1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Korobka, A. Cullinan, D. Cosman, M. Grollman, A.P. Patel, D.J. Eisenberg, M. De Los Santos, C. 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 C11 H14 N3 O7 P 331.219 N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE 6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one 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 O N 145 N P N 146 N N N 147 N C N 148 N O Y 149 N N Y 150 N C Y 151 N N N 152 N C N 153 N C Y 154 N C Y 155 N C N 156 R C N 157 N C N 158 S C N 159 N O N 160 R C N 161 N O N 162 N C N 163 N O N 164 N O N 165 N O N 166 N H 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 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 doub N 159 N sing Y 160 N sing Y 161 N sing Y 162 N doub N 163 N sing Y 164 N sing N 165 N doub N 166 N sing N 167 N sing Y 168 N doub 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 sing 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 sing US Biochemistry BICHAW 0033 0006-2960 35 13310 13318 10.1021/bi9605696 8873597 Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics. 1996 10.2210/pdb1b6y/pdb pdb_00001b6y 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3318.184 5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3' 1 syn polymer 3398.235 5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3' 1 syn polymer no yes (DC)(DG)(DT)(DA)(DC)(EDC)(DC)(DA)(DT)(DG)(DC) CGTACXCATGC A polydeoxyribonucleotide no no (DG)(DC)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DC)(DG) GCATGAGTACG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -9.215 1 19 A 1 B 11 -2.901 A_DC1:DG11_B 1 -9.540 0.527 0.326 -0.218 1.365 1 19 A 2 B 10 -2.543 A_DG2:DC10_B 2 -16.722 -0.831 0.289 -0.384 0.327 1 20 A 3 B 9 -3.490 A_DT3:DA9_B 3 -14.883 -0.055 0.211 -0.175 4.849 1 20 A 4 B 8 -2.968 A_DA4:DT8_B 4 -10.051 0.231 0.386 -0.184 13.399 1 19 A 5 B 7 -1.943 A_DC5:DG7_B 5 -6.817 0.737 0.132 -0.319 -10.563 1 19 A 7 B 5 -1.284 A_DC7:DG5_B 6 1.829 0.623 0.432 -0.231 1.688 1 20 A 8 B 4 -2.820 A_DA8:DT4_B 7 -13.265 0.286 0.153 -0.154 -1.775 1 20 A 9 B 3 -2.554 A_DT9:DA3_B 8 -13.085 -0.169 0.164 -0.170 0.102 1 19 A 10 B 2 -1.817 A_DG10:DC2_B 9 -10.142 -0.504 0.200 -0.198 -10.551 1 19 A 11 B 1 -1.970 A_DC11:DG1_B 10 -2.083 0.691 0.442 -0.266 1.853 30.340 A A 1 2 24.215 B B 11 10 2.567 12.312 -0.239 -1.287 AA_DC1DG2:DC10DG11_BB 1 -2.276 4.477 27.692 -4.215 0.133 3.086 34.990 A A 2 3 2.281 B B 10 9 3.119 1.371 -0.223 -0.879 AA_DG2DT3:DA9DC10_BB 2 -0.585 0.974 34.960 -1.657 0.287 2.646 39.997 A A 3 4 11.439 B B 9 8 2.854 7.778 -0.012 -0.845 AA_DT3DA4:DT8DA9_BB 3 -0.545 0.802 39.260 -1.993 -0.035 2.971 35.517 A A 4 5 -0.853 B B 8 7 2.953 -0.520 0.399 -0.918 AA_DA4DC5:DG7DT8_BB 4 0.548 -0.899 35.509 -1.436 -0.582 1.910 30.542 A A 7 8 20.621 B B 5 4 2.582 10.624 -0.424 -1.345 AA_DC7DA8:DT4DG5_BB 5 3.303 -6.411 28.489 -4.055 1.272 3.263 34.306 A A 8 9 -7.160 B B 4 3 3.154 -4.213 -0.093 -1.105 AA_DA8DT9:DA3DT4_BB 6 0.015 -0.025 34.054 -1.223 0.160 2.486 35.204 A A 9 10 14.306 B B 3 2 2.859 8.570 0.719 -1.301 AA_DT9DG10:DC2DA3_BB 7 0.792 -1.322 34.168 -3.211 -1.091 3.819 42.894 A A 10 11 -15.775 B B 2 1 3.652 -11.401 -0.124 -1.130 AA_DG10DC11:DG1DC2_BB 8 -3.068 4.246 41.311 -0.224 -0.186 chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_nmr_software struct_conn repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations Other 1 0 1999-01-27 1 1 2008-03-24 1 2 2011-07-13 1 3 2012-01-18 1 4 2024-04-10 _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 1999-01-19 REL REL THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED USING THE FULL RELAXATION MATRIX BACK CALCULATION APPROACH. 2 2 NOESY COSY DQF-COSY 6.9 298 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RESTRAINED MOLECULAR DYNAMICS SIMULATIONS BRUNGER refinement X-PLOR 3.1 structure solution Felix structure solution X-PLOR 500 Bruker AM 600 Bruker AMX C 1 n 1 DC 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A EDC 6 n 6 EDC 6 A C 7 n 7 DC 7 A A 8 n 8 DA 8 A T 9 n 9 DT 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 1 n 1 DG 1 B C 2 n 2 DC 2 B A 3 n 3 DA 3 B T 4 n 4 DT 4 B G 5 n 5 DG 5 B A 6 n 6 DA 6 B G 7 n 7 DG 7 B T 8 n 8 DT 8 B A 9 n 9 DA 9 B C 10 n 10 DC 10 B G 11 n 11 DG 11 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 3.51 0.50 113.10 116.61 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -3.63 0.60 122.90 119.27 A A A C6 C5 C7 DT DT DT 3 3 3 N 1 1.87 0.30 108.30 110.17 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 6.67 0.30 108.30 114.97 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 3.19 0.50 113.10 116.29 B B B N7 C8 N9 DG DG DG 1 1 1 N 1 5.08 0.30 108.30 113.38 B B B O4' C1' N1 DC DC DC 2 2 2 N 1 3.03 0.50 113.10 116.13 B B B N7 C8 N9 DG DG DG 5 5 5 N 1 3.05 0.30 108.30 111.35 B B B O4' C1' N9 DG DG DG 7 7 7 N 1 1.96 0.30 108.30 110.26 B B B O4' C1' N1 DC DC DC 10 10 10 N 1 6.85 0.30 108.30 115.15 B B B O4' C1' N9 DG DG DG 11 11 11 N 1 3.10 0.50 113.10 116.20 B B B N7 C8 N9 DG DG DG 11 11 11 N 2 3.76 0.60 118.90 122.66 A A A N1 C2 O2 DC DC DC 1 1 1 N 2 3.33 0.50 113.10 116.43 A A A N7 C8 N9 DG DG DG 2 2 2 N 2 1.81 0.30 108.30 110.11 A A A O4' C1' N1 DT DT DT 3 3 3 N 2 -3.75 0.60 122.90 119.15 A A A C6 C5 C7 DT DT DT 3 3 3 N 2 2.14 0.30 108.30 110.44 A A A O4' C1' N9 DG DG DG 10 10 10 N 2 6.71 0.30 108.30 115.01 A A A O4' C1' N1 DC DC DC 11 11 11 N 2 3.23 0.50 113.10 116.33 B B B N7 C8 N9 DG DG DG 1 1 1 N 2 5.06 0.30 108.30 113.36 B B B O4' C1' N1 DC DC DC 2 2 2 N 2 2.90 0.30 108.30 111.20 B B B O4' C1' N9 DG DG DG 7 7 7 N 2 2.06 0.30 108.30 110.36 B B B O4' C1' N1 DC DC DC 10 10 10 N 2 6.50 0.30 108.30 114.80 B B B O4' C1' N9 DG DG DG 11 11 11 N 2 3.15 0.50 113.10 116.25 B B B N7 C8 N9 DG DG DG 11 11 11 N 1 A A C4 N4 DC DC 1 1 0.094 0.009 1.335 1.429 N 1 A A C2 N2 DG DG 2 2 0.084 0.010 1.341 1.425 N 1 A A C5 C7 DT DT 3 3 0.037 0.006 1.496 1.533 N 1 A A C6 N6 DA DA 4 4 0.091 0.008 1.335 1.426 N 1 A A C4 N4 DC DC 5 5 0.093 0.009 1.335 1.428 N 1 A A C4 N4 DC DC 7 7 0.093 0.009 1.335 1.428 N 1 A A C6 N6 DA DA 8 8 0.093 0.008 1.335 1.428 N 1 A A C5 C7 DT DT 9 9 0.037 0.006 1.496 1.533 N 1 A A C2 N2 DG DG 10 10 0.082 0.010 1.341 1.423 N 1 A A C4 N4 DC DC 11 11 0.091 0.009 1.335 1.426 N 1 B B C2 N2 DG DG 1 1 0.081 0.010 1.341 1.422 N 1 B B C4 N4 DC DC 2 2 0.095 0.009 1.335 1.430 N 1 B B C6 N6 DA DA 3 3 0.094 0.008 1.335 1.429 N 1 B B C5 C7 DT DT 4 4 0.036 0.006 1.496 1.532 N 1 B B C2 N2 DG DG 5 5 0.081 0.010 1.341 1.422 N 1 B B C6 N6 DA DA 6 6 0.093 0.008 1.335 1.428 N 1 B B C2 N2 DG DG 7 7 0.079 0.010 1.341 1.420 N 1 B B C5 C7 DT DT 8 8 0.039 0.006 1.496 1.535 N 1 B B C6 N6 DA DA 9 9 0.092 0.008 1.335 1.427 N 1 B B C4 N4 DC DC 10 10 0.092 0.009 1.335 1.427 N 1 B B C2 N2 DG DG 11 11 0.086 0.010 1.341 1.427 N 2 A A C4 N4 DC DC 1 1 0.095 0.009 1.335 1.430 N 2 A A C2 N2 DG DG 2 2 0.083 0.010 1.341 1.424 N 2 A A C6 N6 DA DA 4 4 0.092 0.008 1.335 1.427 N 2 A A C4 N4 DC DC 5 5 0.092 0.009 1.335 1.427 N 2 A A C4 N4 DC DC 7 7 0.094 0.009 1.335 1.429 N 2 A A C6 N6 DA DA 8 8 0.092 0.008 1.335 1.427 N 2 A A C2 N2 DG DG 10 10 0.082 0.010 1.341 1.423 N 2 A A C4 N4 DC DC 11 11 0.092 0.009 1.335 1.427 N 2 B B C2 N2 DG DG 1 1 0.080 0.010 1.341 1.421 N 2 B B C4 N4 DC DC 2 2 0.095 0.009 1.335 1.430 N 2 B B C6 N6 DA DA 3 3 0.092 0.008 1.335 1.427 N 2 B B C2 N2 DG DG 5 5 0.082 0.010 1.341 1.423 N 2 B B C6 N6 DA DA 6 6 0.093 0.008 1.335 1.428 N 2 B B C2 N2 DG DG 7 7 0.078 0.010 1.341 1.419 N 2 B B C5 C7 DT DT 8 8 0.038 0.006 1.496 1.534 N 2 B B C6 N6 DA DA 9 9 0.094 0.008 1.335 1.429 N 2 B B C4 N4 DC DC 10 10 0.093 0.009 1.335 1.428 N 2 B B C2 N2 DG DG 11 11 0.087 0.010 1.341 1.428 N model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES 1 N N 2 N N covale 1.620 both A DC 5 A O3' DC 5 1_555 A EDC 6 A P EDC 6 1_555 covale 1.619 both A EDC 6 A O3' EDC 6 1_555 A DC 7 A P DC 7 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 11 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 11 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 11 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 9 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 9 B N6 DA 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 7 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 7 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 7 B N2 DG 7 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 5 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 5 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 5 B N2 DG 5 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 4 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 4 B O4 DT 4 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 2 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 2 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 2 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 1 B N2 DG 1 1_555 DNA DEOXYRIBONUCLEIC ACID, ETHENODC, EDC, EXOCYCLIC LESION, DNA 1B6Y PDB 1 1B6Y 1B6Y PDB 2 1B6Y 1 11 1B6Y 1 11 1B6Y A 1 1 11 1 11 1B6Y 1 11 1B6Y B 2 1 11 1 P 1