1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Tuma, J. Connors, W.H. Stitelman, D.H. Richert, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H15 N3 O4 241.244 n 5'-AMINO-5'-DEOXYTHYMIDINE DNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C13 H11 N O5 261.230 OXOLINIC ACID non-polymer N 1 N N N 2 N N N 3 N C N 4 N C N 5 N O N 6 N N N 7 N C N 8 N O N 9 N C N 10 N C N 11 N C N 12 N C N 13 R C N 14 N O N 15 R C N 16 S C N 17 N O N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N O N 34 N P N 35 N O N 36 N O N 37 N O N 38 N C N 39 R C N 40 N O N 41 S C N 42 N O N 43 N C N 44 R C Y 45 N N Y 46 N C Y 47 N N Y 48 N C Y 49 N C N 50 N N Y 51 N N Y 52 N C Y 53 N N Y 54 N C N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N O N 70 N P N 71 N O N 72 N O N 73 N O N 74 N C N 75 R C N 76 N O N 77 S C N 78 N O N 79 N C N 80 R C N 81 N N N 82 N C N 83 N O N 84 N N N 85 N C N 86 N N N 87 N C N 88 N C N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N O N 104 N P N 105 N O N 106 N O N 107 N O N 108 N C N 109 R C N 110 N O N 111 S C N 112 N O N 113 N C N 114 R C Y 115 N N Y 116 N C Y 117 N N Y 118 N C N 119 N C N 120 N O N 121 N N N 122 N C N 123 N N N 124 N N Y 125 N C N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N C N 141 N O Y 142 N C Y 143 N C Y 144 N N Y 145 N C N 146 N O Y 147 N C Y 148 N C Y 149 N C Y 150 N C Y 151 N C Y 152 N C N 153 N O N 154 N O N 155 N C N 156 N C N 157 N C N 158 N O N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N doub N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N doub N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing Y 57 N sing Y 58 N sing Y 59 N doub N 60 N sing Y 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N doub N 66 N sing N 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N doub N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing Y 130 N sing Y 131 N sing Y 132 N doub N 133 N sing Y 134 N sing N 135 N sing Y 136 N doub N 137 N doub N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing Y 149 N doub Y 150 N sing Y 151 N sing N 152 N sing Y 153 N sing N 154 N sing N 155 N doub Y 156 N sing Y 157 N doub Y 158 N sing Y 159 N sing Y 160 N doub N 161 N sing Y 162 N doub N 163 N sing Y 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing US J.Am.Chem.Soc. JACSAT 0004 0002-7863 124 4236 4246 10.1021/ja0125117 11960452 On the effect of covalently appended quinolones on termini of DNA duplexes. 2002 10.2210/pdb1kse/pdb pdb_00001kse 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 Quinolone-DNA hybrid 1728.254 5'-D(*(5AT)P*GP*CP*GP*CP*A)-3' 2 syn polymer 261.230 OXOLINIC ACID 2 syn non-polymer no yes (5AT)(DG)(DC)(DG)(DC)(DA) TGCGCA A,B polydeoxyribonucleotide n n n n n n -7.550 1 19 A 2 B 5 -2.740 A_DG2:DC5_B 1 -7.786 -1.510 0.378 -0.658 -5.593 1 19 A 3 B 4 -1.682 A_DC3:DG4_B 2 -5.073 -0.157 0.390 -0.184 7.058 1 19 A 4 B 3 -1.487 A_DG4:DC3_B 3 -2.748 0.001 0.439 -0.194 12.265 1 19 A 5 B 2 -1.904 A_DC5:DG2_B 4 -12.002 0.957 -0.004 -0.427 3.159 47.332 A A 2 3 12.647 B B 5 4 3.238 10.060 0.100 0.112 AA_DG2DC3:DG4DC5_BB 1 -5.886 7.399 45.955 -0.673 -0.599 2.924 33.276 A A 3 4 10.548 B B 4 3 2.831 6.009 0.143 0.786 AA_DC3DG4:DC3DG4_BB 2 -0.282 0.495 32.743 0.484 -0.292 3.077 43.925 A A 4 5 18.153 B B 3 2 3.233 13.276 -0.306 0.432 AA_DG4DC5:DG2DC3_BB 3 9.785 -13.379 40.853 -0.684 1.340 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection 1 0 2002-05-08 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2002-01-12 REL OXI OXOLINIC ACID Custom synthesized by the authors sample closest to the average 1 2D NOESY, DQF-COSY, TOCSY 2D NOESY 165 mM Phosphate buffer(KH2PO4/K2HPO4), NaCl at pH 7 (uncorrected for deuterium effect) 7 ambient 283 K Torsion-Angle Molecular Dynamics analyte buffer, salt, D2O D2O analyte buffer, salt, H2O/D2O (85:15) H2O/D2O (85:15) Brunger structure solution CNS 1.0 Brunger refinement CNS 1.0 600 Bruker DPX T 1 2 OXI OXI 0 A T 1 2 OXI OXI 0 B T 1 n 1 5AT 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A A 6 n 6 DA 6 A T 1 n 1 5AT 1 B G 2 n 2 DG 2 B C 3 n 3 DC 3 B G 4 n 4 DG 4 B C 5 n 5 DC 5 B A 6 n 6 DA 6 B author_defined_assembly 2 dimeric A 5AT 1 5'-AMINO-5'-DEOXYTHYMIDINE A 5AT 1 DT B 5AT 1 5'-AMINO-5'-DEOXYTHYMIDINE B 5AT 1 DT 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 Solution Structure of a quinolone-capped DNA duplex 1 N N 1 N N 2 N N 2 N N covale 1.350 none A OXI 0 C C1 OXI 1_555 A 5AT 1 A N5' 5AT 1 1_555 covale 1.607 both A 5AT 1 A O3' 5AT 1 1_555 A DG 2 A P DG 2 1_555 covale 1.357 none B OXI 0 D C1 OXI 1_555 B 5AT 1 B N5' 5AT 1 1_555 covale 1.611 both B 5AT 1 B O3' 5AT 1 1_555 B DG 2 B P DG 2 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 5 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 5 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 5 B N4 DC 5 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 3 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 3 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 3 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 2 B N2 DG 2 1_555 DNA DNA, quinolone, Synthetic hybrid, disrupted terminal basepairs 1KSE PDB 1 1KSE 1 6 1KSE 1 6 1KSE A 1 1 6 1 6 1KSE 1 6 1KSE B 1 1 6 BINDING SITE FOR RESIDUE OXI A 0 A OXI 0 Software 4 BINDING SITE FOR RESIDUE OXI B 0 B OXI 0 Software 4 A 5AT 1 A 5AT 1 4 1_555 A DG 2 A DG 2 4 1_555 B DC 5 B DC 5 4 1_555 B DA 6 B DA 6 4 1_555 A DC 5 A DC 5 4 1_555 A DA 6 A DA 6 4 1_555 B 5AT 1 B 5AT 1 4 1_555 B DG 2 B DG 2 4 1_555