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7, "chain_name": "B", "nt_resnum": 14, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/14", "linked_nts": [ "///B/13", null ], "nt_type": "DNA", "dbn": ")", "summary": "syn,~C2'-endo,non-stack,canonical,helix-end,stem-end,cap-acceptor", "alpha": 80.948, "beta": -177.904, "gamma": -173.016, "delta": 144.893, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": 72.662, "glyco_bond": "syn", "C5prime_xyz": [ -4.998, 4.257, 2.171 ], "P_xyz": [ -5.178, 2.997, 4.483 ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -24.305, "v1": 37.549, "v2": -35.975, "v3": 22.859, "v4": 0.710, "amplitude": 38.219, "phase_angle": 160.272, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.021, "frame": { "rmsd": 0.021, "origin": [ 8.286, 15.661, 4.177 ], "x_axis": [ 0.923, -0.385, 0.002 ], "y_axis": [ 0.385, 0.923, 0.008 ], "z_axis": [ -0.005, -0.006, 1.000 ], "quaternion": [ 0.980, 0.004, -0.002, -0.197 ] } } ], "num_hbonds": 24, "hbonds": [ { "index": 1, "atom1_serNum": 22, "atom2_serNum": 283, "donAcc_type": "standard", "distance": 3.077, "atom1_id": "///A/2/N3", "atom2_id": "///B/14/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 2, "atom1_serNum": 27, "atom2_serNum": 285, "donAcc_type": "standard", "distance": 3.059, "atom1_id": "///A/2/O2", "atom2_id": "///B/14/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 3, "atom1_serNum": 28, "atom2_serNum": 282, "donAcc_type": "standard", "distance": 2.936, "atom1_id": "///A/2/N4", "atom2_id": "///B/14/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 4, "atom1_serNum": 56, "atom2_serNum": 263, "donAcc_type": "standard", "distance": 2.711, "atom1_id": "///A/3/O6", "atom2_id": "///B/13/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 5, "atom1_serNum": 57, "atom2_serNum": 261, "donAcc_type": "standard", "distance": 2.899, "atom1_id": "///A/3/N1", "atom2_id": "///B/13/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 6, "atom1_serNum": 59, "atom2_serNum": 260, "donAcc_type": "standard", "distance": 2.875, "atom1_id": "///A/3/N2", "atom2_id": "///B/13/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 7, "atom1_serNum": 63, "atom2_serNum": 291, "donAcc_type": "standard", "distance": 2.791, "atom1_id": "///A/4/OP1", "atom2_id": "///A/15/N1", "atom_pair": "O:N", "residue_pair": "nt:ligand" }, { "index": 8, "atom1_serNum": 63, "atom2_serNum": 292, "donAcc_type": "standard", "distance": 2.706, "atom1_id": "///A/4/OP1", "atom2_id": "///A/15/N2", "atom_pair": "O:N", "residue_pair": "nt:ligand" }, { "index": 9, "atom1_serNum": 75, "atom2_serNum": 244, "donAcc_type": "standard", "distance": 2.890, "atom1_id": "///A/4/O2", "atom2_id": "///B/12/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 10, "atom1_serNum": 76, "atom2_serNum": 242, "donAcc_type": "standard", "distance": 2.943, "atom1_id": "///A/4/N3", "atom2_id": "///B/12/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 11, "atom1_serNum": 78, "atom2_serNum": 241, "donAcc_type": "standard", "distance": 2.842, "atom1_id": "///A/4/N4", "atom2_id": "///B/12/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 12, "atom1_serNum": 94, "atom2_serNum": 292, "donAcc_type": "standard", "distance": 3.038, "atom1_id": "///A/5/N7", "atom2_id": "///A/15/N2", "atom_pair": "N:N", "residue_pair": "nt:ligand" }, { "index": 13, "atom1_serNum": 94, "atom2_serNum": 296, "donAcc_type": "standard", "distance": 3.246, "atom1_id": "///A/5/N7", "atom2_id": "///A/15/N6", "atom_pair": "N:N", "residue_pair": "nt:ligand" }, { "index": 14, "atom1_serNum": 97, "atom2_serNum": 222, "donAcc_type": "standard", "distance": 2.881, "atom1_id": "///A/5/O6", "atom2_id": "///B/11/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 15, "atom1_serNum": 97, "atom2_serNum": 291, "donAcc_type": "standard", "distance": 2.856, "atom1_id": "///A/5/O6", "atom2_id": "///A/15/N1", "atom_pair": "O:N", "residue_pair": "nt:ligand" }, { "index": 16, "atom1_serNum": 97, "atom2_serNum": 296, "donAcc_type": "standard", "distance": 3.208, "atom1_id": "///A/5/O6", "atom2_id": "///A/15/N6", "atom_pair": "O:N", "residue_pair": "nt:ligand" }, { "index": 17, "atom1_serNum": 98, "atom2_serNum": 220, "donAcc_type": "standard", "distance": 2.950, "atom1_id": "///A/5/N1", "atom2_id": "///B/11/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 18, "atom1_serNum": 100, "atom2_serNum": 219, "donAcc_type": "standard", "distance": 2.810, "atom1_id": "///A/5/N2", "atom2_id": "///B/11/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 19, "atom1_serNum": 116, "atom2_serNum": 203, "donAcc_type": "standard", "distance": 2.894, "atom1_id": "///A/6/O2", "atom2_id": "///B/10/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 20, "atom1_serNum": 117, "atom2_serNum": 201, "donAcc_type": "standard", "distance": 2.917, "atom1_id": "///A/6/N3", "atom2_id": "///B/10/N1", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 21, "atom1_serNum": 119, "atom2_serNum": 200, "donAcc_type": "standard", "distance": 2.825, "atom1_id": "///A/6/N4", "atom2_id": "///B/10/O6", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 22, "atom1_serNum": 138, "atom2_serNum": 172, "donAcc_type": "standard", "distance": 2.798, "atom1_id": "///A/7/O6", "atom2_id": "///B/9/N4", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 23, "atom1_serNum": 139, "atom2_serNum": 166, "donAcc_type": "standard", "distance": 2.891, "atom1_id": "///A/7/N1", "atom2_id": "///B/9/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 24, "atom1_serNum": 141, "atom2_serNum": 171, "donAcc_type": "standard", "distance": 2.740, "atom1_id": "///A/7/N2", "atom2_id": "///B/9/O2", "atom_pair": "N:O", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "313d", "num_naChains": 2, "naChains": "A=7,B=7", "num_atoms": 349, "num_waters": 55, "num_metals": 2, "metals_desc": "Mg=1,Co=1", "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 14, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 3, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 4, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 5, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 6, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 7, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 8, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 9, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 10, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 11, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 12, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 13, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 14, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }