18.778
−16.804
−23.423
1.00
63.60
N

ATOM
912
C4
C
R
15
18.844
−17.438
−22.251
1.00
62.96
C

ATOM
913
N4
C
R
15
19.798
−18.361
−22.092
1.00
62.20
N

ATOM
914
C5
C
R
15
17.934
−17.154
−21.190
1.00
62.75
C

ATOM
915
C6
C
R
15
17.002
−16.221
−21.407
1.00
62.10
C

ATOM
916
P
A
R
16
11.621
−15.368
−20.554
1.00
37.32
P

ATOM
917
OP1
A
R
16
11.229
−13.970
−20.269
1.00
39.42
O

ATOM
918
OP2
A
R
16
12.364
−16.147
−19.538
1.00
34.93
O

ATOM
919
O5′
A
R
16
10.316
−16.202
−20.956
1.00
37.41
O

ATOM
920
C5′
A
R
16
10.447
−17.438
−21.647
1.00
40.97
C

ATOM
921
C4′
A
R
16
10.817
−17.207
−23.101
1.00
43.94
C

ATOM
922
O4′
A
R
16
12.248
−17.377
−23.266
1.00
45.45
O

ATOM
923
C3′
A
R
16
10.174
−18.172
−24.088
1.00
45.96
C

ATOM
924
O3′
A
R
16
8.943
−17.639
−24.558
1.00
45.94
O

ATOM
925
C2′
A
R
16
11.215
−18.239
−25.200
1.00
47.55
C

ATOM
926
O2′
A
R
16
11.129
−17.140
−26.085
1.00
47.88
O

ATOM
927
C1′
A
R
16
12.513
−18.175
−24.404
1.00
49.77
C

ATOM
928
N9
A
R
16
12.983
−19.481
−23.951
1.00
56.07
N

ATOM
929
C8
A
R
16
13.023
−19.941
−22.664
1.00
58.42
C

ATOM
930
N7
A
R
16
13.496
−21.159
−22.552
1.00
58.57
N

ATOM
931
C5
A
R
16
13.787
−21.524
−23.857
1.00
58.61
C

ATOM
932
C6
A
R
16
14.319
−22.703
−24.417
1.00
58.39
C

ATOM
933
N6
A
R
16
14.664
−23.772
−23.692
1.00
57.70
N

ATOM
934
N1
A
R
16
14.482
−22.740
−25.755
1.00
58.07
N

ATOM
935
C2
A
R
16
14.136
−21.668
−26.477
1.00
58.55
C

ATOM
936
N3
A
R
16
13.628
−20.507
−26.065
1.00
57.81
N

ATOM
937
C4
A
R
16
13.476
−20.501
−24.731
1.00
57.77
C

ATOM
938
P
C
R
17
7.675
−18.598
−24.741
1.00
61.53
P

ATOM
939
OP1
C
R
17
6.649
−17.855
−25.508
1.00
60.91
O

ATOM
940
OP2
C
R
17
7.338
−19.166
−23.416
1.00
62.31
O

ATOM
941
O5′
C
R
17
8.248
−19.781
−25.652
1.00
63.09
O

ATOM
942
C5′
C
R
17
8.663
−19.514
−26.987
1.00
65.80
C

ATOM
943
C4′
C
R
17
8.805
−20.803
−21.116
1.00
68.55
C

ATOM
944
O4′
C
R
17
10.111
−21.381
−27.524
1.00
70.11
O

ATOM
945
C3′
C
R
17
7.803
−21.890
−27.414
1.00
69.61
C

ATOM
946
O3′
C
R
17
6.642
−21.771
−28.227
1.00
67.84
O

ATOM
947
C2′
C
R
17
8.578
−23.163
−27.733
1.00
71.16
C

ATOM
948
O2′
C
R
17
8.546
−23.483
−29.110
1.00
71.96
O

ATOM
949
C1′
C
R
17
9.993
−22.775
−27.316
1.00
71.90
C

ATOM
950
N1
C
R
17
10.291
−23.064
−25.884
1.00
73.05
N

ATOM
951
C2
C
R
17
11.055
−24.187
−25.549
1.00
73.99
C

ATOM
952
O2
C
R
17
11.473
−24.924
−26.450
1.00
73.80
O

ATOM
953
N3
C
R
17
11.317
−24.435
−24.242
1.00
74.55
N

ATOM
954
C4
C
R
17
10.848
−23.616
−23.299
1.00
73.50
C

ATOM
955
N4
C
R
17
11.132
−23.901
−22.024
1.00
72.78
N

ATOM
956
C5
C
R
17
10.067
−22.467
−23.622
1.00
73.09
C

ATOM
957
C6
C
R
17
9.816
−22.232
−24.914
1.00
72.97
C

ATOM
958
P
A
R
18
5.190
−21.755
−27.555
1.00
66.38
P

ATOM
959
OP1
A
R
18
4.353
−20.797
−28.309
1.00
68.14
O

ATOM
960
OP2
A
R
18
5.366
−21.588
−26.093
1.00
64.91
O

ATOM
961
O5′
A
R
18
4.650
−23.227
−27.841
1.00
64.71
O

ATOM
962
C5′
A
R
18
5.416
−24.090
−28.655
1.00
64.16
C

ATOM
963
C4′
A
R
18
5.319
−25.476
−28.083
1.00
64.40
C

ATOM
964
O4′
A
R
18
6.546
−25.800
−27.389
1.00
64.61
O

ATOM
965
C3′
A
R
18
4.255
−25.568
−27.015
1.00
65.62
C

ATOM
966
O3′
A
R
18
2.988
−25.784
−27.605
1.00
66.93
O

ATOM
967
C2′
A
R
18
4.743
−26.763
−26.207
1.00
66.09
C

ATOM
968
O2′
A
R
18
4.447
−28.000
−26.823
1.00
67.04
O

ATOM
969
C1′
A
R
18
6.248
−26.512
−26.202
1.00
65.29
C

ATOM
970
N9
A
R
18
6.672
−25.709
−25.063
1.00
64.91
N

ATOM
971
C8
A
R
18
6.693
−24.346
−24.977
1.00
64.93
C

ATOM
972
N7
A
R
18
7.115
−23.896
−23.820
1.00
65.03
N

ATOM
973
C5
A
R
18
7.392
−25.046
−23.098
1.00
65.49
C

ATOM
974
C6
A
R
18
7.875
−25.253
−21.790
1.00
65.73
C

ATOM
975
N6
A
R
18
8.176
−24.259
−20.950
1.00
65.54
N

ATOM
976
N1
A
R
18
8.033
−26.526
−21.378
1.00
65.39
N

ATOM
977
C2
A
R
18
7.726
−27.517
−22.222
1.00
66.34
C

ATOM
978
N3
A
R
18
7.264
−27.447
−23.469
1.00
66.22
N

ATOM
979
C4
A
R
18
7.119
−26.171
−23.849
1.00
65.27
C

ATOM
980
P
G
R
19
1.769
−26.263
−26.686
1.00
69.45
P

ATOM
981
OP1
G
R
19
0.673
−26.695
−27.580
1.00
71.64
O

ATOM
982
OP2
G
R
19
1.510
−25.216
−25.671
1.00
69.15
O

ATOM
983
O5′
G
R
19
2.378
−27.545
−25.941
1.00
68.11
O

ATOM
984
C5′
G
R
19
1.890
−28.843
−26.244
1.00
66.33
C

ATOM
985
C4′
G
R
19
1.972
−29.741
−25.027
1.00
65.02
C

ATOM
986
O4′
G
R
19
3.309
−29.703
−24.473
1.00
64.30
O

ATOM
987
C3′
G
R
19
1.062
−29.328
−23.888
1.00
64.24
C

ATOM
988
O3′
G
R
19
−0.226
−29.867
−24.114
1.00
64.19
O

ATOM
989
C2′
G
R
19
1.763
−29.960
−22.686
1.00
64.09
C

ATOM
990
O2′
G
R
19
1.416
−31.321
−22.525
1.00
62.48
O

ATOM
991
C1′
G
R
19
3.246
−29.825
−23.061
1.00
64.52
C

ATOM
992
N9
G
R
19
3.928
−28.670
−22.458
1.00
63.92
N

ATOM
993
C8
G
R
19
3.991
−27.391
−22.963
1.00
63.07
C

ATOM
994
N7
G
R
19
4.667
−26.566
−22.216
1.00
62.30
N

ATOM
995
C5
G
R
19
5.086
−27.340
−21.145
1.00
61.35
C

ATOM
996
C6
G
R
19
5.859
−26.981
−20.016
1.00
59.80
C

ATOM
997
O6
G
R
19
6.338
−25.876
−19.734
1.00
57.72
O

ATOM
998
N1
G
R
19
6.063
−28.065
−19.170
1.00
60.06
N

ATOM
999
C2
G
R
19
5.577
−29.331
−19.388
1.00
60.55
C

ATOM
1000
N2
G
R
19
5.874
−30.250
−18.460
1.00
60.30
N

ATOM
1001
N3
G
R
19
4.847
−29.679
−20.440
1.00
61.35
N

ATOM
1002
C4
G
R
19
4.643
−28.637
−21.277
1.00
62.10
C

ATOM
1003
P
G
R
20
−1.281
−29.993
−22.921
1.00
65.98
P

ATOM
1004
OP1
G
R
20
−1.674
−31.420
−22.833
1.00
64.81
O

ATOM
1005
OP2
G
R
20
−2.309
−28.946
−23.123
1.00
65.86
O

ATOM
1006
O5′
G
R
20
−0.428
−29.599
−21.622
1.00
64.18
O

ATOM
1007
C5′
G
R
20
−1.025
−29.609
−20.325
1.00
61.18
C

ATOM
1008
C4′
G
R
20
−0.049
−30.169
−19.305
1.00
59.53
C

ATOM
1009
O4′
G
R
20
1.290
−29.684
−19.597
1.00
60.67
O

ATOM
1010
C3′
G
R
20
−0.292
−29.746
−17.868
1.00
56.31
C

ATOM
1011
O3′
G
R
20
−1.267
−30.571
−17.248
1.00
51.47
O

ATOM
1012
C2′
G
R
20
1.085
−29.983
−17.268
1.00
57.77
C

ATOM
1013
O2′
G
R
20
1.334
−31.350
−17.042
1.00
57.37
O

ATOM
1014
C1′
G
R
20
1.991
−29.471
−18.382
1.00
61.19
C

ATOM
1015
N9
G
R
20
2.285
−28.046
−18.245
1.00
65.31
N

ATOM
1016
C8
G
R
20
1.716
−27.015
−18.956
1.00
67.40
C

ATOM
1017
N7
G
R
20
2.164
−25.836
−18.615
1.00
68.90
N

ATOM
1018
C5
G
R
20
3.089
−26.097
−17.606
1.00
68.11
C

ATOM
1019
C6
G
R
20
3.896
−25.204
−16.849
1.00
67.28
C

ATOM
1020
O6
G
R
20
3.956
−23.966
−16.923
1.00
67.16
O

ATOM
1021
N1
G
R
20
4.693
−25.886
−15.930
1.00
66.06
N

ATOM
1022
C2
G
R
20
4.707
−27.251
−15.761
1.00
65.11
C

ATOM
1023
N2
G
R
20
5.541
−27.724
−14.825
1.00
63.76
N

ATOM
1024
N3
G
R
20
3.958
−28.097
−16.462
1.00
65.24
N

ATOM
1025
C4
G
R
20
3.174
−27.454
−17.364
1.00
66.37
C

ATOM
1026
P
G
R
21
−1.882
−30.090
−15.853
1.00
48.69
P

ATOM
1027
OP1
G
R
21
−2.822
−31.116
−15.356
1.00
46.63
O

ATOM
1028
OP2
G
R
21
−2.326
−28.688
−16.031
1.00
47.64
O

ATOM
1029
O5′
G
R
21
−0.600
−30.072
−14.912
1.00
47.52
O

ATOM
1030
C5′
G
R
21
−0.344
−31.132
−14.020
1.00
45.44
C

ATOM
1031
C4′
G
R
21
0.802
−30.748
−13.110
1.00
45.74
C

ATOM
1032
O4′
G
R
21
1.722
−29.866
−13.806
1.00
47.27
O

ATOM
1033
C3′
G
R
21
0.403
−29.925
−11.905
1.00
44.58
C

ATOM
1034
O3′
G
R
21
−0.112
−30.752
−10.908
1.00
40.38
O

ATOM
1035
C2′
G
R
21
1.751
−29.353
−11.496
1.00
47.32
C

ATOM
1036
O2′
G
R
21
2.534
−30.309
−10.812
1.00
49.04
O

ATOM
1037
C1′
G
R
21
2.371
−29.027
−12.857
1.00
48.10
C

ATOM
1038
N9
G
R
21
2.206
−27.618
−13.233
1.00
48.97
N

ATOM
1039
C8
G
R
21
1.437
−27.121
−14.258
1.00
49.48
C

ATOM
1040
N7
G
R
21
1.470
−25.819
−14.354
1.00
50.25
N

ATOM
1041
C5
G
R
21
2.313
−25.417
−13.326
1.00
50.54
C

ATOM
1042
C6
G
R
21
2.728
−24.114
−12.937
1.00
50.88
C

ATOM
1043
O6
G
R
21
2.421
−23.025
−13.444
1.00
50.70
O

ATOM
1044
N1
G
R
21
3.588
−24.148
−11.841
1.00
50.31
N

ATOM
1045
C2
G
R
21
3.996
−25.294
−11.202
1.00
50.43
C

ATOM
1046
N2
G
R
21
4.828
−25.130
−10.160
1.00
49.83
N

ATOM
1047
N3
G
R
21
3.614
−26.520
−11.556
1.00
50.64
N

ATOM
1048
C4
G
R
21
2.776
−26.510
−12.624
1.00
50.13
C

ATOM
1049
P
C
R
22
−1.326
−30.203
−10.045
1.00
39.59
P

ATOM
1050
OP1
C
R
22
−2.042
−31.354
−9.466
1.00
41.83
O

ATOM
1051
OP2
C
R
22
−2.046
−29.216
−10.877
1.00
40.32
O

ATOM
1052
O5′
C
R
22
−0.615
−29.417
−8.860
1.00
36.89
O

ATOM
1053
C5′
C
R
22
0.381
−30.040
−8.096
1.00
32.65
C

ATOM
1054
C4′
C
R
22
1.202
−28.958
−7.438
1.00
33.09
C

ATOM
1055
O4′
C
R
22
1.721
−28.077
−8.454
1.00
34.36
O

ATOM
1056
C3′
C
R
22
0.409
−28.010
−6.575
1.00
33.94
C

ATOM
1057
O3′
C
R
22
0.204
−28.581
−5.307
1.00
34.30
O

ATOM
1058
C2′
C
R
22
1.356
−26.822
−6.499
1.00
35.12
C

ATOM
1059
O2′
C
R
22
2.418
−27.033
−5.597
1.00
40.17
O

ATOM
1060
C1′
C
R
22
1.943
−26.799
−7.894
1.00
33.76
C

ATOM
1061
N1
C
R
22
1.342
−25.750
−8.759
1.00
34.97
N

ATOM
1062
C2
C
R
22
1.705
−24.421
−8.549
1.00
34.26
C

ATOM
1063
O2
C
R
22
2.512
−24.153
−7.650
1.00
35.64
O

ATOM
1064
N3
C
R
22
1.170
−23.465
−9.335
1.00
34.35
N

ATOM
1065
C4
C
R
22
0.307
−23.794
−10.291
1.00
34.07
C

ATOM
1066
N4
C
R
22
−0.193
−22.807
−11.041
1.00
33.89
N

ATOM
1067
C5
C
R
22
−0.079
−25.143
−10.524
1.00
33.82
C

ATOM
1068
C6
C
R
22
0.459
−26.083
−9.742
1.00
34.43
C

ATOM
1069
P
A
R
23
−1.176
−28.274
−4.588
1.00
34.35
P

ATOM
1070
OP1
A
R
23
−1.213
−28.990
−3.301
1.00
34.14
O

ATOM
1071
OP2
A
R
23
−2.237
−28.454
−5.609
1.00
31.57
O

ATOM
1072
O5′
A
R
23
−1.079
−26.718
−4.279
1.00
35.92
O

ATOM
1073
C5′
A
R
23
−0.016
−26.188
−3.523
1.00
34.82
C

ATOM
1074
C4′
A
R
23
−0.077
−24.680
−3.633
1.00
35.67
C

ATOM
1075
O4′
A
R
23
−0.079
−24.330
−5.043
1.00
34.11
O

ATOM
1076
C3′
A
R
23
−1.345
−24.084
−3.027
1.00
36.21
C

ATOM
1077
O3′
A
R
23
−1.046
−23.010
−2.137
1.00
38.99
O

ATOM
1078
C2′
A
R
23
−2.159
−23.607
−4.224
1.00
35.49
C

ATOM
1079
O2′
A
R
23
−2.805
−22.376
−3.958
1.00
36.90
O

ATOM
1080
C1′
A
R
23
−1.118
−23.425
−5.320
1.00
33.00
C

ATOM
1081
N9
A
R
23
−1.674
−23.715
−6.638
1.00
32.61
N

ATOM
1082
C8
A
R
23
−2.003
−24.937
−7.153
1.00
31.24
C

ATOM
1083
N7
A
R
23
−2.505
−24.884
−8.366
1.00
29.76
N

ATOM
1084
C5
A
R
23
−2.514
−23.533
−8.664
1.00
31.64
C

ATOM
1085
C6
A
R
23
−2.935
−22.810
−9.797
1.00
33.41
C

ATOM
1086
N6
A
R
23
−3.440
−23.384
−10.888
1.00
36.48
N

ATOM
1087
N1
A
R
23
−2.811
−21.470
−9.775
1.00
35.12
N

ATOM
1088
C2
A
R
23
−2.301
−20.893
−8.680
1.00
36.33
C

ATOM
1089
N3
A
R
23
−1.877
−21.461
−7.553
1.00
34.62
N

ATOM
1090
C4
A
R
23
−2.010
−22.798
−7.610
1.00
33.32
C

ATOM
1091
P
A
R
24
−1.961
−22.782
−0.837
1.00
41.29
P

ATOM
1092
OP1
A
R
24
−1.541
−23.723
0.226
1.00
41.28
O

ATOM
1093
OP2
A
R
24
−3.378
−22.750
−1.265
1.00
42.32
O

ATOM
1094
O5′
A
R
24
−1.518
−21.321
−0.402
1.00
41.45
O

ATOM
1095
C5′
A
R
24
−0.164
−21.100
−0.090
1.00
41.29
C

ATOM
1096
C4′
A
R
24
0.091
−19.615
−0.039
1.00
40.62
C

ATOM
1097
O4′
A
R
24
−0.022
−19.064
−1.372
1.00
40.51
O

ATOM
1098
C3′
A
R
24
−0.944
−18.850
0.750
1.00
40.80
C

ATOM
1099
O3′
A
R
24
−0.637
−18.942
2.130
1.00
40.32
O

ATOM
1100
C2′
A
R
24
−0.715
−17.451
0.195
1.00
41.93
C

ATOM
1101
O2′
A
R
24
0.466
−16.871
0.703
1.00
45.53
O

ATOM
1102
C1′
A
R
24
−0.528
−17.748
−1.291
1.00
39.10
C

ATOM
1103
N9
A
R
24
−1.759
−17.703
−2.068
1.00
36.73
N

ATOM
1104
C8
A
R
24
−2.363
−18.757
−2.694
1.00
37.00
C

ATOM
1105
N7
A
R
24
−3.465
−18.434
−3.328
1.00
36.54
N

ATOM
1106
C5
A
R
24
−3.592
−17.075
−3.100
1.00
36.14
C

ATOM
1107
C6
A
R
24
−4.558
−16.140
−3.500
1.00
36.50
C

ATOM
1108
N6
A
R
24
−5.612
−16.466
−4.253
1.00
39.88
N

ATOM
1109
N1
A
R
24
−4.398
−14.862
−3.106
1.00
35.73
N

ATOM
1110
C2
A
R
24
−3.335
−14.549
−2.360
1.00
35.08
C

ATOM
1111
N3
A
R
24
−2.364
−15.341
−1.918
1.00
34.84
N

ATOM
1112
C4
A
R
24
−2.551
−16.605
−2.328
1.00
35.67
C

ATOM
1113
P
A
R
25
−1.808
−19.017
3.212
1.00
37.93
P

ATOM
1114
OP1
A
R
25
−1.167
−18.926
4.544
1.00
36.95
O

ATOM
1115
OP2
A
R
25
−2.690
−20.148
2.863
1.00
34.86
O

ATOM
1116
O5′
A
R
25
−2.629
−17.677
2.950
1.00
36.31
O

ATOM
1117
C5′
A
R
25
−2.062
−16.442
3.308
1.00
34.60
C

ATOM
1118
C4′
A
R
25
−2.970
−15.304
2.891
1.00
34.86
C

ATOM
1119
O4′
A
R
25
−3.073
−15.273
1.452
1.00
36.62
O

ATOM
1120
C3′
A
R
25
−4.404
−15.419
3.372
1.00
32.96
C

ATOM
1121
O3′
A
R
25
−4.502
−14.840
4.627
1.00
29.68
O

ATOM
1122
C2′
A
R
25
−5.153
−14.571
2.362
1.00
35.84
C

ATOM
1123
O2′
A
R
25
−5.136
−13.196
2.694
1.00
37.61
O

ATOM
1124
C1′
A
R
25
−4.370
−14.850
1.086
1.00
36.70
C

ATOM
1125
N9
A
R
25
−4.972
−15.933
0.345
1.00
38.42
N

ATOM
1126
C8
A
R
25
−4.555
−17.231
0.287
1.00
39.28
C

ATOM
1127
N7
A
R
25
−5.317
−17.989
−0.468
1.00
41.59
N

ATOM
1128
C5
A
R
25
−6.301
−17.122
−0.925
1.00
42.81
C

ATOM
1129
C6
A
R
25
−7.422
−17.296
−1.766
1.00
44.39
C

ATOM
1130
N6
A
R
25
−7.755
−18.462
−2.332
1.00
45.89
N

ATOM
1131
N1
A
R
25
−8.197
−16.217
−2.005
1.00
43.54
N

ATOM
1132
C2
A
R
25
−7.868
−15.049
−1.445
1.00
41.47
C

ATOM
1133
N3
A
R
25
−6.847
−14.766
−0.642
1.00
41.10
N

ATOM
1134
C4
A
R
25
−6.100
−15.854
−0.422
1.00
40.77
C

ATOM
1135
P
C
R
26
−5.569
−15.403
5.650
1.00
25.69
P

ATOM
1136
OP1
C
R
26
−5.691
−14.430
6.745
1.00
30.14
O

ATOM
1137
OP2
C
R
26
−5.232
−16.804
5.944
1.00
28.04
O

ATOM
1138
O5′
C
R
26
−6.900
−15.384
4.795
1.00
28.40
O

ATOM
1139
C5′
C
R
26
−7.665
−14.204
4.721
1.00
30.64
C

ATOM
1140
C4′
C
R
26
−8.887
−14.495
3.883
1.00
32.51
C

ATOM
1141
O4′
C
R
26
−8.434
−14.983
2.603
1.00
35.60
O

ATOM
1142
C3′
C
R
26
−9.762
−15.615
4.412
1.00
32.04
C

ATOM
1143
O3′
C
R
26
−10.696
−15.089
5.326
1.00
29.34
O

ATOM
1144
C2′
C
R
26
−10.454
−16.077
3.140
1.00
35.36
C

ATOM
1145
O2′
C
R
26
−11.501
−15.212
2.768
1.00
39.02
O

ATOM
1146
C1′
C
R
26
−9.331
−15.965
2.123
1.00
37.24
C

ATOM
1147
N1
C
R
26
−8.605
−17.244
1.921
1.00
40.41
N

ATOM
1148
C2
C
R
26
−9.195
−18.214
1.119
1.00
41.54
C

ATOM
1149
O2
C
R
26
−10.294
−17.962
0.613
1.00
44.26
O

ATOM
1150
N3
C
R
26
−8.552
−19.390
0.924
1.00
41.65
N

ATOM
1151
C4
C
R
26
−7.367
−19.602
1.501
1.00
43.49
C

ATOM
1152
N4
C
R
26
−6.766
−20.776
1.280
1.00
44.79
N

ATOM
1153
C5
C
R
26
−6.744
−18.621
2.330
1.00
42.89
C

ATOM
1154
C6
C
R
26
−7.394
−17.465
2.512
1.00
42.44
C

ATOM
1155
P
C
R
27
−11.184
−15.967
6.560
1.00
24.80
P

ATOM
1156
OP1
C
R
27
−11.967
−15.084
7.434
1.00
27.56
O

ATOM
1157
OP2
C
R
27
−10.022
−16.679
7.104
1.00
26.43
O

ATOM
1158
O5′
C
R
27
−12.162
−17.025
5.879
1.00
24.88
O

ATOM
1159
C5′
C
R
27
−13.370
−16.556
5.304
1.00
26.61
C

ATOM
1160
C4′
C
R
27
−14.117
−17.636
4.533
1.00
27.61
C

ATOM
1161
O4′
C
R
27
−13.340
−18.041
3.385
1.00
30.52
O

ATOM
1162
C3′
C
R
27
−14.394
−18.947
5.254
1.00
28.44
C

ATOM
1163
O3′
C
R
27
−15.514
−18.822
6.142
1.00
28.77
O

ATOM
1164
C2′
C
R
27
−14.717
−19.826
4.050
1.00
31.32
C

ATOM
1165
O2′
C
R
27
−15.981
−19.541
3.491
1.00
32.10
O

ATOM
1166
C1′
C
R
27
−13.655
−19.381
3.054
1.00
30.27
C

ATOM
1167
N1
C
R
27
−12.406
−20.184
3.084
1.00
30.23
N

ATOM
1168
C2
C
R
27
−12.354
−21.435
2.453
1.00
32.00
C

ATOM
1169
O2
C
R
27
−13.357
−21.868
1.878
1.00
34.04
O

ATOM
1170
N3
C
R
27
−11.202
−22.144
2.490
1.00
32.22
N

ATOM
1171
C4
C
R
27
−10.141
−21.638
3.120
1.00
33.92
C

ATOM
1172
N4
C
R
27
−9.018
−22.363
3.138
1.00
36.01
N

ATOM
1173
C5
C
R
27
−10.175
−20.364
3.761
1.00
31.82
C

ATOM
1174
C6
C
R
27
−11.317
−19.679
3.720
1.00
29.66
C

ATOM
1175
P
A
R
28
−15.614
−19.687
7.488
1.00
27.67
P

ATOM
1176
OP1
A
R
28
−16.793
−19.227
8.249
1.00
30.45
O

ATOM
1177
OP2
A
R
28
−14.296
−19.686
8.150
1.00
30.36
O

ATOM
1178
O5′
A
R
28
−15.909
−21.147
6.922
1.00
29.34
O

ATOM
1179
C5′
A
R
28
−17.039
−21.327
6.093
1.00
30.85
C

ATOM
1180
C4′
A
R
28
−17.140
−22.768
5.654
1.00
33.89
C

ATOM
1181
O4′
A
R
28
−16.249
−22.994
4.535
1.00
35.11
O

ATOM
1182
C3′
A
R
28
−16.687
−23.769
6.697
1.00
34.45
C

ATOM
1183
O3′
A
R
28
−17.741
−24.057
7.577
1.00
35.04
O

ATOM
1184
C2′
A
R
28
−16.367
−24.969
5.828
1.00
35.36
C

ATOM
1185
O2′
A
R
28
−17.529
−25.638
5.398
1.00
36.48
O

ATOM
1186
C1′
A
R
28
−15.684
−24.285
4.650
1.00
36.81
C

ATOM
1187
N9
A
R
28
−14.266
−24.136
4.902
1.00
39.71
N

ATOM
1188
C8
A
R
28
−13.641
−23.079
5.496
1.00
39.99
C

ATOM
1189
N7
A
R
28
−12.344
−23.238
5.603
1.00
41.35
N

ATOM
1190
C5
A
R
28
−12.111
−24.489
5.057
1.00
41.53
C

ATOM
1191
C6
A
R
28
−10.938
−25.245
4.871
1.00
44.83
C

ATOM
1192
N6
A
R
28
−9.722
−24.823
5.240
1.00
46.57
N

ATOM
1193
N1
A
R
28
−11.060
−26.458
4.287
1.00
45.36
N

ATOM
1194
C2
A
R
28
−12.276
−26.875
3.918
1.00
43.99
C

ATOM
1195
N3
A
R
28
−13.446
−26.251
4.042
1.00
42.07
N

ATOM
1196
C4
A
R
28
−13.289
−25.056
4.624
1.00
40.67
C

ATOM
1197
P
U
R
29
−17.415
−24.562
9.056
1.00
36.08
P

ATOM
1198
OP1
U
R
29
−18.697
−24.705
9.773
1.00
36.05
O

ATOM
1199
OP2
U
R
29
−16.340
−23.719
9.626
1.00
38.73
O

ATOM
1200
O5′
U
R
29
−16.775
−25.993
8.601
1.00
36.54
O

ATOM
1201
C5′
U
R
29
−17.582
−27.121
8.606
1.00
37.99
C

ATOM
1202
C4′
U
R
29
−16.659
−28.298
8.447
1.00
39.32
C

ATOM
1203
O4′
U
R
29
−15.742
−28.011
7.359
1.00
42.45
O

ATOM
1204
C3′
U
R
29
−15.732
−28.481
9.624
1.00
39.17
C

ATOM
1205
O3′
U
R
29
−16.347
−29.217
10.636
1.00
39.19
O

ATOM
1206
C2′
U
R
29
−14.611
−29.281
8.984
1.00
40.74
C

ATOM
1207
O2′
U
R
29
−14.973
−30.627
8.744
1.00
41.13
O

ATOM
1208
C1′
U
R
29
−14.459
−28.526
7.671
1.00
41.21
C

ATOM
1209
N1
U
R
29
−13.485
−27.415
7.805
1.00
41.40
N

ATOM
1210
C2
U
R
29
−12.149
−27.686
7.605
1.00
41.92
C

ATOM
1211
O2
U
R
29
−11.734
−28.786
7.297
1.00
43.67
O

ATOM
1212
N3
U
R
29
−11.308
−26.620
7.766
1.00
42.00
N

ATOM
1213
C4
U
R
29
−11.660
−25.332
8.106
1.00
42.74
C

ATOM
1214
O4
U
R
29
−10.785
−24.476
8.212
1.00
43.73
O

ATOM
1215
C5
U
R
29
−13.074
−25.126
8.315
1.00
42.39
C

ATOM
1216
C6
U
R
29
−13.916
−26.154
8.163
1.00
41.71
C

ATOM
1217
P
U
R
30
−15.495
−29.463
11.957
1.00
37.70
P

ATOM
1218
OP1
U
R
30
−16.298
−30.294
12.872
1.00
38.77
O

ATOM
1219
OP2
U
R
30
−14.967
−28.150
12.385
1.00
3'.97
O

ATOM
1220
O5′
U
R
30
−14.258
−30.318
11.440
1.00
37.73
O

ATOM
1221
C5′
U
R
30
−14.402
−31.698
11.223
1.00
36.40
C

ATOM
1222
C4′
U
R
30
−13.034
−32.329
11.267
1.00
36.66
C

ATOM
1223
O4′
U
R
30
−12.223
−31.796
10.193
1.00
37.17
O

ATOM
1224
C3′
U
R
30
−12.228
−31.979
12.499
1.00
36.14
C

ATOM
1225
O3′
U
R
30
−12.639
−32.769
13.582
1.00
33.90
O

ATOM
1226
C2′
U
R
30
−10.835
−32.356
12.017
1.00
38.31
C

ATOM
1227
O2′
U
R
30
−10.640
−33.754
11.937
1.00
41.23
O

ATOM
1228
C1′
U
R
30
−10.869
−31.767
10.612
1.00
37.79
C

ATOM
1229
N1
U
R
30
−10.388
−30.369
10.580
1.00
37.36
N

ATOM
1230
C2
U
R
30
−9.037
−30.137
10.447
1.00
36.55
C

ATOM
1231
O2
U
R
30
−9.215
−31.026
10.341
1.00
36.95
O

ATOM
1232
N3
U
R
30
−8.680
−28.819
10.436
1.00
37.83
N

ATOM
1233
C4
U
R
30
−9.525
−27.730
10.543
1.00
40.09
C

ATOM
1234
O4
U
R
30
−9.057
−26.597
10.510
1.00
42.53
O

ATOM
1235
C5
U
R
30
−10.922
−28.051
10.688
1.00
39.39
C

ATOM
1236
C6
U
R
30
−11.293
−29.335
10.701
1.00
38.10
C

ATOM
1237
P
C
R
31
−11.801
−32.766
14.939
1.00
31.70
P

ATOM
1238
OP1
C
R
31
−12.248
−33.919
15.742
1.00
33.78
O

ATOM
1239
OP2
C
R
31
−11.860
−31.402
15.502
1.00
33.52
O

ATOM
1240
O5′
C
R
31
−10.306
−33.045
14.484
1.00
31.32
O

ATOM
1241
C5′
C
R
31
−9.500
−33.851
15.309
1.00
31.29
C

ATOM
1242
C4′
C
R
31
−8.052
−33.6/5
14.934
1.00
33.06
C

ATOM
1243
O4′
C
R
31
−7.957
−32.965
13.679
1.00
32.53
O

ATOM
1244
C3′
C
R
31
−7.271
−32.793
15.877
1.00
35.37
C

ATOM
1245
O3′
C
R
31
−6.916
−33.515
17.024
1.00
40.10
O

ATOM
1246
C2′
C
R
31
−6.070
−32.487
15.010
1.00
34.33
C

ATOM
1247
O2′
C
R
31
−5.213
−33.598
14.896
1.00
34.21
O

ATOM
1248
C1′
C
R
31
−6.765
−32.207
13.683
1.00
35.12
C

ATOM
1249
N1
C
R
31
−7.106
−30.781
13.560
1.00
40.00
N

ATOM
1250
C2
C
R
31
−6.063
−29.861
13.461
1.00
43.74
C

ATOM
1251
O2
C
R
31
−4.896
−30.277
13.470
1.00
45.39
O

ATOM
1252
N3
C
R
31
−6.355
−28.542
13.355
1.00
47.02
N

ATOM
1253
C4
C
R
31
−7.627
−28.137
13.351
1.00
47.35
C

ATOM
1254
N4
C
R
31
−7.857
−26.819
13.245
1.00
47.55
N

ATOM
1255
C5
C
R
31
−8.710
−29.066
13.456
1.00
44.70
C

ATOM
1256
C6
C
R
31
−8.405
−30.368
13.559
1.00
42.35
C

ATOM
1257
P
G
R
32
−7.364
−32.945
18.447
1.00
43.16
P

ATOM
1258
OP1
G
R
32
−7.578
−34.106
19.336
1.00
43.82
O

ATOM
1259
OP2
G
R
32
−8.457
−31.968
18.223
1.00
42.78
O

ATOM
1260
O5′
G
R
32
−6.077
−32.127
18.937
1.00
45.47
O

ATOM
1261
C5′
G
R
32
−4.795
−32.430
18.404
1.00
47.44
C

ATOM
1262
C4′
G
R
32
−3.799
−31.297
18.615
1.00
49.67
C

ATOM
1263
O4′
G
R
32
−3.543
−30.631
17.351
1.00
50.87
O

ATOM
1264
C3′
G
R
32
−4.215
−30.149
19.525
1.00
49.57
C

ATOM
1265
O3′
G
R
32
−4.048
−30.474
20.892
1.00
51.36
O

ATOM
1266
C2′
G
R
32
−3.189
−29.122
19.083
1.00
49.22
C

ATOM
1267
O2′
G
R
32
−1.879
−29.501
19.442
1.00
49.74
O

ATOM
1268
C1′
G
R
32
−3.382
−29.248
17.588
1.00
49.79
C

ATOM
1269
N9
G
R
32
−4.602
−28.569
17.209
1.00
50.75
N

ATOM
1270
C8
G
R
32
−5.880
−29.061
17.263
1.00
51.16
C

ATOM
1271
N7
G
R
32
−6.776
−28.197
16.879
1.00
52.10
N

ATOM
1272
C5
G
R
32
−6.041
−27.060
16.570
1.00
52.62
C

ATOM
1273
C6
G
R
32
−6.463
−25.798
16.104
1.00
54.79
C

ATOM
1274
O6
G
R
32
−7.614
−25.415
15.861
1.00
59.06
O

ATOM
1275
N1
G
R
32
−5.394
−24.933
15.919
1.00
54.77
N

ATOM
1276
C2
G
R
32
−4.082
−25.248
16.157
1.00
55.31
C

ATOM
1277
N2
G
R
32
−3.183
−24.284
15.919
1.00
57.00
N

ATOM
1278
N3
G
R
32
−3.674
−26.428
16.593
1.00
54.61
N

ATOM
1279
C4
G
R
32
−4.705
−27.276
16.778
1.00
52.20
C

ATOM
1280
P
A
R
33
−5.086
−29.902
21.975
1.00
52.70
P

ATOM
1281
OP1
A
R
33
−4.666
−30.421
23.290
1.00
53.43
O

ATOM
1282
OP2
A
R
33
−6.463
−30.138
21.480
1.00
51.85
O

ATOM
1283
O5′
A
R
33
−4.854
−28.324
21.968
1.00
51.32
O

ATOM
1284
C5′
A
R
33
−5.556
−27.538
22.905
1.00
49.30
C

ATOM
1285
C4′
A
R
33
−4.709
−26.355
23.299
1.00
48.49
C

ATOM
1286
O4′
A
R
33
−3.579
−26.806
24.080
1.00
47.54
O

ATOM
1287
C3′
A
R
33
−4.090
−25.642
22.118
1.00
47.73
C

ATOM
1288
O3′
A
R
33
−5.018
−24.715
21.624
1.00
48.26
O

ATOM
1289
C2′
A
R
33
−2.903
−24.952
22.772
1.00
47.88
C

ATOM
1290
O2′
A
R
33
−3.287
−23.773
23.452
1.00
48.96
O

ATOM
1291
C1′
A
R
33
−2.455
−26.004
23.783
1.00
46.83
C

ATOM
1292
N9
A
R
33
−1.387
−26.872
23.302
1.00
45.20
N

ATOM
1293
C8
A
R
33
−1.463
−28.216
23.079
1.00
45.12
C

ATOM
1294
N7
A
R
33
−0.338
−28.742
22.648
1.00
44.85
N

ATOM
1295
C5
A
R
33
0.534
−27.669
22.588
1.00
41.91
C

ATOM
1296
C6
A
R
33
1.886
−27.564
22.210
1.00
39.30
C

ATOM
1297
N6
A
R
33
2.619
−28.602
21.804
1.00
39.19
N

ATOM
1298
N1
A
R
33
2.459
−26.348
22.266
1.00
38.76
N

ATOM
1299
C2
A
R
33
1.723
−25.308
22.670
1.00
40.66
C

ATOM
1300
N3
A
R
33
0.445
−25.283
23.049
1.00
43.01
N

ATOM
1301
C4
A
R
33
−0.096
−26.508
22.987
1.00
43.58
C

ATOM
1302
P
A
R
34
−5.218
−24.598
20.052
1.00
50.24
P

ATOM
1303
OP1
A
R
34
−6.470
−23.854
19.784
1.00
50.92
O

ATOM
1304
OP2
A
R
34
−5.005
−25.947
19.480
1.00
50.56
O

ATOM
1305
O5′
A
R
34
−3.995
−23.669
19.633
1.00
46.54
O

ATOM
1306
C5′
A
R
34
−3.936
−22.364
20.140
1.00
43.00
C

ATOM
1307
C4′
A
R
34
−2.519
−21.861
20.031
1.00
41.88
C

ATOM
1308
O4′
A
R
34
−1.639
−22.785
20.712
1.00
40.59
O

ATOM
1309
C3′
A
R
34
−2.004
−21.806
18.610
1.00
41.34
C

ATOM
1310
O3′
A
R
34
−2.348
−20.555
18.048
1.00
42.02
O

ATOM
1311
C2′
A
R
34
−0.500
−21.946
18.815
1.00
41.17
C

ATOM
1312
O2′
A
R
34
0.101
−20.716
19.143
1.00
42.01
O

ATOM
1313
C1′
A
R
34
−0.417
−22.888
20.013
1.00
40.56
C

ATOM
1314
N9
A
R
34
−0.238
−24.289
19.658
1.00
41.45
N

ATOM
1315
C8
A
R
34
−1.221
−25.215
19.447
1.00
42.16
C

ATOM
1316
N7
A
R
34
−0.768
−26.407
19.145
1.00
41.17
N

ATOM
1317
C5
A
R
34
0.608
−26.251
19.160
1.00
40.74
C

ATOM
1318
C6
A
R
34
1.668
−27.150
18.923
1.00
40.96
C

ATOM
1319
N6
A
R
34
1.494
−28.441
18.608
1.00
39.52
N

ATOM
1320
N1
A
R
34
2.923
−26.667
19.022
1.00
41.14
N

ATOM
1321
C2
A
R
34
3.095
−25.376
19.334
1.00
41.64
C

ATOM
1322
N3
A
R
34
2.180
−24.441
19.579
1.00
41.44
N

ATOM
1323
C4
A
R
34
0.948
−24.950
19.475
1.00
40.46
C

ATOM
1324
P
A
R
35
−2.482
−20.405
16.462
1.00
45.13
P

ATOM
1325
OP1
A
R
35
−2.845
−19.002
16.166
1.00
47.81
O

ATOM
1326
OP2
A
R
35
−3.335
−21.501
15.960
1.00
45.29
O

ATOM
1327
O5′
A
R
35
−0.987
−20.667
15.954
1.00
46.11
O

ATOM
1328
C5′
A
R
35
−0.119
−19.563
15.698
1.00
45.34
C

ATOM
1329
C4′
A
R
35
1.309
−20.033
15.493
1.00
45.66
C

ATOM
1330
O4′
A
R
35
1.635
−21.039
16.482
1.00
45.85
O

ATOM
1331
C3′
A
R
35
1.585
−20.720
14.167
1.00
45.24
C

ATOM
1332
O3′
A
R
35
1.857
−19.768
13.173
1.00
46.49
O

ATOM
1333
C2′
A
R
35
2.833
−21.520
14.502
1.00
46.01
C

ATOM
1334
O2′
A
R
35
4.005
−20.734
14.531
1.00
47.10
O

ATOM
1335
C1′
A
R
35
2.481
−22.011
15.897
1.00
46.80
C

ATOM
1336
N9
A
R
35
1.754
−23.258
15.806
1.00
47.88
N

ATOM
1337
C8
A
R
35
0.405
−23.418
15.680
1.00
48.84
C

ATOM
1338
N7
A
R
35
0.037
−24.674
15.596
1.00
49.94
N

ATOM
1339
C5
A
R
35
1.232
−25.377
15.661
1.00
48.68
C

ATOM
1340
C6
A
R
35
1.526
−26.753
15.624
1.00
48.87
C

ATOM
1341
N6
A
R
35
0.587
−27.702
15.506
1.00
49.26
N

ATOM
1342
N1
A
R
35
2.826
−27.112
15.711
1.00
48.46
N

ATOM
1343
C2
A
R
35
3.756
−26.153
15.828
1.00
48.10
C

ATOM
1344
N3
A
R
35
3.598
−24.833
15.874
1.00
47.07
N

ATOM
1345
C4
A
R
35
2.300
−24.514
15.783
1.00
47.57
C

ATOM
1346
P
G
R
36
0.806
−19.527
11.995
1.00
48.84
P

ATOM
1347
OP1
G
R
36
1.459
−18.647
10.996
1.00
48.41
O

ATOM
1348
OP2
G
R
36
−0.475
−19.126
12.625
1.00
47.59
O

ATOM
1349
O5′
G
R
36
0.598
−20.982
11.349
1.00
48.60
O

ATOM
1350
C5′
G
R
36
1.659
−21.624
10.631
1.00
48.20
C

ATOM
1351
C4′
G
R
36
1.744
−23.107
10.967
1.00
46.62
C

ATOM
1352
O4′
G
R
36
1.125
−23.366
12.257
1.00
47.75
O

ATOM
1353
C3′
G
R
36
−1.011
−24.031
10.015
1.00
45.51
C

ATOM
1354
O3′
G
R
36
−1.827
−24.319
8.899
1.00
45.39
O

ATOM
1355
C2′
G
R
36
−0.840
−25.256
10.901
1.00
46.27
C

ATOM
1356
O2′
G
R
36
−2.071
−25.941
11.057
1.00
47.35
O

ATOM
1357
C1′
G
R
36
−0.425
−24.598
12.221
1.00
43.29
C

ATOM
1358
N9
G
R
36
−1.011
−24.324
12.336
1.00
37.86
N

ATOM
1359
C8
G
R
36
−1.638
−23.100
12.262
1.00
36.20
C

ATOM
1360
N7
G
R
36
−2.936
−23.168
12.393
1.00
35.24
N

ATOM
1361
C5
G
R
36
−3.188
−24.523
12.569
1.00
35.02
C

ATOM
1362
C6
G
R
36
−4.411
−25.212
12.762
1.00
33.68
C

ATOM
1363
O6
G
R
36
−5.553
−24.750
12.816
1.00
36.12
O

ATOM
1364
N1
G
R
36
−4.223
−26.578
12.901
1.00
31.08
N

ATOM
1365
C2
G
R
36
−3.002
−27.203
12.856
1.00
34.21
C

ATOM
1366
N2
G
R
36
−3.010
−28.534
13.006
1.00
36.11
N

ATOM
1367
N3
G
R
36
−1.847
−26.577
12.671
1.00
35.35
N

ATOM
1368
C4
G
R
36
−2.014
−25.243
12.537
1.00
35.95
C

ATOM
1369
P
A
R
37
1.170
−24.455
7.447
1.00
44.28
P

ATOM
1370
OP1
A
R
37
2.250
−24.331
6.444
1.00
43.71
O

ATOM
1371
OP2
A
R
37
−0.018
−23.570
7.397
1.00
42.86
O

ATOM
1372
O5′
A
R
37
0.676
−25.966
7.432
1.00
45.03
O

ATOM
1373
C5′
A
R
37
1.635
−26.998
7.572
1.00
43.60
C

ATOM
1374
C4′
A
R
37
0.955
−28.312
7.904
1.00
42.00
C

ATOM
1375
O4′
A
R
37
0.356
−28.237
9.228
1.00
42.09
O

ATOM
1376
C3′
A
R
37
−0.190
−28.711
6.983
1.00
38.25
C

ATOM
1377
O3′
A
R
37
0.312
−29.356
5.831
1.00
32.62
O

ATOM
1378
C2′
A
R
37
−0.914
−29.695
7.887
1.00
40.95
C

ATOM
1379
O2′
A
R
37
−0.216
−30.918
7.987
1.00
43.09
O

ATOM
1380
C1′
A
R
37
−0.865
−28.952
9.222
1.00
41.15
C

ATOM
1381
N9
A
R
37
−1.957
−27.997
9.361
1.00
40.05
N

ATOM
1382
C8
A
R
37
−1.874
−26.635
9.315
1.00
39.99
C

ATOM
1383
N7
A
R
37
−3.028
−26.030
9.460
1.00
39.96
N

ATOM
1384
C5
A
R
37
−3.927
−27.068
9.603
1.00
39.70
C

ATOM
1385
C6
A
R
37
−5.316
−27.093
9.796
1.00
40.93
C

ATOM
1386
N6
A
R
37
−6.055
−25.989
9.876
1.00
42.33
N

ATOM
1387
N1
A
R
37
−5.916
−28.295
9.908
1.00
41.57
N

ATOM
1388
C2
A
R
37
−5.164
−29.398
9.832
1.00
40.99
C

ATOM
1389
N3
A
R
37
−3.850
−29.501
9.652
1.00
40.78
N

ATOM
1390
C4
A
R
37
−3.286
−28.287
9.545
1.00
39.98
C

ATOM
1391
P
G
R
38
−0.561
−29.418
4.493
1.00
32.71
P

ATOM
1392
OP1
G
R
38
0.255
−30.063
3.441
1.00
32.07
O

ATOM
1393
OP2
G
R
38
−1.121
−28.075
4.258
1.00
33.79
O

ATOM
1394
O5′
G
R
38
−1.766
−30.388
4.875
1.00
30.99
O

ATOM
1395
C5′
G
R
38
−1.576
−31.781
4.819
1.00
31.41
C

ATOM
1396
C4′
G
R
38
−2.813
−32.506
5.298
1.00
32.76
C

ATOM
1397
O4′
G
R
38
−3.285
−31.915
6.534
1.00
32.81
O

ATOM
1398
C3′
G
R
38
−4.012
−32.390
4.376
1.00
33.98
C

ATOM
1399
O3′
G
R
38
−3.891
−33.284
3.281
1.00
33.41
O

ATOM
1400
C2′
G
R
38
−5.125
−32.800
5.329
1.00
34.81
C

ATOM
1401
O2′
G
R
38
−5.186
−34.197
5.533
1.00
36.11
O

ATOM
1402
C1′
G
R
38
−4.689
−32.091
6.612
1.00
34.68
C

ATOM
1403
N9
G
R
38
−5.335
−30.797
6.722
1.00
34.46
N

ATOM
1404
C8
G
R
38
−4.752
−29.555
6.728
1.00
34.30
C

ATOM
1405
N7
G
R
38
−5.617
−28.584
6.823
1.00
34.37
N

ATOM
1406
C5
G
R
38
−6.848
−29.232
6.873
1.00
37.08
C

ATOM
1407
C6
G
R
38
−8.163
−28.710
6.971
1.00
39.80
C

ATOM
1408
O6
G
R
38
−8.520
−27.525
7.041
1.00
44.16
O

ATOM
1409
N1
G
R
38
−9.121
−29.718
6.992
1.00
37.77
N

ATOM
1410
C2
G
R
38
8.850
−31.055
6.925
1.00
36.63
C

ATOM
1411
N2
G
R
38
9.912
−31.868
6.957
1.00
35.98
N

ATOM
1412
N3
G
R
38
7.628
−31.560
6.831
1.00
36.06
N

ATOM
1413
C4
G
R
38
6.685
−30.592
6.808
1.00
35.35
C

ATOM
1414
P
U
R
39
−3.912
−32.707
1.792
1.00
32.59
P

ATOM
1415
OP1
U
R
39
−3.027
−33.545
0.951
1.00
33.07
O

ATOM
1416
OP2
U
R
39
−3.690
−31.253
1.885
1.00
33.21
O

ATOM
1417
O5′
U
R
39
−5.417
−32.964
1.332
1.00
31.69
O

ATOM
1418
C5′
U
R
39
−6.132
−34.012
1.935
1.00
32.33
C

ATOM
1419
C4′
U
R
39
−7.589
−33.631
2.037
1.00
33.41
C

ATOM
1420
O4′
U
R
39
−7.829
−32.868
3.242
1.00
33.54
O

ATOM
1421
C3′
U
R
39
−8.050
−32.696
0.946
1.00
32.92
C

ATOM
1422
O3′
U
R
39
−8.267
−33.416
−0.259
1.00
28.28
O

ATOM
1423
C2′
U
R
39
−9.340
−32.168
1.567
1.00
33.53
C

ATOM
1424
O2′
U
R
39
−10.400
−33.090
1.460
1.00
35.14
O

ATOM
1425
C1′
U
R
39
−8.937
−32.014
3.032
1.00
33.73
C

ATOM
1426
N1
U
R
39
−8.509
−30.649
3.338
1.00
36.60
N

ATOM
1427
C2
U
R
39
−9.451
−29.658
3.478
1.00
38.85
C

ATOM
1428
O2
U
R
39
−10.646
−29.852
3.382
1.00
39.45
O

ATOM
1429
N3
U
R
39
−8.940
−28.421
3.752
1.00
40.72
N

ATOM
1430
C4
U
R
39
−7.610
−28.083
3.882
1.00
41.31
C

ATOM
1431
O4
U
R
39
−7.299
−26.923
4.129
1.00
44.50
O

ATOM
1432
C5
U
R
39
−6.689
−29.174
3.713
1.00
40.42
C

ATOM
1433
C6
U
R
39
−7.165
−30.390
3.451
1.00
38.82
C

ATOM
1434
P
G
R
40
−8.209
−32.602
−1.619
1.00
27.07
P

ATOM
1435
OP1
G
R
40
−8.380
−33.536
−2.745
1.00
32.26
O

ATOM
1436
OP2
G
R
40
−7.026
−31.726
−1.553
1.00
25.98
O

ATOM
1437
O5′
G
R
40
−9.520
−31.696
−1.527
1.00
29.97
O

ATOM
1438
C5′
G
R
40
−10.722
−32.131
−2.149
1.00
30.41
C

ATOM
1439
C4′
G
R
40
−11.855
−31.115
−2.001
1.00
32.37
C

ATOM
1440
O4′
G
R
40
−12.025
−30.712
−0.621
1.00
33.17
O

ATOM
1441
C3′
G
R
40
−11.670
−29.792
−2.719
1.00
33.26
C

ATOM
1442
O3′
G
R
40
−12.007
−29.911
−4.061
1.00
35.92
O

ATOM
1443
C2′
G
R
40
−12.709
−28.949
−2.021
1.00
32.31
C

ATOM
1444
O2′
G
R
40
−14.009
−29.317
−2.422
1.00
30.96
O

ATOM
1445
C1′
G
R
40
−12.429
−29.351
−0.585
1.00
33.47
C

ATOM
1446
N9
G
R
40
−11.344
−26.549
−0.040
1.00
33.76
N

ATOM
1447
C8
G
R
40
−10.027
−28.907
0.086
1.00
34.31
C

ATOM
1448
N7
G
R
40
−9.287
−27.966
0.610
1.00
36.04
N

ATOM
1449
C5
G
R
40
−10.173
−26.912
0.830
1.00
35.52
C

ATOM
1450
C6
G
R
40
−9.955
−25.616
1.374
1.00
35.56
C

ATOM
1451
O6
G
R
40
−8.897
−25.110
1.787
1.00
34.65
O

ATOM
1452
N1
G
R
40
−11.132
−24.876
1.413
1.00
34.19
N

ATOM
1453
C2
G
R
40
−12.354
−25.324
0.989
1.00
32.44
C

ATOM
1454
N2
G
R
40
−13.375
−24.468
1.107
1.00
32.59
N

ATOM
1455
N3
G
R
40
−12.568
−26.524
0.482
1.00
32.95
N

ATOM
1456
C4
G
R
40
−11.439
−27.260
0.431
1.00
33.21
C

ATOM
1457
P
G
R
41
−11.182
−29.031
−5.099
1.00
38.61
P

ATOM
1458
OP1
G
R
41
−11.332
−29.651
−6.432
1.00
41.91
O

ATOM
1459
OP2
G
R
41
−9.837
−28.807
−4.514
1.00
37.08
O

ATOM
1460
O5′
G
R
41
−11.940
−27.626
−5.114
1.00
39.51
O

ATOM
1461
C5′
G
R
41
−13.345
−27.557
−4.952
1.00
39.49
C

ATOM
1462
C4′
G
R
41
−13.750
−26.176
−4.457
1.00
37.68
C

ATOM
1463
O4′
G
R
41
−13.401
−26.019
−3.058
1.00
35.06
O

ATOM
1464
C3′
G
R
41
−13.051
−25.005
−5.120
1.00
35.16
C

ATOM
1465
O3′
G
R
41
−13.629
−24.735
−6.375
1.00
34.70
O

ATOM
1466
C2′
G
R
41
−13.380
−23.910
−4.123
1.00
35.31
C

ATOM
1467
O2′
G
R
41
−14.728
−23.498
−4.213
1.00
34.90
O

ATOM
1468
C1′
G
R
41
−13.155
−24.651
−2.811
1.00
34.33
C

ATOM
1469
N9
G
R
41
−11.793
−24.521
−2.337
1.00
33.73
N

ATOM
1470
C8
G
R
41
−10.787
−25.441
−2.441
1.00
33.48
C

ATOM
1471
N7
G
R
41
−9.663
−25.031
−1.922
1.00
34.72
N

ATOM
1472
C5
G
R
41
−9.949
−23.757
−1.448
1.00
35.68
C

ATOM
1473
C6
G
R
41
−9.125
−22.818
−0.784
1.00
37.29
C

ATOM
1474
O6
G
R
41
−7.935
−22.923
−0.465
1.00
39.70
O

ATOM
1475
N1
G
R
41
−9.814
−21.654
−0.481
1.00
37.16
N

ATOM
1476
C2
G
R
41
−11.134
−21.424
−0.778
1.00
37.02
C

ATOM
1477
N2
G
R
41
−11.630
−20.235
−0.398
1.00
35.94
N

ATOM
1478
N3
G
R
41
−11.917
−22.296
−1.399
1.00
36.04
N

ATOM
1479
C4
G
R
41
−11.257
−23.433
−1.701
1.00
34.87
C

ATOM
1480
P
G
R
42
−12.753
−23.954
−7.448
1.00
36.22
P

ATOM
1481
OP1
G
R
42
−13.661
−23.346
−8.442
1.00
37.19
O

ATOM
1482
OP2
G
R
42
−11.659
−24.845
−7.872
1.00
37.80
O

ATOM
1483
O5′
G
R
42
−12.100
−22.795
−6.580
1.00
38.11
O

ATOM
1484
C5′
G
R
42
−12.683
−21.509
−6.615
1.00
39.13
C

ATOM
1485
C4′
G
R
42
−11.789
−20.507
−5.911
1.00
38.23
C

ATOM
1486
O4′
G
R
42
−11.216
−21.116
−4.729
1.00
37.53
O

ATOM
1487
C3′
G
R
42
−10.617
−20.030
−6.748
1.00
36.27
C

ATOM
1488
O3′
G
R
42
−11.019
−18.862
−7.456
1.00
32.96
O

ATOM
1489
C2′
G
R
42
−9.542
−19.737
−5.699
1.00
37.70
C

ATOM
1490
O2′
G
R
42
−9.568
−18.403
−5.243
1.00
40.34
O

ATOM
1491
C1′
G
R
42
−9.893
−20.668
−4.539
1.00
37.08
C

ATOM
1492
N9
G
R
42
−9.035
−21.840
−4.471
1.00
35.46
N

ATOM
1493
C8
G
R
42
−9.259
−23.040
−5.082
1.00
35.58
C

ATOM
1494
N7
G
R
42
−8.320
−23.912
−4.851
1.00
37.27
N

ATOM
1495
C5
G
R
42
−7.421
−23.244
−4.040
1.00
35.82
C

ATOM
1496
C6
G
R
42
−6.207
−23.692
−3.477
1.00
38.85
C

ATOM
1497
O6
G
R
42
−5.678
−24.805
−3.594
1.00
42.98
O

ATOM
1498
N1
G
R
42
−5.596
−22.703
−2.714
1.00
36.45
N

ATOM
1499
C2
G
R
42
−6.102
−21.442
−2.527
1.00
34.62
C

ATOM
1500
N2
G
R
42
−5.373
−20.620
−1.760
1.00
35.43
N

ATOM
1501
N3
G
R
42
−7.239
−21.015
−3.054
1.00
33.12
N

ATOM
1502
C4
G
R
42
−7.844
−21.967
−3.795
1.00
33.82
C

ATOM
1503
P
A
R
43
−10.148
−18.290
−8.668
1.00
32.63
P

ATOM
1504
OP1
A
R
43
−10.726
−16.998
−9.076
1.00
35.34
O

ATOM
1505
OP2
A
R
43
−9.968
−19.351
−9.672
1.00
31.81
O

ATOM
1506
O5′
A
R
43
−8.733
−18.023
−8.000
1.00
34.24
O

ATOM
1507
C5′
A
R
43
−7.749
−17.363
−8.747
1.00
36.54
C

ATOM
1508
C4′
A
R
43
−6.697
−16.811
−7.817
1.00
39.07
C

ATOM
1509
O4′
A
R
43
−6.388
−17.794
−6.799
1.00
38.59
O

ATOM
1510
C3′
A
R
43
−5.369
−16.507
−8.481
1.00
42.00
C

ATOM
1511
O3′
A
R
43
−4.733
−15.531
−7.721
1.00
45.25
O

ATOM
1512
C2′
A
R
43
−4.636
−17.830
−8.349
1.00
41.77
C

ATOM
1513
O2′
A
R
43
−3.232
−17.676
−8.415
1.00
44.07
O

ATOM
1514
C1′
A
R
43
−5.043
−18.206
−6.938
1.00
40.29
C

ATOM
1515
N9
A
R
43
−4.983
−19.632
−6.702
1.00
40.50
N

ATOM
1516
C8
A
R
43
−4.403
−20.271
−5.648
1.00
41.27
C

ATOM
1517
N7
A
R
43
−4.514
−21.574
−5.700
1.00
41.00
N

ATOM
1518
C5
A
R
43
−5.217
−21.798
−6.867
1.00
40.97
C

ATOM
1519
C6
A
R
43
−5.661
−22.973
−7.488
1.00
41.57
C

ATOM
1520
N6
A
R
43
−5.442
−24.191
−6.990
1.00
43.37
N

ATOM
1521
N1
A
R
43
−6.334
−22.850
−8.647
1.00
43.05
N

ATOM
1522
C2
A
R
43
−6.548
−21.624
−9.140
1.00
44.44
C

ATOM
1523
N3
A
R
43
−6.183
−20.443
−8.643
1.00
43.97
N

ATOM
1524
C4
A
R
43
−5.513
−20.609
−7.496
1.00
41.75
C

ATOM
1525
P
C
R
44
−4.767
−14.034
−8.233
1.00
46.32
P

ATOM
1526
OP1
C
R
44
−5.734
−13.298
−7.394
1.00
47.76
O

ATOM
1527
OP2
C
R
44
−4.955
−14.082
−9.701
1.00
47.65
O

ATOM
1528
O5′
C
R
44
−3.277
−13.542
−7.911
1.00
41.08
O

ATOM
1529
C5′
C
R
44
−3.072
−12.496
−6.999
1.00
36.13
C

ATOM
1530
C4′
C
R
44
−1.869
−12.777
−6.124
1.00
34.68
C

ATOM
1531
O4′
C
R
44
−2.052
−14.012
−5.405
1.00
33.81
O

ATOM
1532
C3′
C
R
44
−0.549
−13.034
−6.825
1.00
34.58
C

ATOM
1533
O3′
C
R
44
0.010
−11.834
−7.353
1.00
34.09
O

ATOM
1534
C2′
C
R
44
0.255
−13.560
−5.640
1.00
34.22
C

ATOM
1535
O2′
C
R
44
0.696
−12.527
−4.786
1.00
35.16
O

ATOM
1536
C1′
C
R
44
−0.783
−14.408
−4.913
1.00
33.17
C

ATOM
1537
N1
C
R
44
−0.591
−15.858
−5.149
1.00
36.50
N

ATOM
1538
C2
C
R
44
0.430
−16.526
−4.462
1.00
37.81
C

ATOM
1539
O2
C
R
44
1.138
−15.888
−3.675
1.00
40.26
O

ATOM
1540
N3
C
R
44
0.611
−17.852
−4.670
1.00
37.02
N

ATOM
1541
C4
C
R
44
−0.180
−18.500
−5.526
1.00
38.36
C

ATOM
1542
N4
C
R
44
0.039
−19.808
−5.699
1.00
40.51
N

ATOM
1543
C5
C
R
44
−1.225
−17.838
−6.245
1.00
37.69
C

ATOM
1544
C6
C
R
44
−1.394
−16.528
−6.031
1.00
37.28
C

ATOM
1545
P
G
R
45
0.991
−11.903
−8.614
1.00
33.92
P

ATOM
1546
OP1
G
R
45
1.023
−10.574
−9.255
1.00
35.35
O

ATOM
1547
OP2
G
R
45
0.652
−13.103
−9.404
1.00
34.05
O

ATOM
1548
O5′
G
R
45
2.412
−12.169
−7.966
1.00
32.54
O

ATOM
1549
C5′
G
R
45
3.247
−13.111
−8.581
1.00
30.31
C

ATOM
1550
C4′
G
R
45
3.691
−14.125
−7.556
1.00
30.77
C

ATOM
1551
O4′
G
R
45
2.555
−14.880
−7.070
1.00
30.30
O

ATOM
1552
C3′
G
R
45
4.659
−15.155
−8.086
1.00
29.54
C

ATOM
1553
O3′
G
R
45
5.960
−14.604
−8.005
1.00
26.34
O

ATOM
1554
C2′
G
R
45
4.415
−16.316
−7.121
1.00
29.97
C

ATOM
1555
O2′
G
R
45
5.001
−16.111
−5.854
1.00
31.17
O

ATOM
1556
C1′
G
R
45
2.904
−16.244
−6.960
1.00
28.81
C

ATOM
1557
N9
G
R
45
2.153
−16.969
−7.973
1.00
28.49
N

ATOM
1558
C8
G
R
45
1.342
−16.430
−8.935
1.00
27.78
C

ATOM
1559
N7
G
R
45
0.786
−17.321
−9.705
1.00
27.76
N

ATOM
1560
C5
G
R
45
1.252
−18.528
−9.214
1.00
28.93
C

ATOM
1561
C6
G
R
45
0.986
−19.847
−9.642
1.00
31.75
C

ATOM
1562
O6
G
R
45
0.262
−20.228
−10.577
1.00
32.96
O

ATOM
1563
N1
G
R
45
1.663
−20.778
−8.865
1.00
33.24
N

ATOM
1564
C2
G
R
45
2.483
−20.476
−7.809
1.00
34.60
C

ATOM
1565
N2
G
R
45
3.042
−21.518
−7.182
1.00
39.58
N

ATOM
1566
N3
G
R
45
2.742
−19.246
−7.396
1.00
32.48
N

ATOM
1567
C4
G
R
45
2.093
−18.327
−8.146
1.00
30.05
C

ATOM
1568
P
C
R
46
7.071
−15.112
−9.014
1.00
23.86
P

ATOM
1569
OP1
C
R
46
8.368
−14.524
−8.617
1.00
24.29
O

ATOM
1570
OP2
C
R
46
6.547
−14.953
−10.385
1.00
22.07
O

ATOM
1571
O5′
C
R
46
7.117
−16.657
−8.668
1.00
25.56
O

ATOM
1572
C5′
C
R
46
8.083
−17.109
−7.735
1.00
28.11
C

ATOM
1573
C4′
C
R
46
7.965
−18.610
−7.598
1.00
29.56
C

ATOM
1574
O4′
C
R
46
6.574
−18.952
−7.770
1.00
29.30
O

ATOM
1575
C3′
C
R
46
8.658
−19.415
−8.687
1.00
31.66
C

ATOM
1576
O3′
C
R
46
10.062
−19.582
−8.408
1.00
32.12
O

ATOM
1577
C2′
C
R
46
7.885
−20.734
−8.624
1.00
31.06
C

ATOM
1578
O2′
C
R
46
8.402
−21.630
−7.664
1.00
33.30
O

ATOM
1579
C1′
C
R
46
6.486
−20.290
−8.202
1.00
30.31
C

ATOM
1580
N1
C
R
46
5.531
−20.362
−9.306
1.00
30.10
N

ATOM
1581
C2
C
R
46
5.145
−21.611
−9.761
1.00
33.01
C

ATOM
1582
O2
C
R
46
5.620
−22.608
−9.209
1.00
36.21
O

ATOM
1583
N3
C
R
46
4.265
−21.697
−10.784
1.00
34.73
N

ATOM
1584
C4
C
R
46
3.793
−20.586
−11.339
1.00
35.40
C

ATOM
1585
N4
C
R
46
2.932
−20.713
−12.350
1.00
36.80
N

ATOM
1586
C5
C
R
46
4.182
−19.294
−10.886
1.00
35.24
C

ATOM
1587
C6
C
R
46
5.048
−19.230
−9.870
1.00
33.15
C

ATOM
1588
P
A
R
47
11.156
−19.120
−9.478
1.00
26.50
P

ATOM
1589
OP1
A
R
47
12.229
−18.433
−8.733
1.00
26.42
O

ATOM
1590
OP2
A
R
47
10.436
−18.482
−10.593
1.00
22.22
O

ATOM
1591
O5′
A
R
47
11.747
−20.474
−10.037
1.00
27.93
O

ATOM
1592
C5′
A
R
47
11.028
−21.183
−11.006
1.00
31.70
C

ATOM
1593
C4′
A
R
47
11.763
−22.477
−11.255
1.00
35.56
C

ATOM
1594
O4′
A
R
47
10.979
−23.358
−12.098
1.00
38.64
O

ATOM
1595
C3′
A
R
47
13.078
−22.301
−11.981
1.00
35.70
C

ATOM
1596
O3′
A
R
47
13.887
−23.414
−11.670
1.00
33.85
O

ATOM
1597
C2′
A
R
47
12.614
−22.353
−13.432
1.00
39.07
C

ATOM
1598
O2′
A
R
47
13.669
−22.671
−14.316
1.00
42.41
O

ATOM
1599
C1′
A
R
47
11.630
−23.517
−13.344
1.00
38.63
C

ATOM
1600
N9
A
R
47
10.597
−23.543
−14.373
1.00
36.40
N

ATOM
1601
C8
A
R
47
10.079
−22.484
−15.058
1.00
37.83
C

ATOM
1602
N7
A
R
47
9.140
−22.822
−15.913
1.00
38.36
N

ATOM
1603
C5
A
R
47
9.036
−24.192
−15.768
1.00
36.08
C

ATOM
1604
C6
A
R
47
8.222
−25.148
−16.392
1.00
37.75
C

ATOM
1605
N6
A
R
47
7.319
−24.847
−17.329
1.00
39.78
N

ATOM
1606
N1
A
R
47
8.370
−26.433
−16.020
1.00
38.82
N

ATOM
1607
C2
A
R
47
9.274
−26.727
−15.084
1.00
38.45
C

ATOM
1608
N3
A
R
47
10.090
−25.911
−14.426
1.00
37.52
N

ATOM
1609
C4
A
R
47
9.920
−24.648
−14.820
1.00
35.35
C

ATOM
1610
P
A
R
48
15.162
−23.238
−10.736
1.00
30.38
P

ATOM
1611
OP1
A
R
48
15.263
−21.805
−10.395
1.00
33.17
O

ATOM
1612
OP2
A
R
48
16.279
−23.945
−11.399
1.00
31.50
O

ATOM
1613
O5′
A
R
48
14.790
−24.036
−9.405
1.00
29.56
O

ATOM
1614
C5′
A
R
48
14.364
−25.383
−9.476
1.00
28.10
C

ATOM
1615
C4′
A
R
48
12.870
−25.478
−9.259
1.00
27.96
C

ATOM
1616
O4′
A
R
48
12.413
−26.773
−9.722
1.00
28.23
O

ATOM
1617
C3′
A
R
48
12.429
−25.394
−7.801
1.00
29.14
C

ATOM
1618
O3′
A
R
48
11.123
−24.814
−7.711
1.00
27.70
O

ATOM
1619
C2′
A
R
48
12.411
−26.866
−7.422
1.00
30.44
C

ATOM
1620
O2′
A
R
48
11.633
−27.141
−6.273
1.00
33.37
O

ATOM
1621
C1′
A
R
48
11.741
−27.414
−8.666
1.00
28.28
C

ATOM
1622
N9
A
R
48
11.879
−28.851
−8.826
1.00
28.23
N

ATOM
1623
C8
A
R
48
13.024
−29.588
−8.751
1.00
29.50
C

ATOM
1624
N7
A
R
48
12.830
−30.874
−8.938
1.00
29.93
N

ATOM
1625
C5
A
R
48
11.467
−30.979
−9.148
1.00
27.69
C

ATOM
1626
C6
A
R
48
10.629
−32.074
−9.402
1.00
28.04
C

ATOM
1627
N6
A
R
48
11.070
−33.334
−9.498
1.00
30.64
N

ATOM
1628
N1
A
R
48
9.317
−31.830
−9.559
1.00
27.32
N

ATOM
1629
C2
A
R
48
8.882
−30.573
−9.469
1.00
27.65
C

ATOM
1630
N3
A
R
48
9.572
−29.464
−9.232
1.00
27.86
N

ATOM
1631
C4
A
R
48
10.870
−29.741
−9.083
1.00
27.76
C

ATOM
1632
P
A
R
49
10.815
−23.708
−6.599
1.00
25.46
P

ATOM
1633
OP1
A
R
49
10.779
−22.385
−7.263
1.00
25.93
O

ATOM
1634
OP2
A
R
49
11.724
−23.936
−5.454
1.00
26.41
O

ATOM
1635
O5′
A
R
49
9.366
−24.127
−6.111
1.00
23.58
O

ATOM
1636
C5′
A
R
49
9.249
−25.306
−5.342
1.00
23.21
C

ATOM
1637
C4′
A
R
49
7.799
−25.560
−5.024
1.00
22.78
C

ATOM
1638
O4′
A
R
49
7.362
−24.553
−4.083
1.00
24.48
O

ATOM
1639
C3′
A
R
49
6.881
−25.411
−6.219
1.00
22.64
C

ATOM
1640
O3′
A
R
49
5.728
−26.176
−6.018
1.00
24.89
O

ATOM
1641
C2′
A
R
49
6.552
−23.924
−6.216
1.00
22.62
C

ATOM
1642
O2′
A
R
49
5.260
−23.674
−6.722
1.00
22.06
O

ATOM
1643
C1′
A
R
49
6.576
−23.583
−4.733
1.00
23.33
C

ATOM
1644
N9
A
R
49
7.133
−22.264
−4.457
1.00
27.10
N

ATOM
1645
C8
A
R
49
8.395
−21.955
−4.019
1.00
28.06
C

ATOM
1646
N7
A
R
49
8.598
−20.661
−3.865
1.00
27.59
N

ATOM
1647
C5
A
R
49
7.386
−20.087
−4.227
1.00
27.49
C

ATOM
1648
C6
A
R
49
6.935
−18.751
−4.282
1.00
28.20
C

ATOM
1649
N6
A
R
49
7.690
−17.701
−3.960
1.00
30.25
N

ATOM
1650
N1
A
R
49
5.670
−18.529
−4.686
1.00
29.21
N

ATOM
1651
C2
A
R
49
4.906
−19.579
−5.015
1.00
30.33
C

ATOM
1652
N3
A
R
49
5.213
−20.877
−5.003
1.00
28.42
N

ATOM
1653
C4
A
R
49
6.478
−21.064
−4.595
1.00
28.23
C

ATOM
1654
P
G
R
50
5.600
−27.584
−6.756
1.00
26.43
P

ATOM
1655
OP1
G
R
50
5.634
−27.308
−8.207
1.00
28.65
O

ATOM
1656
OP2
G
R
50
4.459
−28.323
−6.164
1.00
24.73
O

ATOM
1657
O5′
G
R
50
6.950
−28.333
−6.334
1.00
26.57
O

ATOM
1658
C5′
G
R
50
7.044
−28.993
−5.071
1.00
27.03
C

ATOM
1659
C4′
G
R
50
7.089
−30.503
−5.246
1.00
28.31
C

ATOM
1660
O4′
G
R
50
7.926
−30.855
−6.375
1.00
29.76
O

ATOM
1661
C3′
G
R
50
7.687
−31.270
−4.079
1.00
29.62
C

ATOM
1662
O3′
G
R
50
6.670
−31.592
−3.156
1.00
28.63
O

ATOM
1663
C2′
G
R
50
8.179
−32.530
−4.763
1.00
31.33
C

ATOM
1664
O2′
G
R
50
7.115
−33.405
−5.075
1.00
36.10
O

ATOM
1665
C1′
G
R
50
8.753
−31.951
−6.037
1.00
29.95
C

ATOM
1666
N9
G
R
50
10.112
−31.476
−5.861
1.00
31.22
N

ATOM
1667
C8
G
R
50
10.550
−30.181
−5.954
1.00
33.72
C

ATOM
1668
N7
G
R
50
11.834
−30.053
−5.749
1.00
34.73
N

ATOM
1669
C5
G
R
50
12.271
−31.346
−5.497
1.00
33.41
C

ATOM
1670
C6
G
R
50
13.567
−31.832
−5.199
1.00
33.70
C

ATOM
1671
O6
G
R
50
14.626
−31.193
−5.098
1.00
33.22
O

ATOM
1672
N1
G
R
50
13.569
−33.213
−5.015
1.00
34.83
N

ATOM
1673
C2
G
R
50
12.461
−34.019
−5.100
1.00
36.21
C

ATOM
1674
N2
G
R
50
12.659
−35.327
−4.890
1.00
39.01
N

ATOM
1675
N3
G
R
50
11.241
−33.575
−5.375
1.00
36.39
N

ATOM
1676
C4
G
R
50
11.220
−32.233
−5.562
1.00
33.63
C

ATOM
1677
P
C
R
51
6.820
−31.179
−1.626
1.00
24.85
P

ATOM
1678
OP1
C
R
51
5.491
−31.337
−0.997
1.00
27.25
O

ATOM
1679
OP2
C
R
51
7.537
−29.882
−1.563
1.00
26.07
O

ATOM
1680
O5′
C
R
51
7.793
−32.297
−1.047
1.00
28.74
O

ATOM
1681
C5′
C
R
51
7.596
−33.671
−1.347
1.00
29.84
C

ATOM
1682
C4′
C
R
51
8.869
−34.439
−1.057
1.00
30.06
C

ATOM
1683
O4′
C
R
51
9.797
−34.203
−2.143
1.00
31.25
O

ATOM
1684
C3′
C
R
51
9.639
−33.987
0.177
1.00
30.60
C

ATOM
1685
O3′
C
R
51
9.115
−34.574
1.366
1.00
31.55
O

ATOM
1686
C2′
C
R
51
11.022
−34.523
−0.153
1.00
31.67
C

ATOM
1687
O2′
C
R
51
11.113
−35.916
0.025
1.00
33.44
O

ATOM
1688
C1′
C
R
51
11.116
−34.189
−1.633
1.00
32.52
C

ATOM
1689
N1
C
R
51
11.696
−32.857
−1.833
1.00
33.23
N

ATOM
1690
C2
C
R
51
13.079
−32.722
−1.774
1.00
33.75
C

ATOM
1691
O2
C
R
51
13.759
−33.734
−1.577
1.00
32.94
O

ATOM
1692
N3
C
R
51
13.628
−31.494
−1.950
1.00
34.37
N

ATOM
1693
C4
C
R
51
12.839
−30.439
−2.162
1.00
33.81
C

ATOM
1694
N4
C
R
51
13.418
−29.246
−2.330
1.00
34.11
N

ATOM
1695
C5
C
R
51
11.418
−30.561
−2.213
1.00
33.53
C

ATOM
1696
C6
C
R
51
10.893
−31.778
−2.042
1.00
32.83
C

ATOM
1697
P
C
R
52
9.152
−33.795
2.773
1.00
30.80
P

ATOM
1698
OP1
C
R
52
8.215
−34.476
3.687
1.00
32.71
O

ATOM
1699
OP2
C
R
52
8.995
−32.349
2.517
1.00
31.51
O

ATOM
1700
O5′
C
R
52
10.642
−34.041
3.302
1.00
31.72
O

ATOM
1701
C5′
C
R
52
11.140
−35.364
3.490
1.00
31.55
C

ATOM
1702
C4′
C
R
52
12.639
−35.346
3.748
1.00
32.39
C

ATOM
1703
O4′
C
R
52
13.342
−34.814
2.592
1.00
31.44
O

ATOM
1704
C3′
C
R
52
13.074
−34.444
4.885
1.00
32.78
C

ATOM
1705
O3′
C
R
52
12.892
−35.099
6.129
1.00
31.63
O

ATOM
1706
C2′
C
R
52
14.544
−34.226
4.539
1.00
33.35
C

ATOM
1707
O2′
C
R
52
15.341
−35.344
4.860
1.00
35.86
O

ATOM
1708
C1′
C
R
52
14.486
−34.096
3.023
1.00
32.12
C

ATOM
1709
N1
C
R
52
14.399
−32.692
2.524
1.00
33.23
N

ATOM
1710
C2
C
R
52
15.559
−31.907
2.439
1.00
34.11
C

ATOM
1711
O2
C
R
52
16.642
−32.380
2.792
1.00
35.49
O

ATOM
1712
N3
C
R
52
15.466
−30.641
1.971
1.00
35.27
N

ATOM
1713
C4
C
R
52
14.285
−30.153
1.594
1.00
35.56
C

ATOM
1714
N4
C
R
52
14.249
−28.895
1.139
1.00
34.89
N

ATOM
1715
C5
C
R
52
13.092
−30.933
1.669
1.00
35.12
C

ATOM
1716
C6
C
R
52
13.195
−32.186
2.131
1.00
33.87
C

ATOM
1717
P
U
R
53
12.445
−34.266
7.419
1.00
34.99
P

ATOM
1718
OP1
U
R
53
12.137
−35.237
8.489
1.00
36.58
O

ATOM
1719
OP2
U
R
53
11.422
−33.273
7.012
1.00
35.60
O

ATOM
1720
O5′
U
R
53
13.771
−33.478
7.822
1.00
36.43
O

ATOM
1721
C5′
U
R
53
14.101
−33.327
9.196
1.00
41.35
C

ATOM
1722
C4′
U
R
53
15.480
−32.719
9.362
1.00
43.85
C

ATOM
1723
O4′
U
R
53
15.563
−31.504
8.579
1.00
46.58
O

ATOM
1724
C3′
U
R
53
15.801
−32.261
10.769
1.00
45.62
C

ATOM
1725
O3′
U
R
53
17.196
−32.053
10.883
1.00
47.35
O

ATOM
1726
C2′
U
R
53
15.055
−30.934
10.810
1.00
45.94
C

ATOM
1727
O2′
U
R
53
15.550
−30.065
11.810
1.00
45.46
O

ATOM
1728
C1′
U
R
53
15.404
−30.384
9.432
1.00
47.26
C

ATOM
1729
N1
U
R
53
14.370
−29.481
8.847
1.00
48.00
N

ATOM
1730
C2
U
R
53
14.750
−28.256
8.349
1.00
48.39
C

ATOM
1731
O2
U
R
53
15.899
−27.862
8.362
1.00
50.98
O

ATOM
1732
N3
U
R
53
13.735
−27.499
7.829
1.00
48.51
N

ATOM
1733
C4
U
R
53
12.397
−27.840
7.758
1.00
49.68
C

ATOM
1734
O4
U
R
53
11.591
−27.057
7.262
1.00
51.19
O

ATOM
1735
C5
U
R
53
12.077
−29.134
8.299
1.00
49.43
C

ATOM
1736
C6
U
R
53
13.055
−29.889
8.811
1.00
49.22
C

ATOM
1737
P
C
R
54
18.196
−33.239
11.286
1.00
49.19
P

ATOM
1738
OP1
C
R
54
17.906
−34.430
10.446
1.00
45.20
O

ATOM
1739
OP2
C
R
54
18.193
−33.340
12.762
1.00
48.94
O

ATOM
1740
O5′
C
R
54
19.599
−32.606
10.849
1.00
50.38
O

ATOM
1741
C5′
C
R
54
20.813
−33.308
10.996
1.00
51.83
C

ATOM
1742
C4′
C
R
54
21.899
−32.555
10.257
1.00
52.85
C

ATOM
1743
O4′
C
R
54
21.663
−32.663
8.834
1.00
54.99
O

ATOM
1744
C3′
C
R
54
21.897
−31.061
10.505
1.00
53.04
C

ATOM
1745
O3′
C
R
54
22.630
−30.762
11.664
1.00
53.92
O

ATOM
1746
C2′
C
R
54
22.619
−30.546
9.275
1.00
54.61
C

ATOM
1747
O2′
C
R
54
24.020
−30.681
9.395
1.00
55.41
O

ATOM
1748
C1′
C
R
54
22.084
−31.475
8.189
1.00
55.65
C

ATOM
1749
N1
C
R
54
20.932
−30.888
7.438
1.00
57.81
N

ATOM
1750
C2
C
R
54
21.173
−29.901
6.475
1.00
58.67
C

ATOM
1751
O2
C
R
54
22.338
−29.541
6.263
1.00
59.72
O

ATOM
1752
N3
C
R
54
20.125
−29.368
5.798
1.00
58.58
N

ATOM
1753
C4
C
R
54
18.883
−29.781
6.055
1.00
58.87
C

ATOM
1754
N4
C
R
54
17.884
−29.221
5.361
1.00
58.57
N

ATOM
1755
C5
C
R
54
18.614
−30.785
7.038
1.00
59.04
C

ATOM
1756
C6
C
R
54
19.657
−31.305
7.699
1.00
58.57
C

ATOM
1757
P
C
R
55
22.192
−29.514
12.557
1.00
55.31
P

ATOM
1758
OP1
C
R
55
22.960
−29.570
13.818
1.00
56.85
O

ATOM
1759
OP2
C
R
55
20.714
−29.484
12.602
1.00
54.69
O

ATOM
1760
O5′
C
R
55
22.693
−28.259
11.697
1.00
57.08
O

ATOM
1761
C5′
C
R
55
24.077
−28.089
11.396
1.00
57.39
C

ATOM
1762
C4′
C
R
55
24.308
−26.804
10.622
1.00
58.02
C

ATOM
1763
O4′
C
R
55
23.937
−26.977
9.228
1.00
58.21
O

ATOM
1764
C3′
C
R
55
23.464
−25.617
11.047
1.00
59.17
C

ATOM
1765
O3′
C
R
55
23.955
−25.031
12.250
1.00
60.84
O

ATOM
1766
C2′
C
R
55
23.670
−24.719
9.835
1.00
59.98
C

ATOM
1767
O2′
C
R
55
24.973
−24.169
9.770
1.00
61.51
O

ATOM
1768
C1′
C
R
55
23.471
−25.736
8.719
1.00
58.50
C

ATOM
1769
N1
C
R
55
22.042
−25.872
8.359
1.00
58.34
N

ATOM
1770
C2
C
R
55
21.335
−24.754
7.905
1.00
58.79
C

ATOM
1771
O2
C
R
55
21.920
−23.673
7.802
1.00
61.06
O

ATOM
1772
N3
C
R
55
20.029
−24.884
7.584
1.00
58.16
N

ATOM
1773
C4
C
R
55
19.431
−26.064
7.709
1.00
57.98
C

ATOM
1774
N4
C
R
55
18.139
−26.146
7.382
1.00
56.81
N

ATOM
1775
C5
C
R
55
20.130
−27.214
8.178
1.00
59.34
C

ATOM
1776
C6
C
R
55
21.422
−27.075
8.490
1.00
59.08
C

ATOM
1777
P
G
R
56
23.051
−23.995
13.081
1.00
61.30
P

ATOM
1778
OP1
G
R
56
23.859
−23.481
14.203
1.00
62.37
O

ATOM
1779
OP2
G
R
56
21.727
−24.601
13.335
1.00
62.69
O

ATOM
1780
O5′
G
R
56
22.854
−22.802
12.059
1.00
60.52
O

ATOM
1781
C5′
G
R
56
23.724
−21.719
12.147
1.00
60.30
C

ATOM
1782
C4′
G
R
56
23.106
−20.602
11.367
1.00
60.08
C

ATOM
1783
O4′
G
R
56
22.666
−21.125
10.093
1.00
59.18
O

ATOM
1784
C3′
G
R
56
21.813
−20.105
11.961
1.00
60.57
C

ATOM
1785
O3′
G
R
56
22.067
−19.287
13.089
1.00
62.14
O

ATOM
1786
C2′
G
R
56
21.308
−19.324
10.761
1.00
60.14
C

ATOM
1787
O2′
G
R
56
22.092
−18.181
10.496
1.00
61.57
O

ATOM
1788
C1′
G
R
56
21.539
−20.374
9.677
1.00
58.08
C

ATOM
1789
N9
G
R
56
20.390
−21.254
9.563
1.00
53.88
N

ATOM
1790
C8
G
R
56
20.253
−22.530
10.046
1.00
52.98
C

ATOM
1791
N7
G
R
56
19.080
−23.047
9.797
1.00
52.36
N

ATOM
1792
C5
G
R
56
18.402
−22.039
9.118
1.00
52.30
C

ATOM
1793
C6
G
R
56
17.090
−22.004
8.589
1.00
52.73
C

ATOM
1794
O6
G
R
56
16.228
−22.890
8.614
1.00
53.80
O

ATOM
1795
N1
G
R
56
16.808
−20.786
7.974
1.00
51.75
N

ATOM
1796
C2
G
R
56
17.682
−19.736
7.882
1.00
50.48
C

ATOM
1797
N2
G
R
56
17.229
−18.647
7.253
1.00
50.03
N

ATOM
1798
N3
G
R
56
18.910
−19.753
8.373
1.00
51.07
N

ATOM
1799
C4
G
R
56
19.198
−20.931
8.973
1.00
52.10
C

ATOM
1800
P
G
R
57
20.861
−18.893
14.069
1.00
63.33
P

ATOM
1801
OP1
G
R
57
21.346
−17.829
14.980
1.00
63.10
O

ATOM
1802
OP2
G
R
57
20.285
−20.143
14.624
1.00
63.45
O

ATOM
1803
O5′
G
R
57
19.791
−18.270
13.058
1.00
60.33
O

ATOM
1804
C5′
G
R
57
19.060
−17.133
13.440
1.00
56.06
C

ATOM
1805
C4′
G
R
57
18.265
−16.607
12.270
1.00
53.75
C

ATOM
1806
O4′
G
R
57
18.327
−17.535
11.159
1.00
51.40
O

ATOM
1807
C3′
G
R
57
16.787
−16.458
12.556
1.00
54.39
C

ATOM
1808
O3′
G
R
57
16.554
−15.225
13.223
1.00
55.47
O

ATOM
1809
C2′
G
R
57
16.218
−16.485
11.144
1.00
53.28
C

ATOM
1810
O2′
G
R
57
16.435
−15.278
10.447
1.00
53.14
O

ATOM
1811
C1′
G
R
57
17.060
−17.592
10.527
1.00
50.99
C

ATOM
1812
N9
G
R
57
16.506
−16.918
10.748
1.00
49.53
N

ATOM
1813
C8
G
R
57
17.109
−19.949
11.423
1.00
50.90
C

ATOM
1814
N7
G
R
57
16.386
−21.034
11.469
1.00
49.61
N

ATOM
181b
C5
G
R
57
15.229
−20.703
10.782
1.00
47.66
C

ATOM
1816
C6
G
R
57
14.086
−21.486
10.508
1.00
46.12
C

ATOM
1817
O6
G
R
57
13.865
−22.661
10.833
1.00
45.89
O

ATOM
1816
N1
G
R
57
13.138
−20.769
9.786
1.00
45.46
N

ATOM
1819
C2
G
R
57
13.285
−19.465
9.374
1.00
45.89
C

ATOM
1820
N2
G
R
57
12.261
−18.946
8.681
1.00
45.55
N

ATOM
1821
N3
G
R
57
14.354
−18.719
9.626
1.00
46.43
N

ATOM
1822
C4
G
R
57
15.284
−19.401
10.333
1.00
47.68
C

ATOM
1823
P
C
R
58
16.069
−15.213
14.750
1.00
56.04
P

ATOM
1824
OP1
C
R
58
16.522
−13.944
15.364
1.00
54.91
O

ATOM
1825
OP2
C
R
58
16.429
−16.507
15.379
1.00
56.90
O

ATOM
1826
O5′
C
R
58
14.485
−15.160
14.562
1.00
53.40
O

ATOM
1827
C5′
C
R
58
13.961
−14.307
13.559
1.00
50.46
C

ATOM
1828
C4′
C
R
58
12.718
−14.901
12.935
1.00
47.80
C

ATOM
1829
O4′
C
R
58
13.053
−16.091
12.184
1.00
47.63
O

ATOM
1830
C3′
C
R
58
11.698
−15.419
13.921
1.00
45.98
C

ATOM
1831
O3′
C
R
58
10.990
−14.361
14.526
1.00
42.43
O

ATOM
1832
C2′
C
R
58
10.833
−16.261
12.992
1.00
46.23
C

ATOM
1833
O2′
C
R
58
10.002
−15.467
12.171
1.00
47.28
O

ATOM
1834
C1′
C
R
58
11.909
−16.930
12.139
1.00
45.50
C

ATOM
1835
N1
C
R
58
12.293
−18.269
12.626
1.00
42.40
N

ATOM
1836
C2
C
R
58
11.460
−19.352
12.356
1.00
42.50
C

ATOM
1837
O2
C
R
58
10.422
−19.151
11.720
1.00
43.79
O

ATOM
1838
N3
C
R
58
11.811
−20.585
12.795
1.00
42.63
N

ATOM
1839
C4
C
R
58
12.947
−20.740
13.480
1.00
43.80
C

ATOM
1840
N4
C
R
58
13.265
−21.970
13.902
1.00
44.23
N

ATOM
1841
C5
C
R
58
13.811
−19.639
13.763
1.00
43.65
C

ATOM
1842
C6
C
R
58
13.450
−18.431
13.320
1.00
41.89
C

ATOM
1843
P
C
R
59
10.438
−14.604
16.001
1.00
41.16
P

ATOM
1844
OP1
C
R
59
9.824
−13.346
16.479
1.00
40.34
O

ATOM
1845
OP2
C
R
59
11.496
−15.289
16.777
1.00
37.81
O

ATOM
1846
O5′
C
R
59
9.275
−15.660
15.760
1.00
42.26
O

ATOM
1847
C5′
C
R
59
8.140
−15.261
15.029
1.00
42.28
C

ATOM
1848
C4′
C
R
59
7.182
−16.423
14.921
1.00
41.82
C

ATOM
1849
O4′
C
R
59
7.811
−17.516
14.211
1.00
42.53
O

ATOM
1850
C3′
C
R
59
6.812
−17.049
16.244
1.00
41.46
C

ATOM
1851
O3′
C
R
59
5.848
−16.246
16.886
1.00
38.99
O

ATOM
1852
C2′
C
R
59
6.215
−18.344
15.726
1.00
42.84
C

ATOM
1853
O2′
C
R
59
4.970
−18.099
15.110
1.00
45.14
O

ATOM
1854
C1′
C
R
59
7.252
−18.731
14.672
1.00
41.90
C

ATOM
1855
N1
C
R
59
8.347
−19.597
15.202
1.00
40.68
N

ATOM
1856
C2
C
R
59
8.089
−20.946
15.467
1.00
41.84
C

ATOM
1857
O2
C
R
59
6.952
−21.395
15.256
1.00
43.71
O

ATOM
1858
N3
C
R
59
9.088
−21.725
15.950
1.00
40.28
N

ATOM
1859
C4
C
R
59
10.293
−21.199
16.162
1.00
39.98
C

ATOM
1860
N4
C
R
59
11.248
−22.003
16.637
1.00
42.53
N

ATOM
1861
C5
C
R
59
10.576
−19.829
15.899
1.00
38.92
C

ATOM
1862
C6
C
R
59
9.584
−19.072
15.424
1.00
39.71
C

ATOM
1863
P
U
R
60
5.678
−16.320
18.468
1.00
35.18
P

ATOM
1864
OP1
U
R
60
4.582
−15.398
18.832
1.00
35.17
O

ATOM
1865
OP2
U
R
60
7.014
−16.216
19.098
1.00
32.01
O

ATOM
1866
O5′
U
R
60
5.147
−17.798
18.677
1.00
36.72
O

ATOM
1867
C5′
U
R
60
3.762
−18.016
18.549
1.00
38.81
C

ATOM
1868
C4′
U
R
60
3.450
−19.465
18.829
1.00
39.95
C

ATOM
1869
O4′
U
R
60
4.398
−20.301
18.132
1.00
39.48
O

ATOM
1870
C3′
U
R
60
3.626
−19.872
20.272
1.00
42.22
C

ATOM
1871
O3′
U
R
60
2.486
−19.468
21.023
1.00
48.13
O

ATOM
1872
C2′
U
R
60
3.738
−21.388
20.129
1.00
38.70
C

ATOM
1873
O2′
U
R
60
2.485
−22.016
19.934
1.00
36.45
O

ATOM
1874
C1′
U
R
60
4.574
−21.501
18.859
1.00
36.87
C

ATOM
1875
N1
U
R
60
6.016
−21.6b6
19.096
1.00
34.13
N

ATOM
1876
C2
U
R
60
6.491
−22.873
19.514
1.00
35.29
C

ATOM
1877
O2
U
R
60
5.769
−23.832
19.718
1.00
36.56
O

ATOM
1878
N3
U
R
60
7.848
−22.929
19.699
1.00
36.14
N

ATOM
1879
C4
U
R
60
8.757
−21.907
19.503
1.00
36.37
C

ATOM
1880
O4
U
R
60
9.952
−22.113
19.709
1.00
37.70
O

ATOM
1881
C5
U
R
60
8.178
−20.661
19.061
1.00
34.50
C

ATOM
1882
C6
U
R
60
6.855
−20.587
18.875
1.00
33.37
C

ATOM
1883
P
A
R
61
2.645
−19.005
22.551
1.00
50.38
P

ATOM
1884
OP1
A
R
61
1.284
−16.908
23.123
1.00
51.37
O

ATOM
1885
OP2
A
R
61
3.564
−17.843
22.590
1.00
49.60
O

ATOM
1886
O5′
A
R
61
3.395
−20.235
23.237
1.00
53.19
O

ATOM
1887
C5′
A
R
61
2.668
−21.381
23.638
1.00
57.37
C

ATOM
1888
C4′
A
R
61
3.650
−22.461
24.026
1.00
62.94
C

ATOM
1889
O4′
A
R
61
4.737
−22.462
23.071
1.00
64.25
O

ATOM
1890
C3′
A
R
61
4.317
−22.231
25.372
1.00
66.53
C

ATOM
1891
O3′
A
R
61
3.565
−22.883
26.387
1.00
69.34
O

ATOM
1892
C2′
A
R
61
5.688
−22.889
25.205
1.00
68.01
C

ATOM
1893
O2′
A
R
61
5.730
−24.205
25.727
1.00
71.52
O

ATOM
1894
C1′
A
R
61
5.917
−22.914
23.694
1.00
65.87
C

ATOM
1895
N9
A
R
61
7.015
−22.046
23.302
1.00
66.65
N

ATOM
1896
C8
A
R
61
6.940
−20.739
22.913
1.00
67.28
C

ATOM
1897
N7
A
R
61
8.108
−20.207
22.631
1.00
68.45
N

ATOM
1898
C5
A
R
61
9.009
−21.237
22.861
1.00
69.21
C

ATOM
1899
C6
A
R
61
10.416
−21.324
22.748
1.00
70.28
C

ATOM
1900
N6
A
R
61
11.193
−20.308
22.355
1.00
70.67
N

ATOM
1901
N1
A
R
61
10.997
−22.505
23.055
1.00
70.34
N

ATOM
1902
C2
A
R
61
10.220
−23.522
23.448
1.00
69.66
C

ATOM
1903
N3
A
R
61
8.895
−23.561
23.590
1.00
68.66
N

ATOM
1904
C4
A
R
61
8.347
−22.376
23.278
1.00
68.22
C

ATOM
1905
P
A
R
62
2.577
−22.060
27.340
1.00
70.12
P

ATOM
1906
OP1
A
R
62
1.802
−21.115
26.499
1.00
70.76
O

ATOM
1907
OP2
A
R
62
3.388
−21.547
28.466
1.00
70.03
O

ATOM
1908
O5′
A
R
62
1.596
−23.203
27.907
1.00
67.05
O

ATOM
1909
C5′
A
R
62
0.487
−23.683
27.135
1.00
64.41
C

ATOM
1910
C4′
A
R
62
−0.136
−24.898
27.804
1.00
63.06
C

ATOM
1911
O4′
A
R
62
−0.580
−25.861
26.807
1.00
63.66
O

ATOM
1912
C3′
A
R
62
0.810
−25.684
28.704
1.00
62.70
C

ATOM
1913
O3′
A
R
62
0.712
−25.225
30.042
1.00
61.63
O

ATOM
1914
C2′
A
R
62
0.266
−27.097
28.540
1.00
63.29
C

ATOM
1915
O2′
A
R
62
−0.984
−27.270
29.173
1.00
63.97
O

ATOM
1916
C1′
A
R
62
0.081
−27.086
27.040
1.00
62.98
C

ATOM
1917
N9
A
R
62
1.352
−27.003
26.339
1.00
63.62
N

ATOM
1918
C8
A
R
62
2.072
−25.866
26.109
1.00
62.72
C

ATOM
1919
N7
A
R
62
3.188
−26.068
25.453
1.00
62.25
N

ATOM
1920
C5
A
R
62
3.201
−27.432
25.233
1.00
63.50
C

ATOM
1921
C6
A
R
62
4.125
−28.273
24.586
1.00
64.67
C

ATOM
1922
N6
A
R
62
5.251
−27.824
24.020
1.00
65.62
N

ATOM
1923
N1
A
R
62
3.844
−29.593
24.544
1.00
65.24
N

ATOM
1924
C2
A
R
62
2.713
−30.031
25.113
1.00
66.08
C

ATOM
1925
N3
A
R
62
1.768
−29.336
25.751
1.00
66.30
N

ATOM
1926
C4
A
R
62
2.078
−26.028
25.777
1.00
64.66
C

ATOM
1927
P
A
R
63
1.693
−25.811
31.162
1.00
59.90
P

ATOM
1928
OP1
A
R
63
1.008
−25.702
32.469
1.00
59.95
O

ATOM
1929
OP2
A
R
63
3.023
−25.190
30.972
1.00
60.87
O

ATOM
1930
O5′
A
R
63
1.810
−27.356
30.764
1.00
56.02
O

ATOM
1931
C5′
A
R
63
1.095
−28.337
31.507
1.00
54.43
C

ATOM
1932
C4′
A
R
63
1.673
−29.721
31.270
1.00
53.54
C

ATOM
1933
O4′
A
R
63
1.881
−29.921
29.849
1.00
54.73
O

ATOM
1934
C3′
A
R
63
3.030
−29.969
31.913
1.00
51.61
C

ATOM
1935
O3′
A
R
63
2.860
−30.468
33.233
1.00
49.28
O

ATOM
1936
C2′
A
R
63
3.631
−31.023
30.990
1.00
52.89
C

ATOM
1937
O2′
A
R
63
3.160
−32.325
31.279
1.00
53.74
O

ATOM
1938
C1′
A
R
63
3.120
−30.568
29.627
1.00
54.07
C

ATOM
1939
N9
A
R
63
4.015
−29.632
28.953
1.00
54.62
N

ATOM
1940
C8
A
R
63
3.906
−28.270
28.916
1.00
55.31
C

ATOM
1941
N7
A
R
63
4.859
−27.681
28.232
1.00
56.29
N

ATOM
1942
C5
A
R
63
5.647
−28.730
27.789
1.00
56.54
C

ATOM
1943
C6
A
R
63
6.819
−28.774
27.009
1.00
58.45
C

ATOM
1944
N6
A
R
63
7.419
−27.683
26.521
1.00
60.12
N

ATOM
1945
N1
A
R
63
7.353
−29.985
26.750
1.00
59.33
N

ATOM
1946
C2
A
R
63
6.750
−31.074
27.241
1.00
58.51
C

ATOM
1947
N3
A
R
63
5.648
−31.159
27.984
1.00
56.30
N

ATOM
1948
C4
A
R
63
5.141
−29.940
28.225
1.00
55.33
C

ATOM
1949
P
C
R
64
3.836
−29.982
34.404
1.00
47.39
P

ATOM
1950
OP1
C
R
64
3.288
−30.475
35.688
1.00
48.36
O

ATOM
1951
OP2
C
R
64
4.088
−28.536
34.216
1.00
46.79
O

ATOM
1952
O5′
C
R
64
5.195
−30.764
34.086
1.00
47.13
O

ATOM
1953
C5′
C
R
64
5.181
−31.893
33.220
1.00
45.23
C

ATOM
1954
C4′
C
R
64
6.575
−32.472
33.066
1.00
43.98
C

ATOM
1955
O4′
C
R
64
6.973
−32.407
31.672
1.00
43.08
O

ATOM
1956
C3′
C
R
64
7.663
−31.737
33.836
1.00
43.75
C

ATOM
1957
O3′
C
R
64
7.819
−32.313
35.127
1.00
44.90
O

ATOM
1958
C2′
C
R
64
8.893
−31.973
32.967
1.00
42.82
C

ATOM
1959
O2′
C
R
64
9.474
−33.243
33.188
1.00
43.77
O

ATOM
1960
C1′
C
R
64
8.291
−31.905
31.567
1.00
43.19
C

ATOM
1961
N1
C
R
64
8.226
−30.523
31.015
1.00
43.73
N

ATOM
1962
C2
C
R
64
9.290
−30.031
30.252
1.00
44.24
C

ATOM
1963
O2
C
R
64
10.272
−30.755
30.048
1.00
45.12
O

ATOM
1964
N3
C
R
64
9.215
−28.771
29.757
1.00
43.72
N

ATOM
1965
C4
C
R
64
8.138
−28.021
29.999
1.00
42.48
C

ATOM
1966
N4
C
R
64
8.109
−26.785
29.490
1.00
40.92
N

ATOM
1967
C5
C
R
64
7.044
−28.506
30.775
1.00
42.71
C

ATOM
1968
C6
C
R
64
7.129
−29.749
31.258
1.00
42.83
C

ATOM
1969
P
C
R
65
8.705
−31.569
36.233
1.00
45.21
P

ATOM
1970
OP1
C
R
65
9.079
−32.566
37.262
1.00
45.32
O

ATOM
1971
OP2
C
R
65
7.996
−30.332
36.628
1.00
46.64
O

ATOM
1972
O5′
C
R
65
10.015
−31.147
35.418
1.00
43.43
O

ATOM
1973
C5′
C
R
65
10.962
−32.136
35.031
1.00
43.15
C

ATOM
1974
C4′
C
R
65
12.343
−31.527
34.867
1.00
43.13
C

ATOM
1975
O4′
C
R
65
12.539
−31.145
33.482
1.00
43.27
O

ATOM
1976
C3′
C
R
65
12.585
−30.260
35.677
1.00
42.99
C

ATOM
1977
O3′
C
R
65
13.124
−30.592
36.950
1.00
40.05
O

ATOM
1978
C2′
C
R
65
13.599
−29.516
34.817
1.00
44.59
C

ATOM
1979
O2′
C
R
65
14.917
−29.994
35.002
1.00
46.73
O

ATOM
1980
C1′
C
R
65
13.109
−29.852
33.412
1.00
44.11
C

ATOM
1981
N1
C
R
65
12.073
−28.909
32.904
1.00
45.09
N

ATOM
1982
C2
C
R
65
12.463
−27.766
32.197
1.00
44.95
C

ATOM
1983
O2
C
R
65
13.667
−27.558
32.004
1.00
46.52
O

ATOM
1984
N3
C
R
65
11.508
−26.919
31.741
1.00
44.59
N

ATOM
1985
C4
C
R
65
10.220
−27.179
31.970
1.00
45.08
C

ATOM
1986
N4
C
R
65
9.314
−26.314
31.501
1.00
46.12
N

ATOM
1987
C5
C
R
65
9.803
−28.338
32.689
1.00
45.63
C

ATOM
1988
C6
C
R
65
10.754
−29.167
33.133
1.00
45.79
C

ATOM
1989
P
A
R
660
13.449
−29.436
38.007
1.00
51.54
P

ATOM
1990
OP1
A
R
660
14.202
−30.041
39.128
1.00
50.64
O

ATOM
1991
OP2
A
R
660
12.194
−28.698
38.274
1.00
52.62
O

ATOM
1992
O5′
A
R
660
14.425
−28.467
37.190
1.00
52.42
O

ATOM
1993
C5′
A
R
660
15.711
−28.150
37.710
1.00
52.98
C

ATOM
1994
C4′
A
R
660
16.478
−27.262
36.747
1.00
53.33
C

ATOM
1995
O4′
A
R
660
15.894
−27.366
35.424
1.00
54.26
O

ATOM
1996
C3′
A
R
660
16.453
−25.777
37.085
1.00
53.00
C

ATOM
1997
O3′
A
R
660
17.545
−25.453
37.935
1.00
53.10
O

ATOM
1998
C2′
A
R
660
16.603
−25.134
35.711
1.00
54.59
C

ATOM
1999
O2′
A
R
660
17.948
−25.103
35.274
1.00
54.12
O

ATOM
2000
C1′
A
R
660
15.787
−26.082
34.839
1.00
56.09
C

ATOM
2001
N9
A
R
660
14.373
−25.727
34.760
1.00
59.20
N

ATOM
2002
C8
A
R
660
13.316
−26.440
35.254
1.00
60.59
C

ATOM
2003
N7
A
R
660
12.150
−25.878
35.037
1.00
60.51
N

ATOM
2004
C5
A
R
660
12.464
−24.716
34.352
1.00
59.89
C

ATOM
2005
C6
A
R
660
11.668
−23.676
33.832
1.00
60.19
C

ATOM
2006
N6
A
R
660
10.335
−23.650
33.931
1.00
61.67
N

ATOM
2007
N1
A
R
660
12.298
−22.662
33.204
1.00
59.46
N

ATOM
2008
C2
A
R
660
13.632
−22.693
33.106
1.00
58.77
C

ATOM
2009
N3
A
R
660
14.484
−23.613
33.554
1.00
58.79
N

ATOM
2010
C4
A
R
660
13.830
−24.608
34.173
1.00
59.05
C

ATOM
2011
P
U
R
661
17.309
−24.534
39.224
1.00
55.11
P

ATOM
2012
OP1
U
R
661
18.552
−24.550
40.029
1.00
55.87
O

ATOM
2013
OP2
U
R
661
16.026
−24.936
39.841
1.00
55.57
O

ATOM
2014
O5′
U
R
661
17.117
−23.076
38.594
1.00
55.90
O

ATOM
2015
C5′
U
R
661
17.866
−22.693
37.446
1.00
55.88
C

ATOM
2016
C4′
U
R
661
17.571
−21.253
37.066
1.00
54.46
C

ATOM
2017
O4′
U
R
661
16.763
−21.229
35.862
1.00
53.71
O

ATOM
2018
C3′
U
R
661
16.783
−20.466
38.104
1.00
55.35
C

ATOM
2019
O3′
U
R
661
17.674
−19.803
38.992
1.00
56.58
O

ATOM
2020
C2′
U
R
661
16.012
−19.473
37.241
1.00
54.97
C

ATOM
2021
O2′
U
R
661
16.799
−18.360
36.866
1.00
57.44
O

ATOM
2022
C1′
U
R
661
15.687
−20.325
36.019
1.00
53.09
C

ATOM
2023
N1
U
R
661
14.429
−21.110
36.160
1.00
49.78
N

ATOM
2024
C2
U
R
661
13.288
−20.681
35.516
1.00
48.74
C

ATOM
2025
O2
U
R
661
13.250
−19.678
34.825
1.00
49.75
O

ATOM
2026
N3
U
R
661
12.183
−21.473
35.709
1.00
46.78
N

ATOM
2027
C4
U
R
661
12.109
−22.628
36.467
1.00
46.14
C

ATOM
2028
O4
U
R
661
11.046
−23.236
36.549
1.00
45.54
O

ATOM
2029
C5
U
R
661
13.340
−23.010
37.108
1.00
46.87
C

ATOM
2030
C6
U
R
661
14.429
−22.253
36.934
1.00
48.37
C

ATOM
2031
P
U
R
662
17.130
−19.205
40.373
1.00
59.24
P

ATOM
2032
OP1
U
R
662
18.015
−19.686
41.457
1.00
61.19
O

ATOM
2033
OP2
U
R
662
15.674
−19.464
40.439
1.00
58.64
O

ATOM
2034
O5′
U
R
662
17.342
−17.630
40.189
1.00
60.84
O

ATOM
2035
C5′
U
R
662
16.257
−16.810
39.771
1.00
61.60
C

ATOM
2036
C4′
U
R
662
15.998
−15.704
40.778
1.00
61.86
C

ATOM
2037
O4′
U
R
662
14.569
−15.481
40.891
1.00
62.17
O

ATOM
2038
C3′
U
R
662
16.479
−16.000
42.193
1.00
63.15
C

ATOM
2039
O3′
U
R
662
16.834
−14.789
42.849
1.00
65.16
O

ATOM
2040
C2′
U
R
662
15.248
−16.638
42.827
1.00
62.81
C

ATOM
2041
O2′
U
R
662
15.224
−16.483
44.232
1.00
61.06
O

ATOM
2042
C1′
U
R
662
14.125
−15.829
42.188
1.00
64.10
C

ATOM
2043
N1
U
R
662
12.847
−16.585
42.060
1.00
67.70
N

ATOM
2044
C2
U
R
662
11.651
−15.899
42.079
1.00
70.05
C

ATOM
2045
O2
U
R
662
11.579
−14.689
42.196
1.00
72.14
O

ATOM
2046
N3
U
R
662
10.533
−16.686
41.955
1.00
69.92
N

ATOM
2047
C4
U
R
662
10.493
−18.062
41.817
1.00
69.34
C

ATOM
2048
O4
U
R
662
9.412
−18.634
41.716
1.00
69.08
O

ATOM
2049
C5
U
R
662
11.781
−18.705
41.807
1.00
68.55
C

ATOM
2050
C6
U
R
662
12.885
−17.958
41.926
1.00
68.08
C

ATOM
2051
P
G
R
663
17.423
−13.564
42.004
1.00
67.37
P

ATOM
2052
OP1
G
R
663
18.495
−12.933
42.805
1.00
67.09
O

ATOM
2053
OP2
G
R
663
16.282
−12.751
41.526
1.00
66.99
O

ATOM
2054
O5′
G
R
663
18.079
−14.286
40.736
1.00
66.33
O

ATOM
2055
C5′
G
R
663
18.855
−13.533
39.812
1.00
65.29
C

ATOM
2056
C4′
G
R
663
18.184
−13.492
38.452
1.00
64.37
C

ATOM
2057
O4′
G
R
663
16.986
−14.305
38.473
1.00
63.96
O

ATOM
2058
C3′
G
R
663
17.660
−12.130
38.030
1.00
64.37
C

ATOM
2059
O3′
G
R
663
18.696
−11.303
37.526
1.00
67.13
O

ATOM
2060
C2′
G
R
663
16.661
−12.514
36.948
1.00
62.68
C

ATOM
2061
O2′
G
R
663
17.289
−12.837
35.723
1.00
60.21
O

ATOM
2062
C1′
G
R
663
16.040
−13.761
37.569
1.00
62.06
C

ATOM
2063
N9
G
R
663
14.787
−13.500
38.275
1.00
60.02
N

ATOM
2064
C8
G
R
663
14.405
−12.372
38.955
1.00
58.61
C

ATOM
2065
N7
G
R
663
13.210
−12.455
39.470
1.00
58.95
N

ATOM
2066
C5
G
R
663
12.770
−13.716
39.091
1.00
59.72
C

ATOM
2067
C6
G
R
663
11.548
−14.372
39.346
1.00
59.11
C

ATOM
2068
O6
G
R
663
10.573
−13.953
39.986
1.00
58.95
O

ATOM
2069
N1
G
R
663
11.510
−15.643
38.777
1.00
59.98
N

ATOM
2070
C2
G
R
663
12.529
−16.209
38.048
1.00
61.01
C

ATOM
2071
N2
G
R
663
12.312
−17.447
37.579
1.00
59.66
P

ATOM
2072
N3
G
R
663
13.683
−15.603
37.802
1.00
61.82
O

ATOM
2073
C4
G
R
663
13.730
−14.365
38.352
1.00
60.79
O

ATOM
2074
P
C
R
664
18.730
−9.810
38.086
1.00
69.26
O

ATOM
2075
OP1
C
R
664
20.082
−9.544
38.634
1.00
69.54
C

ATOM
2076
OP2
C
R
664
17.539
−9.688
38.959
1.00
69.49
C

ATOM
2077
O5′
C
R
664
18.486
−8.895
36.803
1.00
66.72
O

ATOM
2078
C5′
C
R
664
17.359
−9.156
35.988
1.00
63.20
C

ATOM
2079
C4′
C
R
664
16.990
−7.886
35.268
1.00
58.94
C

ATOM
2080
O4′
C
R
664
16.104
−7.089
36.089
1.00
55.05
O

ATOM
2081
C3′
C
R
664
18.195
−7.008
35.016
1.00
58.63
C

ATOM
2082
O3′
C
R
664
17.967
−6.267
33.886
1.00
63.55
O

ATOM
2083
C2′
C
R
664
18.193
−6.064
36.198
1.00
55.93
C

ATOM
2084
O2′
C
R
664
18.834
−4.858
35.846
1.00
57.75
O

ATOM
2085
C1′
C
R
664
16.697
−5.832
36.327
1.00
51.71
C

ATOM
2086
N1
C
R
664
16.246
−5.364
37.663
1.00
45.36
N

ATOM
2087
C2
C
R
664
15.816
−4.039
37.825
1.00
41.76
C

ATOM
2088
O2
C
R
664
15.837
−3.277
36.854
1.00
41.93
O

ATOM
2089
N3
C
R
664
15.394
−3.624
39.044
1.00
39.36
N

ATOM
2090
C4
C
R
664
15.386
−4.475
40.070
1.00
38.33
C

ATOM
2091
N4
C
R
664
14.961
−4.017
41.253
1.00
34.24
N

ATOM
2092
C5
C
R
664
15.815
−5.832
39.924
1.00
40.19
C

ATOM
2093
C6
C
R
664
16.232
−6.233
38.714
1.00
42.67
C

ATOM
2094
P
A
R
665
19.232
−5.649
33.169
1.00
67.44
P

ATOM
2095
OP1
A
R
665
20.378
−6.532
33.481
1.00
67.16
O

ATOM
2096
OP2
A
R
665
19.287
−4.215
33.519
1.00
69.15
O

ATOM
2097
O5′
A
R
665
18.848
−5.802
31.622
1.00
70.90
O

ATOM
2098
C5′
A
R
665
18.162
−6.980
31.189
1.00
74.99
C

ATOM
2099
C4′
A
R
665
16.776
−6.653
30.661
1.00
78.85
C

ATOM
2100
O4′
A
R
665
15.902
−6.236
31.742
1.00
77.37
O

ATOM
2101
C3′
A
R
665
16.723
−5.490
29.685
1.00
82.97
C

ATOM
2102
O3′
A
R
665
17.122
−5.922
28.381
1.00
90.17
O

ATOM
2103
C2′
A
R
665
15.250
−5.075
29.764
1.00
79.48
C

ATOM
2104
O2′
A
R
665
14.398
−5.847
28.935
1.00
79.19
O

ATOM
2105
C1′
A
R
665
14.923
−5.339
31.236
1.00
75.08
C

ATOM
2106
N9
A
R
665
14.920
−4.136
32.064
1.00
68.85
N

ATOM
2107
C8
A
R
665
15.786
−3.839
33.076
1.00
66.97
C

ATOM
2108
N7
A
R
665
15.544
−2.687
33.654
1.00
65.34
N

ATOM
2109
C5
A
R
665
14.445
−2.192
32.975
1.00
62.44
C

ATOM
2110
C6
A
R
665
13.703
−1.006
33.114
1.00
59.13
C

ATOM
2111
N6
A
R
665
13.977
−0.066
34.023
1.00
57.59
N

ATOM
2112
N1
A
R
665
12.667
−0.823
32.278
1.00
58.32
N

ATOM
2113
C2
A
R
665
12.397
−1.764
31.369
1.00
59.47
C

ATOM
2114
N3
A
R
665
13.016
−2.919
31.144
1.00
61.63
N

ATOM
2115
C4
A
R
665
14.045
−3.073
31.990
1.00
64.52
C

ATOM
2116
P
C
R
666
18.00b
−4.961
27.447
1.00
95.68
P

ATOM
2117
OP1
C
R
666
18.562
−5.789
26.351
1.00
95.98
O

ATOM
2118
OP2
C
R
666
18.917
−4.173
28.314
1.00
95.40
O

ATOM
2119
O5′
C
R
666
16.904
−3.963
26.837
1.00
97.99
O

ATOM
2120
C5′
C
R
666
15.894
−4.467
25.957
1.00
100.08
C

ATOM
2121
C4′
C
R
666
14.826
−3.423
25.654
1.00
101.81
C

ATOM
2122
O4′
C
R
666
13.952
−3.260
26.805
1.00
102.03
O

ATOM
2123
C3′
C
R
666
15.338
−2.021
25.333
1.00
102.73
C

ATOM
2124
O3′
C
R
666
15.648
−1.895
23.933
1.00
103.05
O

ATOM
2125
C2′
C
R
666
14.141
−1.160
25.744
1.00
102.60
C

ATOM
2126
O2′
C
R
666
13.110
−1.135
24.773
1.00
102.63
O

ATOM
2127
C1′
C
R
666
13.665
−1.887
27.000
1.00
102.13
C

ATOM
2128
N1
C
R
666
14.360
−1.426
28.236
1.00
101.44
N

ATOM
2129
C2
C
R
666
13.837
−0.355
28.965
1.00
100.61
C

ATOM
2130
O2
C
R
666
12.798
−0.187
28.571
1.00
100.55
O

ATOM
2131
N3
C
R
666
14.484
−0.056
30.083
1.00
100.11
N

ATOM
2132
C4
C
R
666
15.603
−0.558
30.471
1.00
100.49
C

ATOM
2133
N4
C
R
666
16.205
−0.119
31.580
1.00
100.47
N

ATOM
2134
C5
C
R
666
16.153
−1.651
29.740
1.00
101.06
C

ATOM
2135
C6
C
R
666
15.506
−2.047
28.640
1.00
101.49
C

ATOM
2136
P
U
R
667
17.168
−1.875
23.397
1.00
102.17
P

ATOM
2137
OP1
U
R
667
18.056
−2.387
24.468
1.00
102.34
O

ATOM
2138
OP2
U
R
667
17.428
−0.536
22.817
1.00
102.32
O

ATOM
2139
O5′
U
R
667
17.127
−2.941
22.195
1.00
98.04
O

ATOM
2140
C5′
U
R
667
15.897
−3.207
21.512
1.00
92.13
C

ATOM
2141
C4′
U
R
667
16.055
−4.295
20.461
1.00
87.61
C

ATOM
2142
O4′
U
R
667
17.429
−4.359
20.002
1.00
85.34
O

ATOM
2143
C3′
U
R
667
15.765
−5.711
20.934
1.00
85.21
C

ATOM
2144
O3′
U
R
667
14.350
−5.957
20.967
1.00
84.64
O

ATOM
2145
C2′
U
R
667
16.466
−6.527
19.849
1.00
83.16
C

ATOM
2146
O2′
U
R
667
15.648
−6.719
18.713
1.00
81.91
O

ATOM
2147
C1′
U
R
667
17.673
−5.653
19.483
1.00
82.71
C

ATOM
2148
N1
U
R
667
18.964
−6.173
20.030
1.00
80.25
N

ATOM
2149
C2
U
R
667
19.464
−7.359
19.535
1.00
79.13
C

ATOM
2150
O2
U
R
667
18.908
−8.002
18.665
1.00
80.66
O

ATOM
2151
N3
U
R
667
20.649
−7.773
20.092
1.00
77.10
N

ATOM
2152
C4
U
R
667
21.372
−7.132
21.081
1.00
76.65
C

ATOM
2153
O4
U
R
667
22.422
−7.626
21.484
1.00
75.37
O

ATOM
2154
C5
U
R
667
20.789
−5.900
21.550
1.00
77.28
C

ATOM
2155
C6
U
R
667
19.631
−5.476
21.021
1.00
78.88
C

ATOM
2156
P
C
R
668
13.644
−6.619
22.257
1.00
83.28
P

ATOM
2157
OP1
C
R
668
12.195
−6.313
22.187
1.00
82.79
O

ATOM
2158
OP2
C
R
668
14.421
−6.240
23.460
1.00
83.48
O

ATOM
2159
O5′
C
R
668
13.850
−8.189
22.030
1.00
79.00
O

ATOM
2160
C5′
C
R
668
13.566
−8.761
20.761
1.00
74.41
C

ATOM
2161
C4′
C
R
668
14.440
−9.972
20.509
1.00
69.98
C

ATOM
2162
O4′
C
R
668
15.814
−9.561
20.313
1.00
67.82
O

ATOM
2163
C3′
C
R
668
14.566
−10.932
21.672
1.00
68.45
C

ATOM
2164
O3′
C
R
668
13.411
−11.736
21.814
1.00
68.86
O

ATOM
2165
C2′
C
R
668
15.752
−11.756
21.194
1.00
67.42
C

ATOM
2166
O2′
C
R
668
15.373
−12.722
20.238
1.00
69.90
O

ATOM
2167
C1′
C
R
668
16.631
−10.695
20.535
1.00
65.05
C

ATOM
2168
N1
C
R
668
17.815
−10.366
21.380
1.00
60.49
N

ATOM
2169
C2
C
R
668
18.925
−11.208
21.294
1.00
58.73
C

ATOM
2170
O2
C
R
668
18.884
−12.167
20.515
1.00
59.31
O

ATOM
2171
N3
C
R
668
20.014
−10.955
22.054
1.00
56.52
N

ATOM
2172
C4
C
R
668
20.013
−9.915
22.881
1.00
56.01
C

ATOM
2173
N4
C
R
668
21.115
−9.710
23.607
1.00
55.29
N

ATOM
2174
C5
C
R
668
18.886
−9.041
22.992
1.00
56.81
C

ATOM
2175
C6
C
R
668
17.814
−9.301
22.233
1.00
58.11
C

ATOM
2176
P
C
R
669
13.440
−12.921
22.940
1.00
43.16
P

ATOM
2177
OP1
C
R
669
12.163
−13.665
22.845
1.00
44.05
O

ATOM
2178
OP2
C
R
669
13.848
−12.327
24.235
1.00
45.24
O

ATOM
2179
O5′
C
R
669
14.627
−13.873
22.440
1.00
40.49
O

ATOM
2180
C5′
C
R
669
14.364
−15.236
22.127
1.00
37.22
C

ATOM
2181
C4′
C
R
669
15.588
−16.097
22.372
1.00
32.78
C

ATOM
2182
O4′
C
R
669
16.777
−15.388
21.949
1.00
30.36
O

ATOM
2183
C3′
C
R
669
l5.867
−16.412
23.827
1.00
30.90
C

ATOM
2184
O3′
C
R
669
15.079
−17.488
24.257
1.00
32.41
O

ATOM
2185
C2′
C
R
669
17.341
−16.785
23.749
1.00
28.68
C

ATOM
2186
O2′
C
R
669
17.550
−18.043
23.147
1.00
28.56
O

ATOM
2187
C1′
C
R
669
17.847
−15.680
22.836
1.00
27.16
C

ATOM
2188
N1
C
R
669
18.216
−14.444
23.585
1.00
25.16
N

ATOM
2189
C2
C
R
669
19.490
−14.333
24.148
1.00
23.50
C

ATOM
2190
O2
C
R
669
20.286
−15.268
24.004
1.00
23.07
O

ATOM
2191
N3
C
R
669
19.814
−13.206
24.834
1.00
23.05
N

ATOM
2192
C4
C
R
669
18.918
−12.221
24.965
1.00
24.12
C

ATOM
2193
N4
C
R
669
19.266
−11.125
25.654
1.00
24.47
N

ATOM
2194
C5
C
R
669
17.613
−12.322
24.408
1.00
25.02
C

ATOM
2195
C6
C
R
669
17.307
−13.436
23.730
1.00
25.70
C

ATOM
2196
P
G
R
75
14.945
−17.807
25.819
1.00
35.78
P

ATOM
2197
OP1
G
R
75
13.504
−17.855
26.152
1.00
38.67
O

ATOM
2198
OP2
G
R
75
15.841
−16.884
26.551
1.00
35.73
O

ATOM
2199
O5′
G
R
75
15.554
−19.282
25.938
1.00
36.84
O

ATOM
2200
C5′
G
R
75
16.878
−19.543
25.487
1.00
38.04
C

ATOM
2201
C4′
G
R
75
17.562
−20.560
26.383
1.00
38.18
C

ATOM
2202
O4′
G
R
75
17.147
−20.350
27.756
1.00
39.44
O

ATOM
2203
C3′
G
R
75
17.227
−22.013
26.077
1.00
39.29
C

ATOM
2204
O3′
G
R
75
18.141
−22.534
25.121
1.00
37.39
O

ATOM
2205
C2′
G
R
75
17.403
−22.675
27.439
1.00
41.16
C

ATOM
2206
O2′
G
R
75
18.758
−22.956
27.730
1.00
42.86
O

ATOM
2207
C1′
G
R
75
16.877
−21.593
28.376
1.00
42.07
C

ATOM
2208
N9
G
R
75
15.440
−21.684
28.620
1.00
44.73
N

ATOM
2209
C8
G
R
75
14.480
−20.769
28.260
1.00
46.04
C

ATOM
2210
N7
G
R
75
13.274
−21.116
28.611
1.00
47.41
N

ATOM
2211
C5
G
R
75
13.443
−22.340
29.245
1.00
45.94
C

ATOM
2212
C6
G
R
75
12.487
−23.200
29.837
1.00
45.75
C

ATOM
2213
O6
G
R
75
11.261
−23.043
29.920
1.00
45.60
O

ATOM
2214
N1
G
R
75
13.081
−24.342
30.370
1.00
45.09
N

ATOM
2215
C2
G
R
75
14.428
−24.617
30.335
1.00
44.14
C

ATOM
2216
N2
G
R
75
14.814
−25.769
30.901
1.00
44.69
N

ATOM
2217
N3
G
R
75
15.334
−23.820
29.783
1.00
43.50
N

ATOM
2218
C4
G
R
75
14.771
−22.703
29.260
1.00
44.64
C

ATOM
2219
P
G
R
76
17.621
−23.511
23.966
1.00
61.74
P

ATOM
2220
OP1
G
R
76
18.616
−23.492
22.872
1.00
63.98
O

ATOM
2221
OP2
G
R
76
16.212
−23.161
23.675
1.00
61.01
O

ATOM
2222
O5′
G
R
76
17.658
−24.949
24.670
1.00
59.36
O

ATOM
2223
C5′
G
R
76
18.565
−25.196
25.743
1.00
57.70
C

ATOM
2224
C4′
G
R
76
18.295
−26.546
26.380
1.00
57.24
C

ATOM
2225
O4′
G
R
76
17.460
−26.379
27.559
1.00
57.20
O

ATOM
2226
C3′
G
R
76
17.510
−27.518
25.516
1.00
58.02
C

ATOM
2227
O3′
G
R
76
18.355
−28.181
24.574
1.00
58.08
O

ATOM
2228
C2′
G
R
76
17.003
−28.466
26.590
1.00
59.16
C

ATOM
2229
O2′
G
R
76
18.043
−29.271
27.105
1.00
61.17
O

ATOM
2230
C1′
G
R
76
16.545
−27.464
27.648
1.00
58.36
C

ATOM
2231
N9
G
R
76
15.162
−26.987
27.450
1.00
57.90
N

ATOM
2232
C8
G
R
76
14.753
−25.888
26.725
1.00
56.99
C

ATOM
2233
N7
G
R
76
13.459
−25.713
26.717
1.00
55.40
N

ATOM
2234
C5
G
R
76
12.967
−26.759
27.486
1.00
54.63
C

ATOM
2235
C6
G
R
76
11.633
−27.084
27.835
1.00
53.65
C

ATOM
2236
O6
G
R
76
10.587
−26.495
27.526
1.00
51.09
O

ATOM
2237
N1
G
R
76
11.574
−26.224
28.629
1.00
54.76
N

ATOM
2238
C2
G
R
76
12.662
−28.956
29.035
1.00
54.32
C

ATOM
2239
N2
G
R
76
12.402
−30.024
29.802
1.00
54.01
N

ATOM
2240
N3
G
R
76
13.916
−28.663
28.719
1.00
55.06
N

ATOM
2241
C4
G
R
76
13.997
−27.555
27.944
1.00
55.84
C

ATOM
2242
P
U
R
77
17.732
−29.246
23.544
1.00
56.98
P

ATOM
2243
OP1
U
R
77
18.729
−30.320
23.350
1.00
57.39
O

ATOM
2244
OP2
U
R
77
17.205
−28.513
22.371
1.00
55.04
O

ATOM
2245
O5′
U
R
77
16.476
−29.826
24.355
1.00
58.00
O

ATOM
2246
C5′
U
R
77
16.320
−31.222
24.564
1.00
56.58
C

ATOM
2247
C4′
U
R
77
14.863
−31.569
24.816
1.00
56.20
C

ATOM
2248
O4′
U
R
77
14.269
−30.611
25.724
1.00
55.75
O

ATOM
2249
C3′
U
R
77
13.949
−31.502
23.607
1.00
56.73
C

ATOM
2250
O3′
U
R
77
14.089
−32.659
22.811
1.00
58.43
O

ATOM
2251
C2′
U
R
77
12.596
−31.457
24.301
1.00
55.94
C

ATOM
2252
O2′
U
R
77
12.249
−32.684
24.905
1.00
55.47
O

ATOM
2253
C1′
U
R
77
12.902
−30.438
25.383
1.00
55.28
C

ATOM
2254
N1
U
R
77
12.705
−29.061
24.906
1.00
54.01
N

ATOM
2255
C2
U
R
77
11.423
−28.599
24.741
1.00
53.75
C

ATOM
2256
O2
U
R
77
10.439
−29.276
24.978
1.00
54.94
O

ATOM
2257
N3
U
R
77
11.335
−27.309
24.293
1.00
52.96
N

ATOM
2258
C4
U
R
77
12.381
−26.459
23.993
1.00
53.12
C

ATOM
2259
O4
U
R
77
12.149
−25.323
23.596
1.00
53.74
O

ATOM
2260
C5
U
R
77
13.690
−27.020
24.185
1.00
53.06
C

ATOM
2261
C6
U
R
77
13.798
−28.277
24.624
1.00
53.78
C

ATOM
2262
P
A
R
78
13.611
−32.610
21.290
1.00
59.77
P

ATOM
2263
OP1
A
R
78
13.699
−33.985
20.750
1.00
61.30
O

ATOM
2264
OP2
A
R
78
14.305
−31.491
20.619
1.00
60.55
O

ATOM
2265
O5′
A
R
78
12.080
−32.207
21.416
1.00
57.72
O

ATOM
2266
C5′
A
R
78
11.185
−33.128
21.972
1.00
56.32
C

ATOM
2267
C4′
A
R
78
9.801
−32.590
21.763
1.00
55.42
C

ATOM
2268
O4′
A
R
78
9.673
−31.385
22.555
1.00
53.20
O

ATOM
2269
C3′
A
R
78
9.564
−32.116
20.344
1.00
55.19
C

ATOM
2270
O3′
A
R
78
9.144
−33.183
19.524
1.00
55.86
O

ATOM
2271
C2′
A
R
78
8.447
−31.112
20.559
1.00
54.84
C

ATOM
2272
O2′
A
R
78
7.197
−31.730
20.790
1.00
56.97
O

ATOM
2273
C1′
A
R
78
8.941
−30.427
21.821
1.00
51.98
C

ATOM
2274
N9
A
R
78
9.809
−29.319
21.485
1.00
49.67
N

ATOM
2275
C8
A
R
78
11.174
−29.286
21.446
1.00
48.36
C

ATOM
2276
N7
A
R
78
11.651
−28.116
21.085
1.00
47.49
N

ATOM
2277
C5
A
R
78
10.519
−27.343
20.869
1.00
46.49
C

ATOM
2278
C6
A
R
78
10.328
−26.007
20.468
1.00
46.91
C

ATOM
2279
N6
A
R
78
11.328
−25.163
20.199
1.00
49.02
N

ATOM
2280
N1
A
R
78
9.061
−25.560
20.355
1.00
46.55
N

ATOM
2281
C2
A
R
78
8.054
−26.395
20.624
1.00
46.99
C

ATOM
2282
N3
A
R
78
8.107
−27.668
21.005
1.00
47.63
N

ATOM
2283
C4
A
R
78
9.380
−28.078
21.106
1.00
48.06
C

ATOM
2284
P
G
R
79
9.449
−33.121
17.958
1.00
57.84
P

ATOM
2285
OP1
G
R
79
9.026
−34.406
17.363
1.00
58.51
O

ATOM
2286
OP2
G
R
79
10.832
−32.622
17.778
1.00
57.80
O

ATOM
2287
O5′
G
R
79
8.455
−31.996
17.435
1.00
57.15
O

ATOM
2288
C5′
G
R
79
7.116
−32.339
17.154
1.00
55.74
C

ATOM
2289
C4′
G
R
79
6.287
−31.078
17.123
1.00
55.38
C

ATOM
2290
O4′
G
R
79
6.820
−30.125
18.077
1.00
55.60
O

ATOM
2291
C3′
G
R
79
6.383
−30.299
15.831
1.00
54.57
C

ATOM
2292
O3′
G
R
79
5.618
−30.908
14.824
1.00
52.79
O

ATOM
2293
C2′
G
R
79
5.807
−28.969
16.288
1.00
53.27
C

ATOM
2294
O2′
G
R
79
4.417
−29.067
16.539
1.00
53.14
O

ATOM
2295
C1′
G
R
79
6.568
−28.808
17.602
1.00
52.08
C

ATOM
2296
N9
G
R
79
7.836
−28.085
17.481
1.00
48.27
N

ATOM
2297
C8
G
R
79
9.108
−28.575
17.683
1.00
46.23
C

ATOM
2298
N7
G
R
79
10.043
−27.680
17.504
1.00
45.65
N

ATOM
2299
C5
G
R
79
9.348
−26.518
17.172
1.00
46.42
C

ATOM
2300
C6
G
R
79
9.819
−25.212
16.865
1.00
46.85
C

ATOM
2301
O6
G
R
79
10.990
−24.804
16.826
1.00
49.41
O

ATOM
2302
N1
G
R
79
8.776
−24.331
16.581
1.00
44.25
N

ATOM
2303
C2
G
R
79
7.443
−24.667
16.593
1.00
45.44
C

ATOM
2304
N2
G
R
79
6.578
−23.684
16.296
1.00
45.42
N

ATOM
2305
N3
G
R
79
6.986
−25.883
16.8/8
1.00
46.11
N

ATOM
2306
C4
G
R
79
7.990
−26.754
17.154
1.00
46.95
C

ATOM
2307
P
G
R
80
6.319
31.060
13.409
1.00
51.21
P

ATOM
2308
OP1
G
R
80
5.507
31.999
12.603
1.00
51.71
O

ATOM
2309
OP2
G
R
80
7.753
31.328
13.668
1.00
51.23
O

ATOM
2310
O5′
G
R
80
6.209
−29.583
12.793
1.00
47.94
O

ATOM
2311
C5′
G
R
80
4.931
−28.992
12.624
1.00
44.18
C

ATOM
2312
C4′
G
R
80
5.006
−27.476
12.518
1.00
41.11
C

ATOM
2313
O4′
G
R
80
5.826
−26.901
13.555
1.00
40.30
O

ATOM
2314
C3′
G
R
80
5.672
−26.922
11.284
1.00
39.21
C

ATOM
2315
O3′
G
R
80
4.834
−27.094
10.189
1.00
40.26
O

ATOM
2316
C2′
G
R
80
5.742
−25.463
11.685
1.00
38.17
C

ATOM
2317
O2′
G
R
80
4.457
−24.865
11.678
1.00
38.61
O

ATOM
2318
C1′
G
R
80
6.242
−25.619
13.115
1.00
36.18
C

ATOM
2319
N9
G
R
80
7.688
−25.534
13.256
1.00
33.20
N

ATOM
2320
C8
G
R
80
8.552
−26.531
13.639
1.00
30.79
C

ATOM
2321
N7
G
R
80
9.798
−26.145
13.690
1.00
30.84
N

ATOM
2322
C5
G
R
80
9.755
−24.804
13.319
1.00
32.41
C

ATOM
2323
C6
G
R
80
10.795
−23.849
13.193
1.00
33.17
C

ATOM
2324
O6
G
R
80
12.011
−24.005
13.390
1.00
35.62
O

ATOM
2325
N1
G
R
80
10.311
−22.602
12.792
1.00
30.88
N

ATOM
2326
C2
G
R
80
8.990
−22.314
12.549
1.00
31.55
C

ATOM
2327
N2
G
R
80
8.713
−21.060
12.176
1.00
31.65
N

ATOM
2328
N3
G
R
80
8.005
−23.195
12.663
1.00
33.83
N

ATOM
2329
C4
G
R
80
8.461
−24.415
13.052
1.00
34.15
C

ATOM
2330
P
U
R
81
5.470
−27.671
8.857
1.00
38.61
P

ATOM
2331
OP1
U
R
81
4.365
−28.212
8.032
1.00
38.58
O

ATOM
2332
OP2
U
R
81
6.625
−28.520
9.231
1.00
38.37
O

ATOM
2333
O5′
U
R
81
6.033
−26.347
8.173
1.00
37.87
O

ATOM
2334
C5′
U
R
81
5.185
−25.225
8.085
1.00
36.91
C

ATOM
2335
C4′
U
R
81
6.027
−23.990
7.900
1.00
36.44
C

ATOM
2336
O4′
U
R
81
6.841
−23.807
9.079
1.00
36.72
O

ATOM
2337
C3′
U
R
81
7.044
−24.082
6.778
1.00
36.90
C

ATOM
2338
O3′
U
R
81
6.417
−23.819
5.516
1.00
35.87
O

ATOM
2339
C2′
U
R
81
7.994
−22.962
7.188
1.00
37.75
C

ATOM
2340
O2′
U
R
81
7.502
−21.686
6.827
1.00
39.32
O

ATOM
2341
C1′
U
R
81
8.015
−23.105
8.716
1.00
36.73
C

ATOM
2342
N1
U
R
81
9.200
−23.851
9.226
1.00
35.90
N

ATOM
2343
C2
U
R
81
10.394
−23.176
9.409
1.00
35.48
C

ATOM
2344
O2
U
R
81
10.529
−21.984
9.180
1.00
34.82
O

ATOM
2345
N3
U
R
81
11.432
−23.952
9.873
1.00
34.33
N

ATOM
2346
C4
U
R
81
11.393
−25.306
10.168
1.00
35.01
C

ATOM
2347
O4
U
R
81
12.404
−25.869
10.584
1.00
34.81
O

ATOM
2348
C5
U
R
81
10.112
−25.939
9.951
1.00
34.70
C

ATOM
2349
C6
U
R
81
9.088
−25.204
9.496
1.00
35.20
C

ATOM
2350
P
A
R
82
6.419
−24.914
4.346
1.00
33.24
P

ATOM
2351
OP1
A
R
82
5.953
−24.246
3.115
1.00
32.53
O

ATOM
2352
OP2
A
R
82
5.733
−26.130
4.837
1.00
33.01
O

ATOM
2353
O5′
A
R
82
7.966
−25.273
4.174
1.00
33.43
O

ATOM
2354
C5′
A
R
82
8.883
−24.233
3.942
1.00
32.14
C

ATOM
2355
C4′
A
R
82
9.934
−24.652
2.935
1.00
31.79
C

ATOM
2356
O4′
A
R
82
10.828
−25.624
3.524
1.00
30.72
O

ATOM
2357
C3′
A
R
82
9.409
−25.278
1.653
1.00
30.33
C

ATOM
2358
O3′
A
R
82
10.154
−24.761
0.558
1.00
31.65
O

ATOM
2359
C2′
A
R
82
9.697
−26.755
1.854
1.00
28.70
C

ATOM
2360
O2′
A
R
82
9.920
−27.404
0.624
1.00
28.37
O

ATOM
2361
C1′
A
R
82
10.998
−26.689
2.630
1.00
30.24
C

ATOM
2362
N9
A
R
82
11.279
−27.885
3.415
1.00
33.04
N

ATOM
2363
C8
A
R
82
10.380
−28.834
3.816
1.00
33.64
C

ATOM
2364
N7
A
R
82
10.919
−29.805
4.519
1.00
34.13
N

ATOM
2365
C5
A
R
82
12.261
−29.468
4.585
1.00
32.80
C

ATOM
2366
C6
A
R
82
13.366
−30.090
5.193
1.00
32.45
C

ATOM
2367
N6
A
R
82
13.279
−31.236
5.872
1.00
32.93
N

ATOM
2368
N1
A
R
82
14.569
−29.492
5.077
1.00
33.45
N

ATOM
2369
C2
A
R
82
14.652
−28.346
4.395
1.00
33.62
C

ATOM
2370
N3
A
R
82
13.683
−27.666
3.783
1.00
34.94
N

ATOM
2371
C4
A
R
82
12.500
−28.286
3.916
1.00
33.39
C

ATOM
2372
P
G
R
83
9.437
−24.510
−0.844
1.00
34.01
P

ATOM
2373
OP1
G
R
83
8.346
−25.506
−0.976
1.00
33.23
O

ATOM
2374
OP2
G
R
83
10.494
−24.418
−1.873
1.00
36.17
O

ATOM
2375
O5′
G
R
83
8.788
−23.053
−0.695
1.00
32.99
O

ATOM
2376
C5′
G
R
83
9.523
−22.000
−0.108
1.00
30.16
C

ATOM
2377
C4′
G
R
83
8.585
−20.887
0.325
1.00
29.38
C

ATOM
2378
O4′
G
R
83
7.548
−20.688
−0.674
1.00
27.22
O

ATOM
2379
C3′
G
R
83
7.835
−21.150
1.626
1.00
30.60
C

ATOM
2380
O3′
G
R
83
7.698
−19.940
2.343
1.00
35.69
O

ATOM
2381
C2′
G
R
83
6.472
−21.586
1.128
1.00
26.79
C

ATOM
2382
O2′
G
R
83
5.459
−21.362
2.083
1.00
27.17
O

ATOM
2383
C1′
G
R
83
6.314
−20.599
−0.004
1.00
24.70
C

ATOM
2384
N9
G
R
83
5.231
−20.962
−0.904
1.00
22.46
N

ATOM
2385
C8
G
R
83
4.895
−22.235
−1.287
1.00
21.64
C

ATOM
2386
N7
G
R
83
3.876
−22.282
−2.092
1.00
20.25
N

ATOM
2387
C5
G
R
83
3.501
−20.954
−2.242
1.00
19.91
C

ATOM
2388
C6
G
R
83
2.458
−20.393
−3.008
1.00
19.68
C

ATOM
2389
O6
G
R
83
1.635
−20.980
−3.719
1.00
25.08
O

ATOM
2390
N1
G
R
83
2.419
−19.013
−2.901
1.00
16.78
N

ATOM
2391
C2
G
R
83
3.281
−18.269
−2.147
1.00
17.81
C

ATOM
2392
N2
G
R
83
3.073
−16.946
−2.173
1.00
18.66
N

ATOM
2393
N3
G
R
83
4.269
−18.777
−1.418
1.00
18.40
N

ATOM
2394
C4
G
R
83
4.321
−20.125
−1.516
1.00
20.15
C

ATOM
2395
P
C
R
84
8.475
−19.719
3.721
1.00
38.48
P

ATOM
2396
OP1
C
R
84
8.860
−21.031
4.284
1.00
38.51
O

ATOM
2397
OP2
C
R
84
7.667
−18.784
4.536
1.00
40.51
O

ATOM
2398
O5′
C
R
84
9.796
−18.980
3.217
1.00
38.39
O

ATOM
2399
C5′
C
R
84
9.865
−17.569
3.178
1.00
38.85
C

ATOM
2400
C4′
C
R
84
11.320
−17.166
3.188
1.00
39.35
C

ATOM
2401
O4′
C
R
84
11.791
−16.999
4.554
1.00
38.58
O

ATOM
2402
C3′
C
R
84
12.254
−18.220
2.627
1.00
40.52
C

ATOM
2403
O3′
C
R
84
12.223
−18.205
1.208
1.00
40.79
O

ATOM
2404
C2′
C
R
84
13.555
−17.675
3.183
1.00
40.97
C

ATOM
2405
O2′
C
R
84
13.886
−16.445
2.579
1.00
42.05
O

ATOM
2406
C1′
C
R
84
13.130
−17.455
4.631
1.00
38.25
C

ATOM
2407
N1
C
R
84
13.118
−18.734
5.336
1.00
35.44
N

ATOM
2408
C2
C
R
84
14.241
−19.170
6.045
1.00
34.92
C

ATOM
2409
O2
C
R
84
15.238
−18.454
6.109
1.00
37.10
O

ATOM
2410
N3
C
R
84
14.201
−20.366
6.659
1.00
34.89
N

ATOM
2411
C4
C
R
84
13.104
−21.113
6.574
1.00
37.85
C

ATOM
2412
N4
C
R
84
13.108
−22.294
7.199
1.00
40.54
N

ATOM
2413
C5
C
R
84
11.953
−20.693
5.844
1.00
37.38
C

ATOM
2414
C6
C
R
84
12.010
−19.507
5.238
1.00
36.14
C

ATOM
2415
P
G
R
85
13.270
−19.088
0.375
1.00
42.13
P

ATOM
2416
OP1
G
R
85
13.250
−18.642
−1.038
1.00
39.83
O

ATOM
2417
OP2
G
R
85
13.026
−20.511
0.700
1.00
42.00
O

ATOM
2418
O5′
G
R
85
14.659
−18.664
1.032
1.00
40.66
O

ATOM
2419
C5′
G
R
85
15.851
−18.761
0.284
1.00
41.29
C

ATOM
2420
C4′
G
R
85
17.026
−18.378
1.158
1.00
42.64
C

ATOM
2421
O4′
G
R
85
16.600
−18.339
2.542
1.00
42.68
O

ATOM
2422
C3′
G
R
85
18.167
−19.377
1.164
1.00
42.57
C

ATOM
2423
O3′
G
R
85
18.982
−19.185
0.035
1.00
42.10
O

ATOM
2424
C2′
G
R
85
18.865
−19.051
2.476
1.00
41.38
C

ATOM
2425
O2′
G
R
85
19.654
−17.881
2.417
1.00
40.17
O

ATOM
2426
C1′
G
R
85
17.639
−18.850
3.361
1.00
42.10
C

ATOM
2427
N9
G
R
85
17.206
−20.120
3.916
1.00
41.22
N

ATOM
2428
C8
G
R
85
15.952
−20.685
3.884
1.00
40.86
C

ATOM
2429
N7
G
R
85
15.902
−21.847
4.477
1.00
40.10
N

ATOM
2430
C5
G
R
85
17.208
−22.058
4.918
1.00
39.28
C

ATOM
2431
C6
G
R
85
17.777
−23.141
5.623
1.00
39.33
C

ATOM
2432
O6
G
R
85
17.224
−24.177
6.018
1.00
42.03
O

ATOM
2433
N1
G
R
85
19.131
−22.943
5.870
1.00
37.79
N

ATOM
2434
C2
G
R
85
19.847
−21.843
5.482
1.00
38.15
C

ATOM
2435
N2
G
R
85
21.144
−21.836
5.810
1.00
39.81
N

ATOM
2436
N3
G
R
85
19.332
−20.824
4.819
1.00
38.57
N

ATOM
2437
C4
G
R
85
18.015
−21.003
4.576
1.00
39.41
C

ATOM
2438
P
G
R
86
18.867
−20.259
−1.138
1.00
41.60
P

ATOM
2439
OP1
G
R
86
18.757
−19.519
−2.415
1.00
42.11
O

ATOM
2440
OP2
G
R
86
17.832
−21.245
−0.753
1.00
41.38
O

ATOM
2441
O5′
G
R
86
20.285
−20.987
−1.074
1.00
40.68
O

ATOM
2442
C5′
G
R
86
21.382
−20.281
−0.527
1.00
40.19
C

ATOM
2443
C4′
G
R
86
21.982
−21.044
0.634
1.00
39.11
C

ATOM
2444
O4′
G
R
86
21.014
−21.208
1.699
1.00
40.85
O

ATOM
2445
C3′
G
R
86
22.357
−22.479
0.340
1.00
39.09
C

ATOM
2446
O3′
G
R
86
23.514
−22.555
−0.485
1.00
36.09
O

ATOM
2447
C2′
G
R
86
22.614
−22.943
1.766
1.00
41.07
C

ATOM
2448
O2′
G
R
86
23.810
−22.410
2.292
1.00
44.12
O

ATOM
2449
C1′
G
R
86
21.413
−22.325
2.483
1.00
40.38
C

ATOM
2450
N9
G
R
86
20.312
−23.276
2.612
1.00
40.65
N

ATOM
2451
C8
G
R
86
19.042
−23.176
2.091
1.00
39.95
C

ATOM
2452
N7
G
R
86
18.281
−24.205
2.374
1.00
40.39
N

ATOM
2453
C5
G
R
86
19.102
−25.042
3.128
1.00
41.38
C

ATOM
2454
C6
G
R
86
18.841
−26.305
3.719
1.00
40.00
C

ATOM
2455
O6
G
R
86
17.796
−26.964
3.696
1.00
40.51
O

ATOM
2456
N1
G
R
86
19.955
−26.802
4.391
1.00
40.10
N

ATOM
2457
C2
G
R
86
21.170
−26.165
4.485
1.00
39.73
C

ATOM
2458
N2
G
R
86
22.127
−26.799
5.175
1.00
39.35
N

ATOM
2459
N3
G
R
86
21.430
−24.988
3.938
1.00
40.78
N

ATOM
2460
C4
G
R
86
20.356
−24.485
3.277
1.00
41.70
C

ATOM
2461
P
G
R
87
23.537
−23.583
−1.707
1.00
33.36
P

ATOM
2462
OP1
G
R
87
24.737
−23.307
−2.524
1.00
33.26
O

ATOM
2463
OP2
G
R
87
22.197
−23.570
−2.338
1.00
34.04
O

ATOM
2464
O5′
G
R
87
23.731
−24.986
−0.964
1.00
34.13
O

ATOM
2465
C5′
G
R
87
24.543
−25.062
0.203
1.00
34.15
C

ATOM
2466
C4′
G
R
87
24.491
−26.453
0.804
1.00
34.05
C

ATOM
2467
O4′
G
R
87
23.507
−26.484
1.865
1.00
35.67
O

ATOM
2468
C3′
G
R
87
24.016
−27.535
−0.137
1.00
33.41
C

ATOM
2469
O3′
G
R
87
25.072
−28.003
−0.927
1.00
33.79
O

ATOM
2470
C2′
G
R
87
23.573
−28.594
0.860
1.00
34.76
C

ATOM
2471
O2′
G
R
87
24.655
−29.209
1.520
1.00
37.09
O

ATOM
2472
C1′
G
R
87
22.830
−27.726
1.850
1.00
35.04
C

ATOM
2473
N9
G
R
87
21.454
−27.503
1.442
1.00
35.44
N

ATOM
2474
C8
G
R
87
20.968
−26.439
0.729
1.00
34.50
C

ATOM
2475
N7
G
R
87
19.687
−26.515
0.505
1.00
35.41
N

ATOM
2476
C5
G
R
87
19.304
−27.705
1.107
1.00
34.55
C

ATOM
2477
C6
G
R
87
18.036
−28.312
1.191
1.00
34.73
C

ATOM
2478
O6
G
R
87
16.960
−27.904
0.738
1.00
36.16
O

ATOM
2479
N1
G
R
87
18.084
−29.515
1.884
1.00
35.62
N

ATOM
2480
C2
G
R
87
19.216
−30.063
2.429
1.00
34.97
C

ATOM
2481
N2
G
R
87
19.058
−31.234
3.063
1.00
33.00
N

ATOM
2482
N3
G
R
87
20.415
−29.502
2.361
1.00
35.53
N

ATOM
2483
C4
G
R
87
20.381
−26.328
1.686
1.00
35.01
C

ATOM
2484
P
G
R
88
24.789
−29.243
−1.892
1.00
37.87
P

ATOM
2485
OP1
G
R
88
26.085
−29.864
−2.250
1.00
36.87
O

ATOM
2486
OP2
G
R
88
23.878
−28.764
−2.958
1.00
38.01
O

ATOM
2487
O5′
G
R
88
23.953
−30.252
−0.957
1.00
39.30
O

ATOM
2488
C5′
G
R
88
24.565
−31.422
−0.404
1.00
38.13
C

ATOM
2489
C4′
G
R
88
23.578
−32.572
−0.241
1.00
37.15
C

ATOM
2490
O4′
G
R
88
22.393
−32.150
0.478
1.00
37.45
O

ATOM
2491
C3′
G
R
88
23.031
−33.163
−1.527
1.00
36.02
C

ATOM
2492
O3′
G
R
88
23.972
−34.059
−2.063
1.00
33.44
O

ATOM
2493
C2′
G
R
88
21.798
−33.886
−1.005
1.00
35.34
C

ATOM
2494
O2′
G
R
88
22.144
−35.067
−0.324
1.00
35.40
O

ATOM
2495
C1′
G
R
88
21.270
−32.865
−0.007
1.00
35.84
C

ATOM
2496
N9
G
R
88
20.367
−31.890
−0.599
1.00
37.28
N

ATOM
2497
C8
G
R
88
20.708
−30.668
−1.129
1.00
37.79
C

ATOM
2498
N7
G
R
88
19.688
−29.995
−1.587
1.00
37.77
N

ATOM
2499
C5
G
R
88
18.602
−30.822
−1.339
1.00
37.11
C

ATOM
2500
C6
G
R
88
17.234
−30.628
−1.619
1.00
37.48
C

ATOM
2501
O6
G
R
88
16.688
−29.655
−2.156
1.00
39.25
O

ATOM
2502
N1
G
R
88
16.471
−31.715
−1.208
1.00
36.94
N

ATOM
2503
C2
G
R
88
16.965
−32.841
−0.605
1.00
34.59
C

ATOM
2504
N2
G
R
88
16.071
−33.779
−0.282
1.00
33.20
N

ATOM
2505
N3
G
R
88
18.244
−33.039
−0.341
1.00
36.50
N

ATOM
2506
C4
G
R
88
19.002
−31.990
−0.732
1.00
37.42
C

ATOM
2507
P
U
R
89
23.674
−34.731
−3.470
1.00
30.68
P

ATOM
2508
OP1
U
R
89
24.450
−35.982
−3.547
1.00
31.33
O

ATOM
2509
OP2
U
R
89
23.793
−33.710
−4.530
1.00
31.86
O

ATOM
2510
O5′
U
R
89
22.135
−35.086
−3.334
1.00
31.68
O

ATOM
2511
C5′
U
R
89
21.776
−36.419
−3.121
1.00
31.30
N

ATOM
2512
C4′
U
R
89
20.317
−36.592
−3.438
1.00
29.53
C

ATOM
2513
O4′
U
R
89
19.583
−35.516
−2.813
1.00
28.76
O

ATOM
2514
C3′
U
R
89
19.974
−36.431
−4.904
1.00
28.05
C

ATOM
2515
O3′
U
R
89
20.315
−37.604
−5.634
1.00
25.73
O

ATOM
2516
C2′
U
R
89
18.473
−36.236
−4.767
1.00
28.86
C

ATOM
2517
O2′
U
R
89
17.808
−37.426
−4.413
1.00
30.08
O

ATOM
2518
C1′
U
R
89
18.423
−35.276
−3.585
1.00
29.23
C

ATOM
2519
N1
U
R
89
18.404
−33.865
−3.996
1.00
31.15
N

ATOM
2520
C2
U
R
89
17.185
−33.267
−4.206
1.00
33.63
C

ATOM
2521
O2
U
R
89
16.132
−33.856
−4.057
1.00
36.32
O

ATOM
2522
N3
U
R
89
17.239
−31.955
−4.592
1.00
33.07
N

ATOM
2523
C4
U
R
89
18.3/3
−31.200
−4.789
1.00
33.12
C

ATOM
2524
O4
U
R
89
18.261
−30.029
−5.135
1.00
35.77
O

ATOM
2525
C5
U
R
89
19.616
−31.895
−4.556
1.00
33.71
C

ATOM
2526
C6
U
R
89
19.586
−33.179
−4.175
1.00
32.85
C

ATOM
2527
P
U
R
90
20.173
−37.607
−7.225
1.00
25.12
P

ATOM
2528
OP1
U
R
90
20.604
−36.913
−7.750
1.00
25.48
O

ATOM
2529
OP2
U
R
90
20.772
−36.366
−7.747
1.00
26.78
O

ATOM
2530
O5′
U
R
90
18.609
−37.520
−7.421
1.00
26.63
O

ATOM
2531
C5′
U
R
90
17.967
−38.640
−7.954
1.00
27.14
C

ATOM
2532
C4′
U
R
90
16.505
−36.340
−8.139
1.00
27.35
C

ATOM
2533
O4′
U
R
90
16.053
−37.396
−7.133
1.00
25.50
O

ATOM
2534
C3′
U
R
90
16.197
−37.639
−9.442
1.00
25.29
C

ATOM
2535
O3′
U
R
90
16.188
−38.572
−10.483
1.00
23.41
O

ATOM
2536
C2′
U
R
90
14.812
−37.093
−9.126
1.00
24.66
C

ATOM
2537
O2′
U
R
90
13.827
−38.093
−9.150
1.00
24.34
O

ATOM
2538
C1′
U
R
90
15.026
−36.596
−7.698
1.00
25.04
C

ATOM
2539
N1
U
R
90
15.457
−35.195
−7.731
1.00
25.63
N

ATOM
2540
C2
U
R
90
14.514
−34.240
8.021
1.00
25.98
C

ATOM
2541
O2
U
R
90
13.349
−34.518
8.215
1.00
27.02
O

ATOM
2542
N3
U
R
90
14.982
−32.950
8.071
1.00
25.01
N

ATOM
2543
C4
U
R
90
16.284
−32.538
7.859
1.00
25.69
C

ATOM
2544
O4
U
R
90
16.564
−31.346
7.928
1.00
26.07
O

ATOM
2545
C5
U
R
90
17.217
−33.600
7.570
1.00
27.27
C

ATOM
2546
C6
U
R
90
16.780
−34.867
7.529
1.00
26.58
C

ATOM
2547
P
A
R
91
16.662
−38.102
−11.929
1.00
25.76
P

ATOM
2548
OP1
A
R
91
16.634
−39.265
−12.840
1.00
24.42
O

ATOM
2549
OP2
A
R
91
17.89$
−37.299
−11.764
1.00
27.32
O

ATOM
2550
O5′
A
R
91
15.494
−37.129
−12.377
1.00
27.66
O

ATOM
2551
C5′
A
R
91
14.327
−37.696
−12.925
1.00
29.20
C

ATOM
2552
C4′
A
R
91
13.280
−36.623
−13.100
1.00
30.75
C

ATOM
2553
O4′
A
R
91
13.262
−35.779
−11.925
1.00
31.90
O

ATOM
2554
C3′
A
R
91
13.566
−35.645
−14.210
1.00
32.65
C

ATOM
2555
O3′
A
R
91
13.198
−36.202
−15.463
1.00
36.61
O

ATOM
2556
C2′
A
R
91
12.636
−34.520
−13.797
1.00
32.32
C

ATOM
2557
O2′
A
R
91
11.292
−34.881
−14.005
1.00
34.62
O

ATOM
2558
C1′
A
R
91
12.907
−34.463
−12.300
1.00
30.81
C

ATOM
2559
N9
A
R
91
14.001
−33.577
−11.940
1.00
30.11
N

ATOM
2560
C8
A
R
91
15.231
−33.942
−11.479
1.00
31.61
C

ATOM
2561
N7
A
R
91
16.027
−32.927
−11.228
1.00
32.15
N

ATOM
2562
C5
A
R
91
15.265
−31.819
−11.551
1.00
31.17
C

ATOM
2563
C6
A
R
91
15.537
−30.439
−11.510
1.00
30.65
C

ATOM
2564
N6
A
R
91
16.705
−29.929
−11.111
1.00
30.78
N

ATOM
2565
N1
A
R
91
14.558
−29.599
−11.898
1.00
32.28
N

ATOM
2566
C2
A
R
91
13.388
−30.114
−12.302
1.00
33.94
C

ATOM
2567
N3
A
R
91
13.013
−31.392
−12.384
1.00
33.32
N

ATOM
2568
C4
A
R
91
14.010
−32.202
−11.990
1.00
31.95
C

ATOM
2569
P
C
R
92
13.818
−35.588
−16.808
1.00
38.98
P

ATOM
2570
OP1
C
R
92
14.000
−36.688
−17.781
1.00
39.78
O

ATOM
2571
OP2
C
R
92
14.9/3
−34.743
−16.430
1.00
38.61
O

ATOM
2572
O5′
C
R
92
12.648
−34.635
−17.327
1.00
39.30
O

ATOM
2573
C5′
C
R
92
11.322
−35.134
−17.379
1.00
41.55
C

ATOM
2574
C4′
C
R
92
10.458
−34.170
−18.155
1.00
43.67
C

ATOM
2575
O4′
C
R
92
10.040
−33.109
−17.266
1.00
44.04
O

ATOM
2576
C3′
C
R
92
11.191
−33.479
−19.293
1.00
46.20
C

ATOM
2577
O3′
C
R
92
11.029
−34.225
−20.495
1.00
48.11
O

ATOM
2578
C2′
C
R
92
10.497
−32.123
−19.368
1.00
46.35
C

ATOM
2579
O2′
C
R
92
9.331
−32.151
−20.168
1.00
48.66
O

ATOM
2580
C1′
C
R
92
10.135
−31.854
−17.910
1.00
44.57
C

ATOM
2581
N1
C
R
92
11.143
−31.016
−17.191
1.00
43.42
N

ATOM
2582
C2
C
R
92
10.977
−29.633
−17.152
1.00
43.30
C

ATOM
2583
O2
C
R
92
9.992
−29.136
−17.713
1.00
43.57
O

ATOM
2584
N3
C
R
92
11.898
−28.877
−16.499
1.00
43.42
N

ATOM
2585
C4
C
R
92
12.943
−29.456
−15.905
1.00
42.92
C

ATOM
2586
N4
C
R
92
13.823
−28.672
−15.274
1.00
42.00
N

ATOM
2587
C5
C
R
92
13.130
−30.868
−15.936
1.00
43.71
C

ATOM
2588
C6
C
R
92
12.216
−31.601
−16.584
1.00
44.37
C

ATOM
2589
P
C
R
93
11.782
−33.761
−21.824
1.00
49.66
P

ATOM
2590
OP1
C
R
93
11.145
−34.442
−22.974
1.00
50.18
O

ATOM
2591
OP2
C
R
93
13.235
−33.906
−21.585
1.00
48.60
O

ATOM
2592
O5′
C
R
93
11.449
−32.195
−21.891
1.00
52.13
O

ATOM
2593
C5′
C
R
93
10.362
−31.689
−22.681
1.00
53.55
C

ATOM
2594
C4′
C
R
93
10.506
−30.188
−22.911
1.00
55.33
C

ATOM
2595
O4′
C
R
93
10.691
−29.511
−21.644
1.00
54.45
O

ATOM
2596
C3′
C
R
93
11.724
−29.766
−23.723
1.00
57.28
C

ATOM
2597
O3′
C
R
93
11.461
−29.859
−25.112
1.00
59.28
O

ATOM
2598
C2′
C
R
93
11.943
−28.318
−23.289
1.00
56.35
C

ATOM
2599
O2′
C
R
93
11.146
−27.402
−24.019
1.00
57.28
O

ATOM
2600
C1′
C
R
93
11.496
−28.350
−21.828
1.00
54.24
C

ATOM
2601
N1
C
R
93
12.618
−28.374
−20.829
1.00
51.80
N

ATOM
2602
C2
C
R
93
13.335
−27.204
−20.529
1.00
51.56
C

ATOM
2603
O2
C
R
93
13.049
−26.143
−21.101
1.00
51.96
O

ATOM
2604
N3
C
R
93
14.334
−27.267
−19.612
1.00
50.19
N

ATOM
2605
C4
C
R
93
14.617
−26.422
−19.011
1.00
49.81
C

ATOM
2606
N4
C
R
93
15.604
−28.438
−18.111
1.00
49.44
N

ATOM
2607
C5
C
R
93
13.899
−29.616
−19.301
1.00
50.82
C

ATOM
2608
C6
C
R
93
12.920
−29.545
−20.205
1.00
51.03
C

ATOM
2609
P
G
R
94
12.392
−30.788
−26.013
1.00
59.89
P

ATOM
2610
OP1
G
R
94
11.526
−31.534
−26.955
1.00
60.44
O

ATOM
2611
OP2
G
R
94
13.331
−31.505
−25.122
1.00
60.28
O

ATOM
2612
O5′
G
R
94
13.264
−29.733
−26.810
1.00
59.76
O

ATOM
2613
C5′
G
R
94
14.499
−29.393
−26.264
1.00
62.42
C

ATOM
2614
C4′
G
R
94
14.649
−27.901
−26.296
1.00
66.62
C

ATOM
2615
O4′
G
R
94
14.748
−27.436
−24.927
1.00
67.79
O

ATOM
2616
C3′
G
R
94
15.934
−27.466
−26.969
1.00
69.95
C

ATOM
2617
O3′
G
R
94
15.868
−26.082
−27.333
1.00
75.73
O

ATOM
2618
C2′
G
R
94
16.905
−27.725
−25.826
1.00
68.57
C

ATOM
2619
O2′
G
R
94
18.135
−27.037
−25.968
1.00
68.39
O

ATOM
2620
C1′
G
R
94
16.109
−27.180
−24.639
1.00
67.54
C

ATOM
2621
N9
G
R
94
16.492
−27.826
−23.386
1.00
64.50
N

ATOM
2622
C8
G
R
94
16.397
−29.164
−23.091
1.00
63.34
C

ATOM
2623
N7
G
R
94
16.837
−29.466
−21.901
1.00
61.53
N

ATOM
2624
C5
G
R
94
17.262
−28.251
−21.379
1.00
60.68
C

ATOM
2625
C6
G
R
94
17.840
−27.957
−20.125
1.00
59.45
C

ATOM
2626
O6
G
R
94
18.093
−28.737
−19.199
1.00
60.90
O

ATOM
2627
N1
G
R
94
18.127
−26.601
−19.988
1.00
58.22
N

ATOM
2628
C2
G
R
94
17.886
−25.647
−20.945
1.00
57.90
C

ATOM
2629
N2
G
R
94
18.235
−24.392
−20.625
1.00
54.82
N

ATOM
2630
N3
G
R
94
17.349
−25.909
−22.133
1.00
60.11
N

ATOM
2631
C4
G
R
94
17.061
−27.229
−22.279
1.00
61.90
C

ATOM
2632
P
A
R
95
16.124
−25.587
−28.842
1.00
78.85
P

ATOM
2633
OP1
A
R
95
14.825
−25.564
−29.549
1.00
77.94
O

ATOM
2634
OP2
A
R
95
17.267
−26.337
−29.411
1.00
78.83
O

ATOM
2635
O5′
A
R
95
16.608
−24.086
−28.617
1.00
84.49
O

ATOM
2636
C5′
A
R
95
17.959
−23.762
−28.833
1.00
93.09
C

ATOM
2637
C4′
A
R
95
18.027
−22.476
−29.617
1.00
100.98
C

ATOM
2638
O4′
A
R
95
16.863
−21.670
−29.300
1.00
103.12
O

ATOM
2639
C3′
A
R
95
19.240
−21.616
−29.300
1.00
105.41
C

ATOM
2640
O3′
A
R
95
20.215
−21.807
−30.313
1.00
109.76
O

ATOM
2641
C2′
A
R
95
18.657
−20.205
−29.305
1.00
105.66
C

ATOM
2642
O2′
A
R
95
18.475
−19.699
−30.613
1.00
105.52
O

ATOM
2643
C1′
A
R
95
17.301
−20.490
−28.671
1.00
105.18
C

ATOM
2644
N9
A
R
95
17.378
−20.784
−27.247
1.00
106.48
N

ATOM
2645
C8
A
R
95
17.779
−21.962
−26.685
1.00
107.48
C

ATOM
2646
N7
A
R
95
17.753
−21.958
−25.370
1.00
107.47
N

ATOM
2647
C5
A
R
95
17.296
−20.690
−25.048
1.00
106.91
C

ATOM
2648
C6
A
R
95
17.040
−20.055
−23.815
1.00
106.20
C

ATOM
2649
N6
A
R
95
17.226
−20.647
−22.630
1.00
105.33
N

ATOM
2650
N1
A
R
95
16.590
−18.782
−23.851
1.00
106.13
N

ATOM
2651
C2
A
R
95
16.401
−18.198
−25.042
1.00
106.41
C

ATOM
2652
N3
A
R
95
16.607
−18.690
−26.263
1.00
106.72
N

ATOM
2653
C4
A
R
95
17.057
−19.952
−26.196
1.00
106.82
C

ATOM
2654
P
U
R
96
21.657
−21.157
−30.130
1.00
112.21
P

ATOM
2655
OP1
U
R
96
21.438
−19.789
−29.604
1.00
112.97
O

ATOM
2656
OP2
U
R
96
22.440
−21.372
−31.373
1.00
112.07
O

ATOM
2657
O5′
U
R
96
22.272
−22.080
−28.977
1.00
110.36
O

ATOM
2658
C5′
U
R
96
21.424
−22.489
−27.913
1.00
107.93
C

ATOM
2659
C4′
U
R
96
21.830
−21.770
−26.644
1.00
106.86
C

ATOM
2660
O4′
U
R
96
20.828
−21.907
−25.612
1.00
107.22
O

ATOM
2661
C3′
U
R
96
23.085
−22.327
−26.021
1.00
105.78
C

ATOM
2662
O3′
U
R
96
24.180
−21.812
−26.754
1.00
102.98
O

ATOM
2663
C2′
U
R
96
22.968
−21.768
−24.607
1.00
106.35
C

ATOM
2664
O2′
U
R
96
23.253
−20.385
−24.546
1.00
105.78
O

ATOM
2665
C1′
U
R
96
21.476
−22.000
−24.355
1.00
106.78
C

ATOM
2666
N1
U
R
96
21.175
−23.340
−23.788
1.00
106.29
N

ATOM
2667
C2
U
R
96
21.668
−23.665
−22.544
1.00
105.62
C

ATOM
2668
O2
U
R
96
22.346
−22.899
−21.879
1.00
105.12
O

ATOM
2669
N3
U
R
96
21.335
−24.925
−22.106
1.00
105.14
N

ATOM
2670
C4
U
R
96
20.573
−25.868
−22.777
1.00
105.07
C

ATOM
2671
O4
U
R
96
20.360
−26.960
−22.260
1.00
104.91
O

ATOM
2672
C5
U
R
96
20.097
−25.452
−24.071
1.00
105.24
C

ATOM
2673
C6
U
R
96
20.410
−24.230
−24.518
1.00
105.74
C

ATOM
2674
P
G
R
97
25.147
−22.775
−27.594
1.00
100.22
P

ATOM
2675
OP1
G
R
97
25.214
−22.260
−28.982
1.00
100.05
O

ATOM
2676
OP2
G
R
97
24.768
−24.187
−27.350
1.00
100.16
O

ATOM
2677
O5′
G
R
97
26.537
−22.485
−26.857
1.00
96.14
O

ATOM
2678
C5′
G
R
97
26.664
−21.265
−26.126
1.00
88.97
C

ATOM
2679
C4′
G
R
97
27.324
−21.466
−24.772
1.00
83.18
C

ATOM
2680
O4′
G
R
97
26.321
−21.605
−23.732
1.00
79.67
O

ATOM
2681
C3′
G
R
97
28.169
−22.716
−24.603
1.00
81.48
C

ATOM
2682
O3′
G
R
97
29.430
−22.572
−25.251
1.00
81.66
O

ATOM
2683
C2′
G
R
97
28.295
−22.691
−23.089
1.00
79.39
C

ATOM
2684
O2′
G
R
97
29.058
−21.594
−22.634
1.00
79.63
O

ATOM
2685
C1′
G
R
97
26.833
−22.476
−22.736
1.00
77.03
C

ATOM
2686
N9
G
R
97
26.088
−23.723
−22.792
1.00
72.89
N

ATOM
2687
C8
G
R
97
25.223
−24.119
−23.783
1.00
71.33
C

ATOM
2688
N7
G
R
97
24.698
−25.296
−23.576
1.00
68.96
N

ATOM
2689
C5
G
R
97
25.257
−25.711
−22.372
1.00
68.50
C

ATOM
2690
C6
G
R
97
25.064
−26.910
−21.645
1.00
66.80
C

ATOM
2691
O6
G
R
97
24.336
−27.871
−21.934
1.00
66.25
O

ATOM
2692
N1
G
R
97
25.820
−26.932
−20.473
1.00
64.90
N

ATOM
2693
C2
G
R
97
26.659
−25.925
−20.059
1.00
65.03
C

ATOM
2694
N2
G
R
97
27.301
−26.128
−18.899
1.00
63.35
N

ATOM
2695
N3
G
R
97
26.848
−24.793
−20.731
1.00
67.18
N

ATOM
2696
C4
G
R
97
26.119
−24.755
−21.876
1.00
69.80
C

TER
2697

G
R
97

HETATM
2698
P1
C2E
R
1
6.502
−20.754
−18.401
1.00
30.05
P

HETATM
2699
O2P
C2E
R
1
7.742
−19.829
−18.836
1.00
28.81
O

HETATM
2700
O1P
C2E
R
1
6.847
−22.489
−18.550
1.00
29.16
O

HETATM
2701
O5′
C2E
R
1
6.313
−20.343
−16.869
1.00
33.61
O

HETATM
2702
C5′
C2E
R
1
6.559
−18.996
−16.506
1.00
32.76
C

HETATM
2703
C4′
C2E
R
1
6.865
−18.937
−15.021
1.00
34.17
C

HETATM
2704
O4′
C2E
R
1
6.003
−19.815
−14.274
1.00
34.79
O

HETATM
2705
C3′
C2E
R
1
8.288
−19.364
−14.725
1.00
33.27
C

HETATM
2706
O3′
C2E
R
1
9.134
−18.220
−14.703
1.00
28.21
O

HETATM
2707
C2′
C2E
R
1
8.184
−20.029
−13.358
1.00
36.97
C

HETATM
2708
O2′
C2E
R
1
8.490
−19.107
−12.296
1.00
38.43
O

HETATM
2709
C1′
C2E
R
1
6.732
−20.479
−13.230
1.00
35.05
C

HETATM
2710
N9
C2E
R
1
6.662
−21.952
−13.424
1.00
33.61
N

HETATM
2711
C8
C2E
R
1
6.108
−22.581
−14.487
1.00
34.46
C

HETATM
2712
N7
C2E
R
1
6.218
−23.933
−14.358
1.00
33.49
N

HETATM
2713
C5
C2E
R
1
6.856
−24.175
−13.205
1.00
30.79
C

HETATM
2714
C6
C2E
R
1
7.284
−25.380
−12.488
1.00
30.78
C

HETATM
2715
O6
C2E
R
1
7.044
−26.614
−13.005
1.00
33.98
O

HETATM
2716
N1
C2E
R
1
7.920
−25.228
−11.310
1.00
29.12
N

HETATM
2717
C2
C2E
R
1
8.166
−24.001
−10.782
1.00
28.18
C

HETATM
2718
N2
C2E
R
1
8.810
−23.925
−9.594
1.00
27.61
N

HETATM
2719
N3
C2E
R
1
7.794
−22.852
−11.406
1.00
29.14
N

HETATM
2720
C4
C2E
R
1
7.147
−22.881
−12.593
1.00
30.69
C

HETATM
2721
P11
C2E
R
1
10.674
−18.317
−15.114
1.00
25.34
P

HETATM
2722
O21
C2E
R
1
11.363
−16.696
−15.348
1.00
27.89
O

HETATM
2723
O11
C2E
R
1
11.615
−19.211
−13.902
1.00
27.08
O

HETATM
2724
O5A
C2E
R
1
10.636
−19.098
−16.510
1.00
28.41
O

HETATM
2725
C5A
C2E
R
1
10.602
−16.336
−17.710
1.00
29.50
C

HETATM
2726
C4A
C2E
R
1
10.091
−19.175
−18.871
1.00
30.00
C

HETATM
2727
O4A
C2E
R
1
11.192
−19.889
−19.428
1.00
30.98
O

HETATM
2728
C3A
C2E
R
1
9.054
−20.212
−18.465
1.00
30.60
C

HETATM
2729
O3A
C2E
R
1
5.041
−20.33 7
−19.313
1.00
32.56
O

HETATM
2730
C2A
C2E
R
1
9.413
−21.436
−19.257
1.00
33.12
C

HETATM
2731
O2A
C2E
R
1
8.699
−21.413
−20.497
1.00
34.13
O

HETATM
2732
C1A
C2E
R
1
10.885
−21.281
−19.550
1.00
34.77
C

HETATM
2733
N91
C2E
R
1
11.655
−22.046
−18.538
1.00
39.55
N

HETATM
2734
C81
C2E
R
1
12.593
−21.523
−17.718
1.00
42.02
C

HETATM
2735
N71
C2E
R
1
13.118
−22.490
−16.912
1.00
43.25
N

HETATM
2736
C51
C2E
R
1
12.509
−23.652
−17.212
1.00
41.01
C

HETATM
2737
C61
C2E
R
1
12.606
−25.046
−16.721
1.00
40.60
C

HETATM
2738
O61
C2E
R
1
13.479
−25.383
−15.726
1.00
41.42
O

HETATM
2739
N11
C2E
R
1
11.801
−25.971
−17.288
1.00
40.05
N

HETATM
2740
C21
C2E
R
1
10.922
−25.643
−18.285
1.00
41.02
C

HETATM
2741
N21
C2E
R
1
10.144
−26.622
−18.808
1.00
41.66
N

HETATM
2742
N31
C2E
R
1
10.793
−24.373
−18.772
1.00
39.33
N

HETATM
2743
C41
C2E
R
1
11.548
−23.359
−18.280
1.00
39.99
C

HETATM
2744
IR
IRI
R
670
13.553
−19.985
−5.943
1.00
43.60
IR

HETATM
2745
N1
IRI
R
670
13.723
−18.216
−6.890
1.00
40.61
N

HETATM
2746
N2
IRI
R
670
13.604
−20.915
−7.740
1.00
38.52
N

HETATM
2747
N3
IRI
R
670
13.354
−21.750
−4.983
1.00
38.38
N

HETATM
2748
N4
IRI
R
670
13.464
−19.016
−4.173
1.00
38.30
N

HETATM
2749
N5
IRI
R
670
15.551
−20.166
−5.731
1.00
38.33
N

HETATM
2750
N6
IRI
R
670
11.554
−19.810
−6.155
1.00
39.34
N

HETATM
2751
IR
IRI
R
2
16.326
−25.223
12.163
1.00
75.64
IR

HETATM
2752
N1
IRI
R
2
16.941
−23.312
12.409
1.00
75.42
N

HETATM
2753
N2
IRI
R
2
14.575
−24.758
13.066
1.00
75.32
N

HETATM
2754
N3
IRI
R
2
15.726
−27.143
11.944
1.00
75.64
N

HETATM
2755
N4
IRI
R
2
18.102
−25.650
11.289
1.00
74.63
N

HETATM
2756
N5
IRI
R
2
15.515
−24.825
10.353
1.00
75.53
N

HETATM
2757
N6
IRI
R
2
17.131
−25.623
13.978
1.00
75.87
N

HETATM
2758
IR
IRI
R
3
3.290
−22.237
−20.960
1.00
64.89
IR

HETATM
2759
N1
IRI
R
3
2.654
−20.547
−20.047
1.00
65.08
N

HETATM
2760
N2
IRI
R
3
4.235
−22.808
−19.262
1.00
63.11
N

HETATM
2761
N3
IRI
R
3
3.921
−23.916
−21.897
1.00
65.89
N

HETATM
2762
N4
IRI
R
3
2.372
−21.655
−22.665
1.00
64.73
N

HETATM
2763
N5
IRI
R
3
1.610
−23.218
−20.397
1.00
62.81
N

HETATM
2764
N6
IRI
R
3
4.966
−21.264
−21.545
1.00
63.36
N

HETATM
2765
IR
IRI
R
4
15.656
−24.430
−0.102
1.00
48.52
IR

HETATM
2766
N1
IRI
R
4
16.116
−22.768
0.957
1.00
47.83
N

HETATM
2767
N2
IRI
R
4
15.805
−25.538
1.585
1.00
46.64
N

HETATM
2768
N3
IRI
R
4
15.196
−26.075
−1.189
1.00
47.66
N

HETATM
2769
N4
IRI
R
4
15.540
−23.294
−1.775
1.00
47.65
N

HETATM
2770
N5
IRI
R
4
13.674
−24.156
0.210
1.00
48.80
N

HETATM
2771
N6
IRI
R
4
17.634
−24.704
−0.435
1.00
48.33
N

HETATM
2772
IR
IRI
R
5
23.417
−29.848
−24.640
1.00
111.07
IR

HETATM
2773
N1
IRI
R
5
23.756
−27.856
−24.767
1.00
110.88
N

HETATM
2774
N2
IRI
R
5
21.708
−29.596
−25.694
1.00
110.91
N

HETATM
2775
N3
IRI
R
5
23.089
−31.840
−24.472
1.00
110.63
N

HETATM
2776
N4
IRI
R
5
25.118
−30.045
−23.559
1.00
111.06
N

HETATM
2777
N5
IRI
R
5
24.467
−30.213
−26.333
1.00
110.45
N

HETATM
2778
N6
IRI
R
5
22.370
−29.481
−22.946
1.00
110.68
N

HETATM
2779
IR
IRI
R
6
−10.737
−26.558
18.409
1.00
73.53
IR

HETATM
2780
N1
IRI
R
6
−8.940
−25.713
18.806
1.00
72.33
N

HETATM
2781
N2
IRI
R
6
−11.234
−26.384
20.364
1.00
72.26
N

HETATM
2782
N3
IRI
R
6
−12.524
−27.421
18.001
1.00
72.42
N

HETATM
2783
N4
IRI
R
6
−10.201
−26.742
16.466
1.00
72.77
N

HETATM
2784
N5
IRI
R
6
−11.574
−24.762
17.995
1.00
72.54
N

HETATM
2785
N6
IRI
R
6
−9.901
−28.357
18.813
1.00
72.66
N

HETATM
2786
IR
IRI
R
7
18.223
−26.044
−3.227
1.00
78.01
IR

HETATM
2787
N1
IRI
R
7
18.991
−25.127
−4.863
1.00
77.82
N

HETATM
2788
N2
IRI
R
7
16.632
−24.789
−3.280
1.00
77.54
N

HETATM
2789
N3
IRI
R
7
17.468
−26.946
−1.580
1.00
77.41
N

HETATM
2790
N4
IRI
R
7
19.842
−27.263
−3.181
1.00
77.43
N

HETATM
2791
N5
IRI
R
7
17.239
−27.402
−4.364
1.00
77.68
N

HETATM
2792
N6
IRI
R
7
19.216
−24.689
−2.093
1.00
77.76
N

HETATM
2793
IR
IRI
R
671
3.369
−18.801
4.897
1.00
86.19
IR

HETATM
2794
N1
IRI
R
671
3.219
−16.813
4.542
1.00
86.06
N

HETATM
2795
N2
IRI
R
671
2.472
−18.538
6.693
1.00
85.93
N

HETATM
2796
N3
IRI
R
671
3.543
−20.788
5.249
1.00
86.03
N

HETATM
2797
N4
IRI
R
671
4.294
−19.033
3.110
1.00
85.92
N

HETATM
2798
N5
IRI
R
671
1.581
−19.167
4.016
1.00
85.59
N

HETATM
2799
N6
IRI
R
671
5.159
−18.433
5.772
1.00
85.52
N

HETATM
2800
IR
IRI
R
672
13.492
−28.215
16.395
1.00
76.52
IR

HETATM
2801
N1
IRI
R
672
13.116
−26.513
17.423
1.00
75.71
N

HETATM
2802
N2
IRI
R
672
15.186
−28.474
17.472
1.00
75.94
N

HETATM
2803
N3
IRI
R
672
13.867
−29.905
15.345
1.00
75.61
N

HETATM
2804
N4
IRI
R
672
11.812
−27.913
15.305
1.00
75.57
N

HETATM
2805
N5
IRI
R
672
12.440
−29.329
17.720
1.00
75.59
N

HETATM
2806
N6
IRI
R
672
14.549
−27.101
15.078
1.00
75.75
N

HETATM
2807
MG
MG
R
673
3.239
−24.383
−5.600
1.00
61.87
MG

HETATM
2808
MG
MG
R
674
13.280
−15.470
−14.739
1.00
80.34
MG

HETATM
2809
O
HOH
P
99
10.160
−9.134
31.902
1.00
66.02
O

HETATM
2810
O
HOH
P
100
−6.816
−2.770
42.343
1.00
77.15
O

HETATM
2811
O
HOH
P
101
3.312
−13.193
41.640
1.00
60.06
O

HETATM
2812
O
HOH
P
102
2.037
−14.021
39.455
1.00
35.38
O

HETATM
2813
O
HOH
P
103
−4.720
−13.453
40.181
1.00
40.79
O

HETATM
2814
O
HOH
P
104
5.947
−17.719
46.071
1.00
56.23
O

HETATM
2815
O
HOH
P
105
0.362
−15.182
47.752
1.00
65.09
O

HETATM
2816
O
HOH
P
106
7.290
−12.790
32.812
1.00
55.17
O

HETATM
2817
O
HOH
P
108
11.586
−4.412
34.636
1.00
69.15
O

HETATM
2818
O
HOH
P
109
10.747
−7.744
42.765
1.00
65.33
O

HETATM
2819
O
HOH
P
110
0.870
−14.811
50.378
1.00
55.00
O

HETATM
2820
O
HOH
P
111
−2.736
−2.758
30.800
1.00
44.11
O

HETATM
2821
O
HOH
R
100
18.977
−33.313
−10.884
1.00
49.02
O

HETATM
2822
O
HOH
R
101
4.327
−15.292
−10.841
1.00
50.79
O

HETATM
2823
O
HOH
R
102
17.919
−28.829
10.879
1.00
65.34
O

HETATM
2824
O
HOH
R
103
−15.508
−18.997
0.231
1.00
56.35
O

HETATM
2825
O
HOH
R
104
15.489
−24.366
15.706
1.00
25.16
O

HETATM
2826
O
HOH
R
105
16.916
−30.158
−14.736
1.00
18.68
O

HETATM
2827
O
HOH
R
106
29.823
−19.548
−26.220
1.00
39.98
O

HETATM
2828
O
HOH
R
107
7.879
−32.444
7.642
1.00
18.27
O

HETATM
2829
O
HOH
R
108
7.654
−31.273
5.750
1.00
41.04
O

HETATM
2830
O
HOH
R
109
13.864
−21.138
41.006
1.00
37.79
O

HETATM
2831
O
HOH
R
111
12.113
−15.815
−12.521
1.00
36.53
O

HETATM
2832
O
HOH
R
112
14.969
−26.268
−12.700
1.00
51.16
O

HETATM
2833
O
HOH
R
113
16.940
−25.262
−13.683
1.00
30.68
O

HETATM
2834
O
HOH
R
114
15.065
−28.636
−6.117
1.00
43.05
O

HETATM
2835
O
HOH
R
115
9.512
−29.897
0.330
1.00
43.79
O

HETATM
2836
O
HOH
R
116
6.971
−28.579
2.820
1.00
39.11
O

HETATM
2837
O
HOH
R
117
2.860
−30.293
3.944
1.00
50.32
O

HETATM
2838
O
HOH
R
118
−4.233
−26.157
6.560
1.00
63.25
O

HETATM
2839
O
HOH
R
119
15.672
−33.178
−14.610
1.00
44.45
O

HETATM
2840
O
HOH
R
120
15.995
−35.585
7.500
1.00
46.44
O

HETATM
2841
O
HOH
R
122
11.528
−21.236
40.723
1.00
52.08
O

HETATM
2842
O
HOH
R
123
5.978
−25.490
−1.743
1.00
62.06
O

HETATM
2843
O
HOH
R
124
8.482
−26.766
−9.171
1.00
30.51
O

HETATM
2844
O
HOH
R
125
8.352
−12.975
19.365
1.00
44.03
O

HETATM
2845
O
HOH
R
126
18.298
−32.694
−21.443
1.00
42.31
O

HETATM
2846
O
HOH
R
127
9.774
−32.491
8.965
1.00
25.41
O

HETATM
2847
O
HOH
R
128
−10.257
−31.921
23.076
1.00
61.91
O

HETATM
2848
O
HOH
R
129
1.086
−24.235
−0.532
1.00
96.91
O

HETATM
2849
O
HOH
R
130
21.038
−36.292
−14.129
1.00
49.12
O

HETATM
2850
O
HOH
R
131
−6.055
−27.340
−3.964
1.00
46.40
O

HETATM
2851
O
HOH
R
132
15.288
−19.471
43.254
1.00
51.64
O

HETATM
2852
O
HOH
R
133
−1.895
−23.116
9.280
1.00
37.39
O

HETATM
2853
O
HOH
R
134
11.611
−31.062
11.118
1.00
41.41
O

HETATM
2854
O
HOH
R
135
7.324
−29.192
−16.386
1.00
48.11
O

HETATM
2855
O
HOH
R
136
9.590
−27.632
−2.596
1.00
30.97
O

HETATM
2856
O
HOH
R
137
−4.572
−25.340
−0.827
1.00
49.53
O

HETATM
2857
O
HOH
R
138
−6.812
−26.422
−1.195
1.00
56.21
O

HETATM
2858
O
HOH
R
139
14.112
−20.818
21.910
1.00
63.26
O

HETATM
2859
O
HOH
R
140
−6.090
−26.927
1.287
1.00
63.52
O

HETATM
2860
O
HOH
R
141
14.430
−28.921
−29.580
1.00
24.57
O

HETATM
2861
O
HOH
R
142
21.105
−23.059
25.048
1.00
48.57
O

HETATM
2862
O
HOH
R
143
24.428
−37.553
−10.426
1.00
40.58
O

HETATM
2863
O
HOH
R
144
18.580
−34.892
5.547
1.00
40.86
O

HETATM
2864
O
HOH
R
145
18.756
−36.274
1.101
1.00
60.20
O

HETATM
2865
O
HOH
R
146
19.954
−19.707
23.345
1.00
41.94
O

HETATM
2866
O
HOH
R
148
27.733
−36.664
−12.835
1.00
51.39
O

HETATM
2867
O
HOH
R
150
−12.437
−28.820
13.779
1.00
66.60
O

HETATM
2868
O
HOH
R
151
11.562
−26.960
−12.379
1.00
36.97
O

HETATM
2869
O
HOH
R
152
3.058
−25.809
4.024
1.00
32.95
O

HETATM
2870
O
HOH
R
153
29.256
−24.470
−20.537
1.00
67.94
O

HETATM
2871
O
HOH
R
154
−4.025
−27.394
−8.581
1.00
49.84
O

HETATM
2872
O
HOH
R
155
−7.265
−14.477
−5.041
1.00
34.16
O

HETATM
2873
O
HOH
R
156
−2.425
−12.085
1.766
1.00
63.07
O

HETATM
2874
O
HOH
R
157
−4.670
−31.840
−3.509
1.00
52.72
O

HETATM
2875
O
HOH
R
158
−0.350
−14.270
−0.484
1.00
53.12
O

HETATM
2876
O
HOH
R
159
21.441
−35.405
7.269
1.00
45.81
O

HETATM
2877
O
HOH
R
160
8.859
−26.031
24.215
1.00
37.10
O

HETATM
2878
O
HOH
R
161
23.555
−3.668
33.367
1.00
74.61
O

HETATM
2879
O
HOH
R
162
20.295
−3.381
23.522
1.00
51.66
O

HETATM
2880
O
HOH
R
163
14.354
−17.834
−19.519
1.00
20.35
O

HETATM
2881
O
HOH
R
164
−2.806
−32.357
14.965
1.00
57.06
O

HETATM
2882
O
HOH
R
165
11.749
−26.356
−3.180
1.00
37.91
O

HETATM
2883
O
HOH
R
166
9.488
−14.610
21.938
1.00
49.41
O

HETATM
2884
O
HOH
R
167
2.875
−33.435
3.589
1.00
55.00
O

HETATM
2885
O
HOH
R
168
0.739
−21.707
−15.639
1.00
45.53
O

HETATM
2886
O
HOH
R
169
28.199
−22.167
−30.226
1.00
40.04
O

HETATM
2887
O
HOH
R
170
4.161
−34.723
−4.955
1.00
37.10
O

HETATM
2888
O
HOH
R
171
18.885
−39.836
−5.081
1.00
86.29
O

HETATM
2889
O
HOH
R
172
12.817
−26.726
−0.177
1.00
43.60
O

HETATM
2890
O
HOH
R
173
3.555
−32.843
−3.780
1.00
37.47
O

HETATM
2891
O
HOH
R
174
20.359
−41.531
−13.061
1.00
56.61
O

HETATM
2892
O
HOH
R
175
−0.968
−33.105
−21.302
1.00
27.26
O

HETATM
2893
O
HOH
R
176
−3.359
−31.654
−20.869
1.00
37.10
O

HETATM
2894
O
HOH
R
177
17.534
−18.533
18.004
1.00
57.16
O

HETATM
2895
O
HOH
R
178
−12.703
−18.849
−9.382
1.00
36.76
O

HETATM
2896
O
HOH
R
179
−2.260
−23.004
6.585
1.00
52.35
O

HETATM
2897
O
HOH
R
180
−7.628
−27.731
20.211
1.00
62.69
O

HETATM
2898
O
HOH
R
181
−7.843
−35.086
6.592
1.00
49.86
O

HETATM
2899
O
HOH
R
182
11.262
−17.206
−5.582
1.00
48.13
O

HETATM
2900
O
HOH
R
183
19.859
−20.832
18.139
1.00
52.96
O

CONECT
736
737
738
739
740

CONECT
737
736

CONECT
738
736

CONECT
739
736

CONECT
740
736
741

CONECT
741
740
742
743
744

CONECT
742
741

CONECT
743
741

CONECT
744
741
745

CONECT
745
744
746
747
748

CONECT
746
745

CONECT
747
745

CONECT
748
745
749

CONECT
749
748
750

CONECT
750
749
751
752

CONECT
751
750
756

CONECT
752
750
753
754

CONECT
753
752
768

CONECT
754
752
755
756

CONECT
755
754

CONECT
756
751
754
757

CONECT
757
756
758
767

CONECT
758
757
759

CONECT
759
758
760

CONECT
760
759
761
767

CONECT
761
760
762
763

CONECT
762
761

CONECT
763
761
764

CONECT
764
763
765
766

CONECT
765
764

CONECT
766
764
767

CONECT
767
757
760
766

CONECT
768
753

CONECT
2698
2699
2700
2701
2729

CONECT
2699
2698

CONECT
2700
2698

CONECT
2701
2698
2702

CONECT
2702
2701
2703

CONECT
2703
2702
2704
2705

CONECT
2704
2703
2709

CONECT
2705
2703
2706
2707

CONECT
2706
2705
2721

CONECT
2707
2705
2708
2709

CONECT
2708
2707

CONECT
2709
2704
2707
2710

CONECT
2710
2709
2711
2720

CONECT
2711
2710
2712

CONECT
2712
2711
2713

CONECT
2713
2712
2714
2720

CONECT
2714
2713
2715
2716

CONECT
2715
2714

CONECT
2716
2714
2717

CONECT
2717
2716
2718
2719

CONECT
2718
2717

CONECT
2719
2717
2720

CONECT
2720
2710
2713
2719

CONECT
2721
2706
2722
2723
2724

CONECT
2722
2721

CONECT
2723
2721

CONECT
2724
2721
2725

CONECT
2725
2724
2726

CONECT
2726
2725
2727
2728

CONECT
2727
2726
2732

CONECT
2728
2726
2729
2730

CONECT
2729
2698
2728

CONECT
2730
2728
2731
2732

CONECT
2731
2730

CONECT
2732
2727
2730
2733

CONECT
2733
2732
2734
2743

CONECT
2734
2733
2735

CONECT
2735
2734
2736

CONECT
2736
2735
2737
2743

CONECT
2737
2736
2738
2739

CONECT
2738
2737

CONECT
2739
2737
2740

CONECT
2740
2739
2741
2742

CONECT
2741
2740

CONECT
2742
2740
2743

CONECT
2743
2733
2736
2742

CONECT
2744
2745
2746
2747
2748

CONECT
2744
2749
2750

CONECT
2745
2744

CONECT
2746
2744

CONECT
2747
2744

CONECT
2748
2744

CONECT
2749
2744

CONECT
2750
2744

CONECT
2751
2752
2753
2754
2755

CONECT
2751
2756
2757

CONECT
2752
2751

CONECT
2753
2751

CONECT
2754
2751

CONECT
2755
2751

CONECT
2756
2751

CONECT
2757
2751

CONECT
2758
2759
2760
2761
2762

CONECT
2758
2763
2764

CONECT
2759
2758

CONECT
2760
2758

CONECT
2761
2758

CONECT
2762
2758

CONECT
2763
2758

CONECT
2764
2758

CONECT
2765
2766
2767
2768
2769

CONECT
2765
2770
2771

CONECT
2766
2765

CONECT
2767
2765

CONECT
2768
2765

CONECT
2769
2765

CONECT
2770
2765

CONECT
2771
2765

CONECT
2772
2773
2774
2775
2776

CONECT
2772
2777
2778

CONECT
2773
2772

CONECT
2774
2772

CONECT
2775
2772

CONECT
2776
2772

CONECT
2777
2772

CONECT
2778
2772

CONECT
2779
2780
2781
2782
2783

CONECT
2779
2784
2785

CONECT
2780
2779

CONECT
2781
2779

CONECT
2782
2779

CONECT
2783
2779

CONECT
2784
2779

CONECT
2785
2779

CONECT
2786
2787
2788
2789
2790

CONECT
2786
2791
2792

CONECT
2787
2786

CONECT
2788
2786

CONECT
2789
2786

CONECT
2790
2786

CONECT
2791
2786

CONECT
2792
2786

CONECT
2793
2794
2795
2796
2797

CONECT
2793
2798
2799

CONECT
2794
2793

CONECT
2795
2793

CONECT
2796
2793

CONECT
2797
2793

CONECT
2798
2793

CONECT
2799
2793

CONECT
2800
2801
2802
2803
2804

CONECT
2800
2805
2806

CONECT
2801
2800

CONECT
2802
2800

CONECT
2803
2800

CONECT
2804
2800

CONECT
2805
2800

CONECT
2806
2800

MASTER

383
0
13
3
6
0
23
6
2898
2
151
16

END

It is understood that the disclosed method and compositions are not limited to the particular methodology, protocols, and reagents described as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.

It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a riboswitch” includes a plurality of such riboswitches, reference to “the riboswitch” is a reference to one or more riboswitches and equivalents thereof known to those skilled in the art, and so forth.

“Optional” or “optionally” means that the subsequently described event, circumstance, or material may or may not occur or be present, and that the description includes instances where the event, circumstance, or material occurs or is present and instances where it does not occur or is not present.

Ranges may be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, also specifically contemplated and considered disclosed is the range from the one particular value and/or to the other particular value unless the context specifically indicates otherwise. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another, specifically contemplated embodiment that should be considered disclosed unless the context specifically indicates otherwise. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint unless the context specifically indicates otherwise. Finally, it should be understood that all of the individual values and sub-ranges of values contained within an explicitly disclosed range are also specifically contemplated and should be considered disclosed unless the context specifically indicates otherwise. The foregoing applies regardless of whether in particular cases some or all of these embodiments are explicitly disclosed.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of skill in the art to which the disclosed method and compositions belong. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present method and compositions, the particularly useful methods, devices, and materials are as described. Publications cited herein and the material for which they are cited are hereby specifically incorporated by reference. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such disclosure by virtue of prior invention. No admission is made that any reference constitutes prior art. The discussion of references states what their authors assert, and applicants reserve the right to challenge the accuracy and pertinency of the cited documents. It will be clearly understood that, although a number of publications are referred to herein, such reference does not constitute an admission that any of these documents forms part of the common general knowledge in the art.

Throughout the description and claims of this specification, the word “comprise” and variations of the word, such as “comprising” and “comprises,” means “including but not limited to,” and is not intended to exclude, for example, other additives, components, integers or steps.

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the method and compositions described herein. Such equivalents are intended to be encompassed by the following claims.

REFERENCES

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[2] J. E. Barrick, et al., Proc. Natl. Acad. Sci. USA 2004, 101, 6421-6426.

[3] T. J. McCarthy, M. A. Plog, S. A. Floy, J. A. Jansen, J. K. Soukup, G. A. Soukup, Chem. Biol. 2005, 12, 1221-1226.

[4] S. R. Wilkinson, M. D. Been, RNA 2005, 11, 1788-1794.

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[7] J. A. Jansen, T. J. McCarthy, G. A. Soukup, J. K. Soukup. Nat. Struct. Mol. Biol. 2006 13, 517-523.

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[10] M.-A. Badet-Denisot, L. René, B. Badet, Bull. Soc. Chim. Fr. 1993, 130, 249-255.

[11] S. Milewski, Biochim. Biophys. Acta 2002, 1597, 173-192.

[12] N. Sudarsan, J. K. Wickiser, S, Nakamura, M. S. Ebert, R. R. Breaker, Genes Dev. 2003, 17, 2688-2697.

[13] N. Sudarsan, S. Cohen-Chalamish, S, Nakamura, G. M. Emilsson, R. R. Breaker, Chem. Biol. 2006, 12, 1325-1335.

[14] K. J. Schray, S. J. Benkovic, Acc. Chem. Res. 1978, 11, 136-141.

[17] D. R. Lide, CRC Handbook of Chemistry and Physics, 75th ed., CRC Press, Boca Raton, Fla. 1994, pp. 8-45.

[18] G. Mayer, M. Famulok, Chembiochem 2006, 7, 602-604.

[19] K. F. Blount, I. Puskarz, R. Penchovsky, R. R. Breaker, RNA Biology 2006, (in press).

[20] A. Roth, R. R. Breaker, Proc. Natl. Acad. Sci. USA 1998, 95, 6027-6031.

[21] K. J. Hampel, M. M. Tinsley, Biochemistry 2006, 45, 7861-7871.

[22] J. Lim, W. C. Winkler, S, Nakamura, V. Scott, R. R. Breaker, Angewandte Chem. Int. Ed. 2006, 45, 964-968; Angew Chem. 2006, 118, 978-982.

[23] J. C. Cochrane, S. V. Lipchock, S. A. Strobel, Chem Biol 2007, 14, 97-105.

[24] Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat Rev Micro 7, 263-73 (2009).

[25] Tamayo, R., Pratt, J. T. & Camilli, A. Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu. Rev. Microbiol. 61, 131-48 (2007).

[26] Waters, C. M., Lu, W., Rabinowitz, J. D. & Bassler, B. Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT. Journal of Bacteriology 190, 2527-36 (2008).

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GEMM RIBOSWITCHES, STRUCTURE-BASED COMPOUND DESIGN WITH GEMM RIBOSWITCHES, AND METHODS AND COMPOSITIONS FOR USE OF AND WITH GEMM RIBOSWITCHES

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