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A.277 A.167 A.276] 3 1", "num_nts": 5, "nts_short": "GAGUU", "nts_long": "///A/165,///A/166,///A/167,///A/276,///A/277", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///A/166" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 4, 5 ], "summary": "[2] 1 0 [A.173 A.271 A.175 A.270] 3 2", "num_nts": 5, "nts_short": "CGUAG", "nts_long": "///A/173,///A/174,///A/175,///A/270,///A/271", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///A/174" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] } ], "num_iloops": 8, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 5, -2 ], "summary": "[2] 1 1 [A.176 A.269 A.178 A.267] 2 1", "num_nts": 6, "nts_short": "CUAUGG", "nts_long": "///A/176,///A/177,///A/178,///A/267,///A/268,///A/269", "num_stems": 2, 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{ "index": 107, "atom1_serNum": 2196, "atom2_serNum": 2393, "donAcc_type": "standard", "distance": 2.919, "atom1_id": "///A/253/N6", "atom2_id": "///A/262/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 108, "atom1_serNum": 2197, "atom2_serNum": 2391, "donAcc_type": "standard", "distance": 3.121, "atom1_id": "///A/253/N1", "atom2_id": "///A/262/N3", "atom_pair": "N:N", "residue_pair": "nt:nt" }, { "index": 109, "atom1_serNum": 2215, "atom2_serNum": 2371, "donAcc_type": "standard", "distance": 3.552, "atom1_id": "///A/254/O2", "atom2_id": "///A/261/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 110, "atom1_serNum": 2218, "atom2_serNum": 2393, "donAcc_type": "standard", "distance": 3.897, "atom1_id": "///A/254/N4", "atom2_id": "///A/262/O4", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 111, "atom1_serNum": 2235, "atom2_serNum": 2347, "donAcc_type": "questionable", "distance": 2.980, "atom1_id": "///A/255/O2", "atom2_id": "///A/260/O6", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 112, "atom1_serNum": 2251, "atom2_serNum": 2300, "donAcc_type": "acceptable", "distance": 3.928, "atom1_id": "///A/256/O2'", "atom2_id": "///A/258/N7", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 113, "atom1_serNum": 2261, "atom2_serNum": 2310, "donAcc_type": "standard", "distance": 2.445, "atom1_id": "///A/256/N2", "atom2_id": "///A/259/OP2", "atom_pair": "N:O", "residue_pair": "nt:nt" }, { "index": 114, "atom1_serNum": 2473, "atom2_serNum": 2491, "donAcc_type": "acceptable", "distance": 3.299, "atom1_id": "///A/266/O2'", "atom2_id": "///A/267/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 115, "atom1_serNum": 2814, "atom2_serNum": 2830, "donAcc_type": "acceptable", "distance": 3.264, "atom1_id": "///A/282/O2'", "atom2_id": "///A/283/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 116, "atom1_serNum": 2834, "atom2_serNum": 2850, "donAcc_type": "acceptable", "distance": 3.066, "atom1_id": "///A/283/O2'", "atom2_id": "///A/284/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 117, "atom1_serNum": 2854, "atom2_serNum": 2873, "donAcc_type": "acceptable", "distance": 3.008, "atom1_id": "///A/284/O2'", "atom2_id": "///A/285/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 118, "atom1_serNum": 2884, "atom2_serNum": 2945, "donAcc_type": "standard", "distance": 3.431, "atom1_id": "///A/285/O6", "atom2_id": "///A/288/N3", "atom_pair": "O:N", "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": "8qo5", "num_naChains": 1, "naChains": "A=145", "num_atoms": 3078, "num_waters": 0, "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": 19, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-bulges.pdb", "desc": "an ensemble of bulges" }, { "index": 7, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 8, "name": "dssr-junctions.pdb", "desc": "an ensemble of junctions (multi-branch)" }, { "index": 9, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 10, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 11, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 12, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 13, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 14, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 15, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 16, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 17, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 18, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 19, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }