1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Mao, H. Deng, Z. Wang, F. Harris, T.M. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C27 H28 N5 O15 P 693.509 [1',2'-DIDEOXY[2-AMINO-5-([9-HYDROXY-AFLATOXINB2-8-YL]-FORMYL-AMINO)-6-OXO-1,6-IHYDRO-PYRIMIDIN-4-YLAMINO]-RIBOFURANOSE]-5-MONOPHOSPHATE GROUP DNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C 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 H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 H N 141 N H N 142 N H N 143 N H N 144 N C N 145 N C N 146 N C N 147 N C N 148 N O N 149 N P N 150 N O N 151 N O N 152 N O N 153 N C N 154 R C N 155 N O N 156 R C N 157 N N N 158 N C N 159 N N N 160 N C N 161 N N N 162 N N N 163 N C N 164 N O N 165 N C N 166 N N N 167 N C N 168 N O N 169 N C N 170 S C N 171 N O N 172 R C N 173 R C N 174 N O N 175 R C Y 176 N C N 177 N O N 178 S C N 179 N O Y 180 N C Y 181 N C Y 182 N C N 183 N O N 184 N C Y 185 N C Y 186 N C N 187 N O N 188 N C N 189 N O N 190 N C N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N O N 219 N H N 1 N sing N 2 N sing N 3 N doub 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 N 12 N sing N 13 N sing 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 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 doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub 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 doub 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 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 doub 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 doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N doub N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N doub N 160 N sing N 161 N doub 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 doub N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing 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 N 192 N doub N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing Y 210 N doub Y 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing Y 216 N sing Y 217 N doub N 218 N sing N 219 N sing Y 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing Y 225 N doub N 226 N sing N 227 N sing N 228 N doub N 229 N sing N 230 N sing N 231 N sing US Biochemistry BICHAW 0033 0006-2960 37 4374 4387 10.1021/bi9718292 9521757 An intercalated and thermally stable FAPY adduct of aflatoxin B1 in a DNA duplex: structural refinement from 1H NMR. 1998 10.2210/pdb1hm1/pdb pdb_00001hm1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 CHAIN A, GUA 5 -> FAG, FAPY ADDUCT OF 3365.292 DNA (5'-D(*CP*TP*AP*TP*(FAG)P*AP*TP*TP*CP*A)-3') 1 syn polymer 3068.042 DNA (5'-D(TP*GP*AP*AP*TP*CP*AP*TP*AP*G)-3') 1 syn polymer no yes (DC)(DT)(DA)(DT)(FAG)(DA)(DT)(DT)(DC)(DA) CTATNATTCA A polydeoxyribonucleotide no no (DT)(DG)(DA)(DA)(DT)(DC)(DA)(DT)(DA)(DG) TGAATCATAG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n -2.415 1 19 A 1 B 20 -2.206 A_DC1:DG20_B 1 -1.972 0.283 -0.058 -0.207 10.507 1 20 A 2 B 19 1.980 A_DT2:DA19_B 2 -12.803 0.213 -0.091 -0.119 34.127 1 20 A 3 B 18 0.238 A_DA3:DT18_B 3 1.165 0.035 0.240 -0.111 27.814 1 20 A 4 B 17 11.670 A_DT4:DA17_B 4 10.063 0.243 -0.391 0.051 7.291 1 20 A 6 B 15 -2.178 A_DA6:DT15_B 5 2.141 -0.095 0.570 -0.104 -11.030 1 20 A 7 B 14 -3.080 A_DT7:DA14_B 6 -10.858 -0.373 0.153 -0.087 -18.463 1 20 A 8 B 13 -1.582 A_DT8:DA13_B 7 -5.215 0.016 0.189 -0.180 -7.679 1 19 A 9 B 12 -0.200 A_DC9:DG12_B 8 2.457 0.503 0.020 -0.193 20.119 1 20 A 10 B 11 1.254 A_DA10:DT11_B 9 3.305 0.069 0.295 -0.042 3.033 33.096 A A 1 2 15.403 B B 20 19 3.064 8.662 0.285 0.227 AA_DC1DT2:DA19DG20_BB 1 3.403 -6.050 31.795 -0.993 0.046 2.785 41.233 A A 2 3 -7.371 B B 19 18 2.985 -5.171 0.429 1.055 AA_DT2DA3:DT18DA19_BB 2 -3.907 5.569 40.742 1.993 -0.983 4.152 32.373 A A 3 4 11.896 B B 18 17 4.227 6.581 0.741 -0.190 AA_DA3DT4:DA17DT18_BB 3 2.745 -4.961 31.599 -1.846 -0.701 4.476 35.038 A A 6 7 -10.551 B B 15 14 4.403 -6.319 0.275 -0.782 AA_DA6DT7:DA14DT15_BB 4 0.610 -1.018 34.476 0.000 -0.331 3.535 37.059 A A 7 8 -1.519 B B 14 13 3.517 -0.965 -0.063 -0.777 AA_DT7DT8:DA13DA14_BB 5 -0.183 0.288 37.047 -1.083 0.072 3.318 36.450 A A 8 9 6.663 B B 13 12 3.298 4.155 -0.097 0.384 AA_DT8DC9:DG12DA13_BB 6 -2.828 4.535 36.113 0.029 -0.243 2.161 30.150 A A 9 10 23.634 B B 12 11 2.479 11.965 0.176 -0.286 AA_DC9DA10:DT11DG12_BB 7 -1.397 2.759 27.690 -2.358 -0.549 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other Data collection 1 0 1998-10-14 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id Y BNL 1998-05-11 REL REL MINIMIZED AVERAGE 1 1 NOESY TOCSY DQF-COSY 6.80 1 atm 298.00 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING 0.1 M NACL,10 MM NAH2PO4, 0.05 MM NA2(EDTA) BRUNGER refinement X-PLOR 2.4 structure solution Felix structure solution Insight II structure solution X-PLOR 750 Bruker DMX750 C 1 n 1 DC 1 A T 2 n 2 DT 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A FAG 5 n 5 FAG 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A A 10 n 10 DA 10 A T 11 n 1 DT 11 B G 12 n 2 DG 12 B A 13 n 3 DA 13 B A 14 n 4 DA 14 B T 15 n 5 DT 15 B C 16 n 6 DC 16 B A 17 n 7 DA 17 B T 18 n 8 DT 18 B A 19 n 9 DA 19 B G 20 n 10 DG 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 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DT 4 0.079 SIDE CHAIN 1 4.12 0.30 108.30 112.42 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.32 0.30 108.30 111.62 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 -4.99 0.60 122.90 117.91 A A A C6 C5 C7 DT DT DT 2 2 2 N 1 3.49 0.30 108.30 111.79 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 3.76 0.50 113.80 117.56 A A A N7 C8 N9 DA DA DA 3 3 3 N 1 -2.47 0.40 105.80 103.33 A A A C8 N9 C4 DA DA DA 3 3 3 N 1 -4.30 0.60 122.90 118.60 A A A C6 C5 C7 DT DT DT 4 4 4 N 1 3.36 0.30 108.30 111.66 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 3.61 0.50 113.80 117.41 A A A N7 C8 N9 DA DA DA 6 6 6 N 1 -2.49 0.40 105.80 103.31 A A A C8 N9 C4 DA DA DA 6 6 6 N 1 5.98 0.30 108.30 114.28 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 3.74 0.30 108.30 112.04 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -3.69 0.60 122.90 119.21 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 3.46 0.30 108.30 111.76 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 2.94 0.30 108.30 111.24 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 3.69 0.50 113.80 117.49 A A A N7 C8 N9 DA DA DA 10 10 10 N 1 -2.64 0.40 105.80 103.16 A A A C8 N9 C4 DA DA DA 10 10 10 N 1 3.73 0.30 108.30 112.03 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 4.02 0.30 108.30 112.32 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 4.61 0.50 113.10 117.71 B B B N7 C8 N9 DG DG DG 12 12 12 N 1 -3.27 0.40 106.40 103.13 B B B C8 N9 C4 DG DG DG 12 12 12 N 1 3.81 0.30 108.30 112.11 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 3.71 0.50 113.80 117.51 B B B N7 C8 N9 DA DA DA 13 13 13 N 1 -2.73 0.40 105.80 103.07 B B B C8 N9 C4 DA DA DA 13 13 13 N 1 6.65 0.30 108.30 114.95 B B B O4' C1' N9 DA DA DA 14 14 14 N 1 3.70 0.50 113.80 117.50 B B B N7 C8 N9 DA DA DA 14 14 14 N 1 3.04 0.30 108.30 111.34 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 -4.63 0.60 122.90 118.27 B B B C6 C5 C7 DT DT DT 15 15 15 N 1 4.65 0.30 108.30 112.95 B B B O4' C1' N1 DC DC DC 16 16 16 N 1 3.87 0.30 108.30 112.17 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 3.84 0.50 113.80 117.64 B B B N7 C8 N9 DA DA DA 17 17 17 N 1 -2.41 0.40 105.80 103.39 B B B C8 N9 C4 DA DA DA 17 17 17 N 1 3.38 0.30 108.30 111.68 B B B O4' C1' N1 DT DT DT 18 18 18 N 1 4.16 0.30 108.30 112.46 B B B O4' C1' N9 DA DA DA 19 19 19 N 1 4.02 0.50 113.80 117.82 B B B N7 C8 N9 DA DA DA 19 19 19 N 1 -2.62 0.40 105.80 103.18 B B B C8 N9 C4 DA DA DA 19 19 19 N 1 3.04 0.30 108.30 111.34 B B B O4' C1' N9 DG DG DG 20 20 20 N 1 4.51 0.50 113.10 117.61 B B B N7 C8 N9 DG DG DG 20 20 20 N 1 -2.92 0.40 106.40 103.48 B B B C8 N9 C4 DG DG DG 20 20 20 N model building X-PLOR refinement X-PLOR phasing X-PLOR THE SOLUTION NMR STRUCTURE OF A THERMALLY STABLE FAPY ADDUCT OF AFLATOXIN B1 IN AN OLIGODEOXYNUCLEOTIDE DUPLEX REFINED FROM DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N covale 1.613 both A DT 4 A O3' DT 4 1_555 A FAG 5 A P FAG 5 1_555 covale 1.619 one A FAG 5 A O3' FAG 5 1_555 A DA 6 A P DA 6 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 20 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 20 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 20 B N2 DG 10 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 19 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 19 B N6 DA 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 DA 6 A N1 DA 6 1_555 B DT 15 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 15 B O4 DT 5 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 14 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 14 B N6 DA 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 DA 10 A N1 DA 10 1_555 B DT 11 B N3 DT 1 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 11 B O4 DT 1 1_555 DNA AFLATOXIN B1, FAPY, FORMAMIDOPYRIMIDINE, INTERCALATION, DNA DUPLEX, SOLUTION STRUCTURE, DNA ADDUCT, DEOXYRIBONUCLEIC ACID, DNA 1HM1 PDB 1 1HM1 1HM1 PDB 2 1HM1 1 10 1HM1 1 10 1HM1 A 1 1 10 11 20 1HM1 11 20 1HM1 B 2 1 10 1 P 1