0.030989 0.000000 0.014961 0.000000 0.039124 0.000000 0.000000 0.000000 0.031992 0.00000 0.00000 0.00000 Lipscomb, L.A. Peek, M.E. Morningstar, M.L. Verghis, S.M. Miller, E.M. Rich, A. Essigmann, J.M. Williams, L.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 115.77 90.00 32.270 25.560 34.710 C10 H14 N5 O8 P 363.221 n 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER 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 N 13 N N N 14 N C N 15 N N N 16 N C N 17 N C N 18 N O N 19 N N N 20 N C N 21 N N N 22 N N 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 182 N O N 183 N H N 184 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 N 24 N sing N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N doub N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N doub N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N doub 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 Y 64 N sing Y 65 N sing Y 66 N doub N 67 N sing Y 68 N sing Y 69 N sing Y 70 N doub N 71 N sing Y 72 N doub N 73 N sing N 74 N sing Y 75 N sing Y 76 N doub N 77 N sing Y 78 N sing N 79 N sing N 80 N sing N 81 N doub 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 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 doub N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub 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 Y 137 N sing Y 138 N sing Y 139 N doub N 140 N sing Y 141 N sing N 142 N sing Y 143 N doub N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N doub N 156 N sing N 157 N sing 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 doub N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N doub N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 92 719 723 10.1073/pnas.92.3.719 7846041 X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. 1995 10.2210/pdb183d/pdb pdb_0000183d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 277.00 1 AREA DETECTOR SDMS x-ray 1 1.0 ROTATING ANODE RIGAKU RU200 3061.992 DNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3') 1 syn polymer 18.015 water 42 nat water no yes (DC)(DC)(DA)(8OG)(DC)(DG)(DC)(DT)(DG)(DG) CCAGCGCTGG A polydeoxyribonucleotide n n n n n n n n n n 2.11 41.57 VAPOR DIFFUSION, SITTING DROP 7.60 pH 7.60, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K 277.00 WATER 1 MPD 1 BIS-TRIS-PROPANE_HCL 1 MGCL2 1 WATER 2 MPD 2 -5.284 1 19 A 1 A 10 -1.087 A_DC1:DG10_A 1 -10.523 0.084 0.280 -0.120 -0.577 1 19 A 2 A 9 -1.708 A_DC2:DG9_A 2 -10.021 0.315 -0.057 -0.184 0.883 1 20 A 3 A 8 1.143 A_DA3:DT8_A 3 -7.569 -0.002 0.209 -0.184 2.461 1 19 A 4 A 7 -3.930 A_8OG4:DC7_A 4 -6.679 -0.014 0.467 -0.125 2.715 1 19 A 5 A 6 -1.614 A_DC5:DG6_A 5 -8.767 -0.009 -0.094 -0.048 -2.715 1 19 A 6 A 5 -1.614 A_DG6:DC5_A 6 -8.767 0.009 -0.094 -0.048 -2.462 1 19 A 7 A 4 -3.930 A_DC7:8OG4_A 7 -6.679 0.014 0.467 -0.125 -0.883 1 20 A 8 A 3 1.143 A_DT8:DA3_A 8 -7.569 0.002 0.209 -0.184 0.577 1 19 A 9 A 2 -1.708 A_DG9:DC2_A 9 -10.021 -0.315 -0.057 -0.184 5.284 1 19 A 10 A 1 -1.087 A_DG10:DC1_A 10 -10.523 -0.084 0.280 -0.120 3.236 30.456 A A 1 2 12.563 A A 10 9 3.276 6.526 -0.451 0.653 AA_DC1DC2:DG9DG10_AA 1 4.624 -8.903 29.411 -0.077 1.794 2.831 50.062 A A 2 3 -8.916 A A 9 8 3.265 -7.518 0.170 2.806 AA_DC2DA3:DT8DG9_AA 2 -1.613 1.913 49.505 3.825 -0.310 3.241 24.657 A A 3 4 20.213 A A 8 7 3.383 8.430 0.551 0.515 AA_DA38OG4:DC7DT8_AA 3 -3.620 8.681 22.911 -1.504 -2.455 3.333 37.399 A A 4 5 -1.869 A A 7 6 3.407 -1.195 -0.233 0.369 AA_8OG4DC5:DG6DC7_AA 4 5.129 -8.024 37.040 0.738 1.062 3.515 42.983 A A 5 6 9.559 A A 6 5 3.512 6.976 0.000 0.293 AA_DC5DG6:DC5DG6_AA 5 0.000 0.000 42.440 -0.347 0.000 3.333 37.399 A A 6 7 -1.869 A A 5 4 3.407 -1.195 0.233 0.369 AA_DG6DC7:8OG4DC5_AA 6 -5.129 8.024 37.040 0.738 -1.062 3.241 24.657 A A 7 8 20.213 A A 4 3 3.383 8.430 -0.551 0.515 AA_DC7DT8:DA38OG4_AA 7 3.620 -8.681 22.911 -1.504 2.455 2.831 50.062 A A 8 9 -8.915 A A 3 2 3.265 -7.518 -0.170 2.806 AA_DT8DG9:DC2DA3_AA 8 1.613 -1.913 49.505 3.825 0.310 3.236 30.456 A A 9 10 12.563 A A 2 1 3.276 6.526 0.451 0.653 AA_DG9DG10:DC1DC2_AA 9 -4.624 8.903 29.411 -0.077 -1.794 chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1995-02-27 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag BNL Y NDB 1994-08-01 REL HOH water HOH 11 2 HOH HOH 11 A HOH 12 2 HOH HOH 12 A HOH 13 2 HOH HOH 13 A HOH 14 2 HOH HOH 14 A HOH 15 2 HOH HOH 15 A HOH 16 2 HOH HOH 16 A HOH 17 2 HOH HOH 17 A HOH 18 2 HOH HOH 18 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 21 2 HOH HOH 21 A HOH 22 2 HOH HOH 22 A HOH 23 2 HOH HOH 23 A HOH 24 2 HOH HOH 24 A HOH 25 2 HOH HOH 25 A HOH 26 2 HOH HOH 26 A HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 29 2 HOH HOH 29 A HOH 30 2 HOH HOH 30 A HOH 31 2 HOH HOH 31 A HOH 32 2 HOH HOH 32 A HOH 33 2 HOH HOH 33 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 37 2 HOH HOH 37 A HOH 38 2 HOH HOH 38 A HOH 39 2 HOH HOH 39 A HOH 40 2 HOH HOH 40 A HOH 41 2 HOH HOH 41 A HOH 42 2 HOH HOH 42 A HOH 43 2 HOH HOH 43 A HOH 44 2 HOH HOH 44 A HOH 45 2 HOH HOH 45 A HOH 46 2 HOH HOH 46 A HOH 47 2 HOH HOH 47 A HOH 48 2 HOH HOH 48 A HOH 49 2 HOH HOH 49 A HOH 50 2 HOH HOH 50 A HOH 51 2 HOH HOH 51 A HOH 52 2 HOH HOH 52 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A +G 4 n 4 8OG 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A author_defined_assembly 2 dimeric A 8OG 4 A 8OG 4 DG 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 2_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A C1' 8OG 4 PLANAR 1 A DA 3 0.065 SIDE CHAIN 1 A DG 6 0.094 SIDE CHAIN 1 A DC 7 0.076 SIDE CHAIN 1 4.36 0.30 108.30 112.66 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 1.89 0.30 108.30 110.19 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 -14.35 1.90 104.00 89.65 A A A O3' P O5' 8OG DC DC 4 5 5 Y 1 9.89 1.60 120.90 130.79 A A A P O5' C5' DC DC DC 5 5 5 N 1 4.81 0.60 118.90 123.71 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 9.47 1.20 119.70 129.17 A A A C3' O3' P DC DC DG 5 5 6 Y 1 6.02 0.30 108.30 114.32 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 4.22 0.30 108.30 112.52 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 4.40 0.60 118.90 123.30 A A A N1 C2 O2 DC DC DC 7 7 7 N 1 -3.89 0.60 123.70 119.81 A A A C5 C6 N1 DT DT DT 8 8 8 N 1 -4.52 0.60 122.30 117.78 A A A N3 C2 O2 DT DT DT 8 8 8 N 1 -4.20 0.60 122.90 118.70 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 A A C5' C4' DC DC 1 1 0.043 0.007 1.512 1.555 N 1 A A C5' C4' DG DG 6 6 0.050 0.007 1.512 1.562 N 0.234 0.234 1.600 10.000 3290 95.400 1 2.000 1.600 10.000 42 246 1 203 0 0.020 3.60 1.600 183D 12930 3290 2.000 1 refinement X-PLOR X-RAY STRUCTURE OF A DNA DECAMER CONTAINING 7, 8-DIHYDRO-8-OXOGUANINE 1 N N 2 N N covale 1.625 both A DA 3 A O3' DA 3 1_555 A 8OG 4 A P 8OG 4 1_555 covale 1.572 both A 8OG 4 A O3' 8OG 4 1_555 A DC 5 A P DC 5 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 10 A N1 DG 10 2_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 10 A O6 DG 10 2_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 10 A N2 DG 10 2_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 9 A N1 DG 9 2_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 9 A O6 DG 9 2_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 9 A N2 DG 9 2_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 8 A N3 DT 8 2_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 8 A O4 DT 8 2_555 hydrog WATSON-CRICK A 8OG 4 A N1 8OG 4 1_555 A DC 7 A N3 DC 7 2_555 hydrog WATSON-CRICK A 8OG 4 A N2 8OG 4 1_555 A DC 7 A O2 DC 7 2_555 hydrog WATSON-CRICK A 8OG 4 A O6 8OG 4 1_555 A DC 7 A N4 DC 7 2_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 6 A N1 DG 6 2_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 6 A O6 DG 6 2_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 6 A N2 DG 6 2_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 5 A N3 DC 5 2_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 5 A O2 DC 5 2_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 5 A N4 DC 5 2_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 A 8OG 4 A N1 8OG 4 2_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 A 8OG 4 A O6 8OG 4 2_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 A 8OG 4 A N2 8OG 4 2_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 A DA 3 A N1 DA 3 2_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 A DA 3 A N6 DA 3 2_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 A DC 2 A N3 DC 2 2_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 A DC 2 A O2 DC 2 2_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 A DC 2 A N4 DC 2 2_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 A DC 1 A N3 DC 1 2_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 A DC 1 A O2 DC 1 2_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 A DC 1 A N4 DC 1 2_555 DNA B-DNA, DOUBLE HELIX, MODIFIED, DNA 183D PDB 1 183D 1 10 183D 1 10 183D A 1 1 10 5 C 1 2 1