1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Giri, I. Jenkins, M.D. Schnetz-Boutaud, N.C. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C17 H14 O7 330.289 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 non-polymer 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking N 1 N C N 2 R C N 3 N O N 4 R C Y 5 N C N 6 N O N 7 R C N 8 N O Y 9 N C Y 10 N C Y 11 N C N 12 N O N 13 N C Y 14 N C Y 15 N C Y 16 N O Y 17 N C N 18 N O Y 19 N C Y 20 N C N 21 N C N 22 N C N 23 N C N 24 N O 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 H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 N C N 50 R C Y 51 N N Y 52 N C Y 53 N N Y 54 N C Y 55 N C N 56 N N Y 57 N N Y 58 N C Y 59 N N Y 60 N C 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 H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 N C N 86 R C N 87 N N N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N C N 94 N C 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 H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C Y 121 N N Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N N Y 131 N C 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 H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N O N 147 N P N 148 N O N 149 N O N 150 N O N 151 N C N 152 R C N 153 N O N 154 S C N 155 N O N 156 N C N 157 R C N 158 N N N 159 N C N 160 N O N 161 N N N 162 N C N 163 N O N 164 N C N 165 N C N 166 N C N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 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 sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing Y 12 N doub Y 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing Y 18 N sing Y 19 N doub N 20 N sing N 21 N sing Y 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing Y 27 N doub Y 28 N sing Y 29 N sing Y 30 N sing N 31 N doub Y 32 N sing Y 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N doub 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 N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing Y 66 N sing Y 67 N sing Y 68 N doub N 69 N sing Y 70 N sing Y 71 N sing Y 72 N doub N 73 N sing Y 74 N doub N 75 N sing N 76 N sing Y 77 N sing Y 78 N doub N 79 N sing Y 80 N sing N 81 N sing N 82 N sing N 83 N doub 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 sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub 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 N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing Y 139 N sing Y 140 N sing Y 141 N doub N 142 N sing Y 143 N sing N 144 N sing Y 145 N doub N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N doub N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 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 N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing US Chem.Res.Toxicol. CRTOEC 2140 0893-228X 15 638 647 10.1021/tx010187n 12018984 Structural refinement of the 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct in a 5'-Cp(AFB)G-3' sequence. 2002 10.2210/pdb1mkl/pdb pdb_00001mkl 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 3003.993 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3' 1 syn polymer 3084.041 5'-D(*AP*GP*AP*TP*CP*GP*AP*TP*GP*T)-3' 1 syn polymer 330.289 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 1 syn non-polymer no no (DA)(DC)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DT) ACATCGATCT A polydeoxyribonucleotide no no (DA)(DG)(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT) AGATCGATGT B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n 13.670 1 20 A 1 B 20 -3.303 A_DA1:DT20_B 1 -8.396 0.221 -0.070 0.173 9.156 1 19 A 2 B 19 -0.818 A_DC2:DG19_B 2 -13.718 0.175 -0.344 -0.158 -4.112 1 20 A 3 B 18 0.159 A_DA3:DT18_B 3 11.597 0.144 0.165 -0.025 19.876 1 20 A 4 B 17 -2.894 A_DT4:DA17_B 4 8.578 -0.567 -0.074 0.093 13.795 1 19 A 5 B 16 1.392 A_DC5:DG16_B 5 -0.113 0.322 0.013 -0.068 -26.692 1 19 A 6 B 15 -4.198 A_DG6:DC15_B 6 -8.655 -0.211 0.003 -0.022 -6.472 1 20 A 7 B 14 -4.933 A_DA7:DT14_B 7 -6.126 0.473 0.218 0.029 -9.857 1 20 A 8 B 13 -6.875 A_DT8:DA13_B 8 -1.276 -0.081 0.308 -0.052 -7.165 1 19 A 9 B 12 -1.363 A_DC9:DG12_B 9 10.383 -0.030 0.033 -0.113 -10.989 1 20 A 10 B 11 0.369 A_DT10:DA11_B 10 1.193 0.021 0.533 -0.138 3.675 31.638 A A 1 2 -10.539 B B 20 19 3.550 -5.714 -0.263 -1.095 AA_DA1DC2:DG19DT20_BB 1 1.231 -2.271 31.107 -0.832 0.736 3.337 41.896 A A 2 3 15.255 B B 19 18 3.541 10.755 -0.579 -0.570 AA_DC2DA3:DT18DG19_BB 2 -6.471 9.179 40.053 -2.007 0.083 2.797 19.133 A A 3 4 11.041 B B 18 17 2.981 3.646 0.061 -0.686 AA_DA3DT4:DA17DT18_BB 3 1.066 -3.228 18.756 -3.722 0.301 3.463 33.100 A A 4 5 9.108 B B 17 16 3.583 5.166 0.029 -0.474 AA_DT4DC5:DG16DA17_BB 4 -1.830 3.226 32.656 -1.777 -0.386 6.115 27.669 A A 5 6 31.394 B B 16 15 7.410 14.274 0.486 -0.517 AA_DC5DG6:DC15DG16_BB 5 3.293 -7.243 23.538 -8.843 0.774 2.994 30.154 A A 6 7 -5.033 B B 15 14 2.861 -2.613 -1.106 -0.875 AA_DG6DA7:DT14DC15_BB 6 -2.129 4.100 29.969 -1.203 1.737 3.496 28.444 A A 7 8 -1.763 B B 14 13 3.466 -0.866 -0.049 -1.225 AA_DA7DT8:DA13DT14_BB 7 1.226 -2.497 28.405 -2.281 0.398 3.571 36.986 A A 8 9 4.559 B B 13 12 3.671 2.889 0.620 -0.733 AA_DT8DC9:DG12DA13_BB 8 -1.846 2.914 36.832 -1.586 -1.253 3.583 26.067 A A 9 10 8.762 B B 12 11 3.719 3.937 0.248 -0.680 AA_DC9DT10:DA11DG12_BB 9 0.885 -1.971 25.758 -2.716 -0.278 atom_site chem_comp entity entity_poly entity_poly_seq ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_entity_nonpoly pdbx_entity_src_syn pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_mod_residue pdbx_struct_oper_list pdbx_validate_planes struct_asym struct_conn struct_ref chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software struct_conn repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations Non-polymer description Polymer sequence Source and taxonomy Structure summary Data collection Database references Derived calculations 1 0 2002-10-16 1 1 2008-04-28 1 2 2011-07-13 2 0 2019-01-30 2 1 2024-05-01 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.group_PDB _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly_seq.mon_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.step_name _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _struct_ref.pdbx_align_begin _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE RCSB Y RCSB 2002-08-29 REL REL AFN 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 32630 synthetic construct sample 1 10 32630 synthetic construct sample 1 10 1 2D NOESY DQF-COSY 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.2, in 99.999% D2O 7.2 1 atm 283 K 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2, in 9:1 H2O:D2O 7.2 1 atm 283 K The structures are based on 341 distance retraints, 38 empirical H-bond restraints, 17 sugar pucker restraints, and 89 empirical torsion angle restraints Data was processed using felix 97. The NOE intensities were converted to distance using RANMARDI module of MARDIGRAS. Starting structures were built using InsightII. XPLOR was used for structural refinement. Final averaged structure was solvated using AMBER. And MD simulated annealing was performed in presence of counter ions using SANDER protocol. The back calculations were performed using CORMA. 1 simulated annealing structure, calculaed starting from energy minmized averaged structure from 20 final structures. the enrgy minimized structure was solvated, and md simulation annealing was performed in presence of counter ions 99.999% D2O 90% H2O/10% D2O Bruker collection XwinNMR 3.0 Accelrys Inc. processing Felix 97 Borgias, B. A., and James, T. L. (1990) MARDIGRAS- -a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. Magn. Reson. 87, 475-487 data analysis MARDIGRAS 5.2 A.T.Brunger refinement X-PLOR 3.851 Keepers, J. W., and James, T. L. (1984)J. Magn. Reson. 87, 475-487. iterative matrix relaxation CORMA 5.2 Case, D. A., and Pearlman C. A., et al. (1999) Amber 6.0, University of California, San Francisco, CA. structure solution Amber 6.0 500 Bruker DRX 600 Bruker DRX X 6 3 AFN AFN 11 A A 1 n 1 DA 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A X 6 n 6 DG 6 A A 7 n 7 DA 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A A 11 n 1 DA 11 B G 12 n 2 DG 12 B A 13 n 3 DA 13 B T 14 n 4 DT 14 B C 15 n 5 DC 15 B G 16 n 6 DG 16 B A 17 n 7 DA 17 B T 18 n 8 DT 18 B G 19 n 9 DG 19 B T 20 n 10 DT 20 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DG 6 0.154 SIDE CHAIN 1 A DC 9 0.056 SIDE CHAIN 1 B DG 12 0.101 SIDE CHAIN 1 B DA 13 0.097 SIDE CHAIN 1 B DG 19 0.068 SIDE CHAIN 1 3.18 0.50 117.70 120.88 A A A C5 C6 N1 DA DA DA 1 1 1 N 1 -4.36 0.60 118.60 114.24 A A A N1 C6 N6 DA DA DA 1 1 1 N 1 3.46 0.30 108.30 111.76 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 -4.64 0.70 121.90 117.26 A A A N3 C2 O2 DC DC DC 2 2 2 N 1 -4.00 0.60 118.60 114.60 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 4.52 0.30 108.30 112.82 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 -4.10 0.60 122.90 118.80 A A A C6 C5 C7 DT DT DT 4 4 4 N 1 2.87 0.30 108.30 111.17 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.37 0.50 117.70 121.07 A A A C5 C6 N1 DA DA DA 7 7 7 N 1 -4.51 0.60 118.60 114.09 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 -3.74 0.60 122.90 119.16 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 -4.40 0.70 121.90 117.50 A A A N3 C2 O2 DC DC DC 9 9 9 N 1 2.37 0.30 108.30 110.67 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 -5.07 0.60 122.90 117.83 A A A C6 C5 C7 DT DT DT 10 10 10 N 1 -3.01 0.50 117.00 113.99 B B B C4 C5 C6 DA DA DA 11 11 11 N 1 -3.92 0.60 118.60 114.68 B B B N1 C6 N6 DA DA DA 11 11 11 N 1 3.66 0.30 108.30 111.96 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 3.36 0.50 117.70 121.06 B B B C5 C6 N1 DA DA DA 13 13 13 N 1 2.31 0.30 108.30 110.61 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 -4.18 0.60 122.90 118.72 B B B C6 C5 C7 DT DT DT 14 14 14 N 1 3.11 0.30 108.30 111.41 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 3.67 0.60 118.90 122.57 B B B N1 C2 O2 DC DC DC 15 15 15 N 1 -4.60 0.70 121.90 117.30 B B B N3 C2 O2 DC DC DC 15 15 15 N 1 -4.27 0.60 119.90 115.63 B B B N1 C6 O6 DG DG DG 16 16 16 N 1 -4.87 0.60 118.60 113.73 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 1.83 0.30 108.30 110.13 B B B O4' C1' N1 DT DT DT 18 18 18 N 1 -3.80 0.60 122.90 119.10 B B B C6 C5 C7 DT DT DT 18 18 18 N 1 5.38 0.30 108.30 113.68 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 -5.56 0.60 122.90 117.34 B B B C6 C5 C7 DT DT DT 20 20 20 N NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE 1 N N 2 N N 3 N N covale 1.502 none sing A DG 6 A N7 DG 6 1_555 A AFN 11 C C8A AFN 1_555 hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 20 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 20 B O4 DT 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 19 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 19 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 19 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 18 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 18 B O4 DT 8 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 17 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 17 B N6 DA 7 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 16 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 16 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 16 B N2 DG 6 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 15 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 15 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 15 B N4 DC 5 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 14 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 14 B O4 DT 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 13 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 13 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 12 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 12 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 12 B N2 DG 2 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 11 B N1 DA 1 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 11 B N6 DA 1 1_555 DNA Structure of the 8, 9-Dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B1 Adduct in a 5'-CpAFBG-3' Sequence context, DNA 1MKL PDB 1 1 1MKL 1MKL PDB 2 1 1MKL 1 10 1MKL 1 10 1MKL A 1 1 10 11 20 1MKL 11 20 1MKL B 2 1 10