0.037421 0.021605 0.000000 0.000000 0.043210 0.000000 0.000000 0.000000 0.009848 0.00000 0.00000 0.00000 Freisinger, E. Fernandes, A. Grollman, A.P. Kisker, C.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 26.723 26.723 101.544 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 H2 O 18.015 WATER non-polymer Na 1 22.990 SODIUM ION non-polymer 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 180 N O N 181 N H N 182 N H N 183 N NA 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 N 188 N sing N 189 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 329 685 697 10.1016/S0022-2836(03)00445-5 12787670 Crystallographic Characterization of an Exocyclic DNA Adduct: 3,N4-etheno-2'-deoxycytidine in the Dodecamer 5'-CGCGAATT(ethenoC)GCG-3' 2003 10.2210/pdb1n5c/pdb pdb_00001n5c 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 CCD 2000-06-13 ADSC QUANTUM 4 MIRROR SINGLE WAVELENGTH M x-ray 1 1.1 1.0 X26C NSLS 1.1 SYNCHROTRON NSLS BEAMLINE X26C 3687.414 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*GP*CP*G)-3' 1 syn polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 73 nat water no yes (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(EDC)(DG)(DC)(DG) CGCGAATTXGCG A polydeoxyribonucleotide n n n n n n n n n n n n 1 2.34 47.11 7.00 Drop: MPD, potassium chloride, spermine tetrahydrochloride, cacodylate; Reservoir: MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.00 277 MPD 1 KCl 1 spermine tetrahydrochloride 1 cacodylate 1 MPD 2 -14.509 1 19 A 14 A 23 -4.822 A_DG14:DC23_A 1 -2.925 -0.224 0.112 0.013 -12.906 1 19 A 15 A 22 1.258 A_DC15:DG22_A 2 6.485 0.149 0.564 0.015 -0.075 1 20 A 17 A 20 11.324 A_DA17:DT20_A 3 -19.451 -0.166 -0.523 -0.153 -3.036 1 20 A 18 A 19 5.671 A_DA18:DT19_A 4 -18.457 0.090 0.011 0.058 3.036 1 20 A 19 A 18 5.671 A_DT19:DA18_A 5 -18.457 -0.090 0.011 0.058 0.075 1 20 A 20 A 17 11.324 A_DT20:DA17_A 6 -19.451 0.166 -0.523 -0.153 12.906 1 19 A 22 A 15 1.258 A_DG22:DC15_A 7 6.485 -0.149 0.564 0.015 14.509 1 19 A 23 A 14 -4.822 A_DC23:DG14_A 8 -2.925 0.224 0.112 0.013 3.301 35.783 A A 14 15 -9.402 A A 23 22 3.510 -5.741 0.918 0.264 AA_DG14DC15:DG22DC23_AA 1 -4.126 6.756 35.100 1.298 -2.118 6.334 67.136 A A 15 17 7.286 A A 22 20 6.388 8.038 -0.514 0.174 AA_DC15DA17:DT20DG22_AA 2 4.020 -3.644 66.602 -0.454 0.771 3.357 37.717 A A 17 18 -7.950 A A 20 19 3.385 -5.112 -0.119 -0.096 AA_DA17DA18:DT19DT20_AA 3 -4.757 7.398 37.088 0.540 -0.455 3.073 35.280 A A 18 19 -4.095 A A 19 18 3.045 -2.480 0.000 -0.512 AA_DA18DT19:DA18DT19_AA 4 0.000 0.000 35.195 -0.500 0.000 3.357 37.717 A A 19 20 -7.950 A A 18 17 3.385 -5.112 0.119 -0.096 AA_DT19DT20:DA17DA18_AA 5 4.757 -7.398 37.088 0.540 0.455 6.334 67.136 A A 20 22 7.286 A A 17 15 6.388 8.038 0.514 0.174 AA_DT20DG22:DC15DA17_AA 6 -4.020 3.644 66.602 -0.454 -0.771 3.301 35.783 A A 22 23 -9.402 A A 15 14 3.510 -5.741 -0.918 0.264 AA_DG22DC23:DG14DC15_AA 7 4.126 -6.756 35.100 1.298 2.118 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations Refinement description 1 0 2003-06-03 1 1 2008-04-28 1 2 2011-07-13 1 3 2012-01-18 1 4 2024-02-14 1 5 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _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.ptnr1_symmetry _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_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2002-11-05 REL REL NA SODIUM ION HOH water 1EHV NDB ENTRY BD0032 PDB experimental model NA 1101 2 NA NA 1101 A HOH 1001 3 HOH HOH 1001 A HOH 1001 3 HOH HOH 1002 A HOH 1001 3 HOH HOH 1003 A HOH 1001 3 HOH HOH 1004 A HOH 1001 3 HOH HOH 1005 A HOH 1001 3 HOH HOH 1006 A HOH 1001 3 HOH HOH 1007 A HOH 1001 3 HOH HOH 1008 A HOH 1001 3 HOH HOH 1009 A HOH 1001 3 HOH HOH 1010 A HOH 1001 3 HOH HOH 1011 A HOH 1001 3 HOH HOH 1012 A HOH 1001 3 HOH HOH 1013 A HOH 1001 3 HOH HOH 1014 A HOH 1001 3 HOH HOH 1015 A HOH 1001 3 HOH HOH 1016 A HOH 1001 3 HOH HOH 1017 A HOH 1001 3 HOH HOH 1018 A HOH 1001 3 HOH HOH 1019 A HOH 1001 3 HOH HOH 1020 A HOH 1001 3 HOH HOH 1021 A HOH 1001 3 HOH HOH 1022 A HOH 1001 3 HOH HOH 1023 A HOH 1001 3 HOH HOH 1024 A HOH 1001 3 HOH HOH 1025 A HOH 1001 3 HOH HOH 1026 A HOH 1001 3 HOH HOH 1027 A HOH 1001 3 HOH HOH 1028 A HOH 1001 3 HOH HOH 1029 A HOH 1001 3 HOH HOH 1030 A HOH 1001 3 HOH HOH 1031 A HOH 1001 3 HOH HOH 1032 A HOH 1001 3 HOH HOH 1033 A HOH 1001 3 HOH HOH 1034 A HOH 1001 3 HOH HOH 1035 A HOH 1001 3 HOH HOH 1036 A HOH 1001 3 HOH HOH 1037 A HOH 1001 3 HOH HOH 1038 A HOH 1001 3 HOH HOH 1039 A HOH 1001 3 HOH HOH 1040 A HOH 1001 3 HOH HOH 1041 A HOH 1001 3 HOH HOH 1042 A HOH 1001 3 HOH HOH 1043 A HOH 1001 3 HOH HOH 1044 A HOH 1001 3 HOH HOH 1045 A HOH 1001 3 HOH HOH 1046 A HOH 1001 3 HOH HOH 1047 A HOH 1001 3 HOH HOH 1048 A HOH 1001 3 HOH HOH 1049 A HOH 1001 3 HOH HOH 1050 A HOH 1001 3 HOH HOH 1051 A HOH 1001 3 HOH HOH 1052 A HOH 1001 3 HOH HOH 1053 A HOH 1001 3 HOH HOH 1054 A HOH 1001 3 HOH HOH 1055 A HOH 1001 3 HOH HOH 1056 A HOH 1001 3 HOH HOH 1057 A HOH 1001 3 HOH HOH 1058 A HOH 1001 3 HOH HOH 1059 A HOH 1001 3 HOH HOH 1060 A HOH 1001 3 HOH HOH 1061 A HOH 1001 3 HOH HOH 1062 A HOH 1001 3 HOH HOH 1063 A HOH 1001 3 HOH HOH 1064 A HOH 1001 3 HOH HOH 1065 A HOH 1001 3 HOH HOH 1066 A HOH 1001 3 HOH HOH 1067 A HOH 1001 3 HOH HOH 1068 A HOH 1001 3 HOH HOH 1069 A HOH 1001 3 HOH HOH 1070 A HOH 1001 3 HOH HOH 1071 A HOH 1001 3 HOH HOH 1072 A HOH 1001 3 HOH HOH 1073 A C 13 n 1 DC 13 A G 14 n 2 DG 14 A C 15 n 3 DC 15 A G 16 n 4 DG 16 A A 17 n 5 DA 17 A A 18 n 6 DA 18 A T 19 n 7 DT 19 A T 20 n 8 DT 20 A E 21 n 9 EDC 21 A G 22 n 10 DG 22 A C 23 n 11 DC 23 A G 24 n 12 DG 24 A 0.152 0.164 0.149 0.161 0.215 0.219 172 200 5 5 3141 author_defined_assembly 2 dimeric A DC 13 A N3 DC 1 1_555 A NA 1101 B NA NA 1_555 A DC 13 A O2 DC 1 1_555 56.8 A DC 13 A N3 DC 1 1_555 A NA 1101 B NA NA 1_555 A DG 24 A OP1 DG 12 5_755 112.3 A DC 13 A O2 DC 1 1_555 A NA 1101 B NA NA 1_555 A DG 24 A OP1 DG 12 5_755 93.2 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 5_655 -x+y+1,y,-z+2/3 crystal symmetry operation 26.7230000000 0.0000000000 67.6960000000 1 A NA 1101 B NA 1 A HOH 1002 C HOH 1 A HOH 1042 C HOH 1 A HOH 1050 C HOH 1 A HOH 1056 C HOH 1 -2.66 0.40 120.30 117.64 A A A C6 N1 C2 DC DC DC 13 13 13 N 1 3.13 0.50 119.90 123.03 A A A C2 N3 C4 DC DC DC 13 13 13 N 1 3.32 0.50 121.00 124.32 A A A C5 C6 N1 DC DC DC 13 13 13 N 1 4.65 0.60 118.90 123.55 A A A N1 C2 O2 DC DC DC 13 13 13 N 1 -6.96 0.70 108.00 101.04 A A A O4' C1' N9 DG DG DG 14 14 14 N 1 -5.88 0.70 108.00 102.12 A A A O4' C1' N1 DT DT DT 20 20 20 N 1 11.17 1.20 119.70 130.87 A A A C3' O3' P EDC EDC DG 21 21 22 Y 1 4.93 0.60 119.90 124.83 A A A N1 C6 O6 DG DG DG 22 22 22 N 1 -5.08 0.60 128.60 123.52 A A A C5 C6 O6 DG DG DG 22 22 22 N 0.219 0.164 0.161 1.79 20.00 1327 200 3913 1445 5 99.6 RANDOM 1 THROUGHOUT 0.000 ISOMORPHOUS REPLACEMENT NDB ENTRY BD0032 ENGH & HUBER BABINET'S PRINCIPLE 137 303.75 1.79 20.00 73 319 1 245 0 0.020 2.600 0.025 0.007 0.065 0.143 1.790 50.000 1N5C 4113 5 0.061 1 22 4 99.4 1.79 1.85 2 0.187 1 4 100.0 data reduction DENZO data scaling SCALEPACK model building X-PLOR refinement SHELXL-97 phasing X-PLOR Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG 1 N N 2 N N 3 N N The second part of the biological assembly/double helix is generated by the two fold axis: -x+y+1, y, -z+3/2. covale 1.620 both A DT 20 A O3' DT 8 1_555 A EDC 21 A P EDC 9 1_555 covale 1.573 both A EDC 21 A O3' EDC 9 1_555 A DG 22 A P DG 10 1_555 metalc 2.292 A DC 13 A N3 DC 1 1_555 A NA 1101 B NA NA 1_555 metalc 2.395 A DC 13 A O2 DC 1 1_555 A NA 1101 B NA NA 1_555 metalc 2.279 A DG 24 A OP1 DG 12 5_755 A NA 1101 B NA NA 1_555 hydrog WATSON-CRICK A DG 14 A N1 DG 2 1_555 A DC 23 A N3 DC 11 5_655 hydrog WATSON-CRICK A DG 14 A N2 DG 2 1_555 A DC 23 A O2 DC 11 5_655 hydrog WATSON-CRICK A DG 14 A O6 DG 2 1_555 A DC 23 A N4 DC 11 5_655 hydrog WATSON-CRICK A DC 15 A N3 DC 3 1_555 A DG 22 A N1 DG 10 5_655 hydrog WATSON-CRICK A DC 15 A N4 DC 3 1_555 A DG 22 A O6 DG 10 5_655 hydrog WATSON-CRICK A DC 15 A O2 DC 3 1_555 A DG 22 A N2 DG 10 5_655 hydrog WATSON-CRICK A DA 17 A N1 DA 5 1_555 A DT 20 A N3 DT 8 5_655 hydrog WATSON-CRICK A DA 17 A N6 DA 5 1_555 A DT 20 A O4 DT 8 5_655 hydrog WATSON-CRICK A DA 18 A N1 DA 6 1_555 A DT 19 A N3 DT 7 5_655 hydrog WATSON-CRICK A DA 18 A N6 DA 6 1_555 A DT 19 A O4 DT 7 5_655 hydrog WATSON-CRICK A DT 19 A N3 DT 7 1_555 A DA 18 A N1 DA 6 5_655 hydrog WATSON-CRICK A DT 19 A O4 DT 7 1_555 A DA 18 A N6 DA 6 5_655 hydrog WATSON-CRICK A DT 20 A N3 DT 8 1_555 A DA 17 A N1 DA 5 5_655 hydrog WATSON-CRICK A DT 20 A O4 DT 8 1_555 A DA 17 A N6 DA 5 5_655 hydrog WATSON-CRICK A DG 22 A N1 DG 10 1_555 A DC 15 A N3 DC 3 5_655 hydrog WATSON-CRICK A DG 22 A N2 DG 10 1_555 A DC 15 A O2 DC 3 5_655 hydrog WATSON-CRICK A DG 22 A O6 DG 10 1_555 A DC 15 A N4 DC 3 5_655 hydrog WATSON-CRICK A DC 23 A N3 DC 11 1_555 A DG 14 A N1 DG 2 5_655 hydrog WATSON-CRICK A DC 23 A N4 DC 11 1_555 A DG 14 A O6 DG 2 5_655 hydrog WATSON-CRICK A DC 23 A O2 DC 11 1_555 A DG 14 A N2 DG 2 5_655 DNA B form double helix, 3, N4-etheno-2'-cytidine modification opposite G, DNA 1N5C PDB 1 1N5C 13 24 1N5C 13 24 1N5C A 1 1 12 BINDING SITE FOR RESIDUE NA A 1101 A NA 1101 Software 3 A DC 13 A DC 1 3 1_555 A DC 23 A DC 11 3 5_755 A DG 24 A DG 12 3 5_755 153 P 32 1 2