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"origin": [ 30.267, 32.841, -0.213 ], "x_axis": [ 0.739, 0.638, -0.215 ], "y_axis": [ 0.191, -0.504, -0.842 ], "z_axis": [ -0.646, 0.581, -0.494 ], "quaternion": [ -0.430, 0.827, 0.251, -0.260 ] } }, { "index": 6, "index_chain": 6, "chain_name": "A", "nt_resnum": 6, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/6", "linked_nts": [ "///A/5", "///A/7" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,ss-non-loop", "alpha": -73.141, "beta": 172.780, "gamma": 53.244, "delta": 78.643, "epsilon": -158.559, "zeta": -77.093, "epsilon_zeta": -81.466, "bb_type": "BI", "chi": -158.791, "glyco_bond": "anti", "C5prime_xyz": [ -1.559, 8.813, 0.480 ], "P_xyz": [ 1.027, 9.275, 0.646 ], "form": "A", "ssZp": 4.352, "Dp": 4.585, "splay_angle": 21.305, "splay_distance": 3.340, "splay_ratio": 0.186, "d22": null, "d64": null, "eta": 158.669, "theta": -154.542, "eta_prime": 178.679, "theta_prime": -151.238, "eta_base": -129.349, "theta_base": -132.128, "v0": 3.775, "v1": -30.768, "v2": 44.050, "v3": -43.858, "v4": 25.124, "amplitude": 45.449, "phase_angle": 14.253, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.721, "filter_rmsd": 0.062, "frame": { "rmsd": 0.010, "origin": [ 29.031, 36.030, -1.099 ], "x_axis": [ 0.712, 0.175, -0.680 ], "y_axis": [ -0.357, -0.744, -0.565 ], "z_axis": [ -0.604, 0.645, -0.467 ], "quaternion": [ -0.354, 0.855, -0.053, -0.376 ] } }, { "index": 7, "index_chain": 7, "chain_name": "A", "nt_resnum": 7, "nt_name": "DA", "nt_code": "A", "nt_id": "///A/7", "linked_nts": [ "///A/6", "///A/8" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,ss-non-loop", "alpha": -62.473, "beta": -178.863, "gamma": 49.729, "delta": 86.421, "epsilon": -155.425, "zeta": -67.412, "epsilon_zeta": -88.013, "bb_type": "BI", "chi": -149.353, "glyco_bond": "anti", "C5prime_xyz": [ -1.358, 8.766, -0.086 ], "P_xyz": [ 1.218, 9.054, 0.442 ], "form": "A", "ssZp": 3.838, "Dp": 4.311, "splay_angle": 18.529, "splay_distance": 3.044, "splay_ratio": 0.161, "d22": null, "d64": null, "eta": 176.824, "theta": -140.636, "eta_prime": -173.620, "theta_prime": -135.429, "eta_base": -147.414, "theta_base": -118.326, "v0": 2.179, "v1": -23.544, "v2": 35.578, "v3": -35.088, "v4": 20.491, "amplitude": 36.876, "phase_angle": 15.252, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "33p", "cluster": "1a", "suiteness": 0.841, "filter_rmsd": 0.038, "frame": { "rmsd": 0.012, "origin": [ 27.868, 39.035, -1.980 ], "x_axis": [ 0.565, -0.371, -0.737 ], "y_axis": [ -0.726, -0.648, -0.230 ], "z_axis": [ -0.392, 0.665, -0.636 ], "quaternion": [ -0.265, 0.844, -0.325, -0.334 ] } }, { "index": 8, "index_chain": 8, "chain_name": "A", "nt_resnum": 8, "nt_name": "DC", "nt_code": "C", "nt_id": "///A/8", "linked_nts": [ "///A/7", null ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,non-pair-contact,ss-non-loop", "alpha": -70.974, "beta": 174.704, "gamma": 65.914, "delta": 135.723, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -121.417, "glyco_bond": "anti", "C5prime_xyz": [ -2.110, 8.662, -1.131 ], "P_xyz": [ 0.352, 9.418, -1.247 ], "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": -22.301, "v1": 30.432, "v2": -26.156, "v3": 14.330, "v4": 4.868, "amplitude": 29.695, "phase_angle": 151.741, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "32p", "cluster": "1b", "suiteness": 0.658, "filter_rmsd": 0.067, "frame": { "rmsd": 0.009, "origin": [ 27.577, 41.256, -4.040 ], "x_axis": [ 0.259, -0.747, -0.612 ], "y_axis": [ -0.958, -0.278, -0.066 ], "z_axis": [ -0.121, 0.604, -0.788 ], "quaternion": [ -0.220, 0.762, -0.559, -0.240 ] } } ], "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": "3kq8", "num_naChains": 1, "naChains": "A=8", "num_atoms": 199, "num_waters": 36, "num_metals": 1, "metals_desc": "Mg=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": 9, "auxfiles": [ { "index": 1, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 2, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 3, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 4, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 5, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 6, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 7, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 8, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 9, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }