1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Beger, R.D. Bolton, P.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C5 H11 O7 P 214.110 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE ABASIC DEOXYRIBOSE 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 P N 2 N O 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 R C N 10 N O N 11 N C N 12 S C N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N O N 26 N P N 27 N O N 28 N O N 29 N O N 30 N C N 31 R C N 32 N O N 33 S C N 34 N O N 35 N C N 36 R C Y 37 N N Y 38 N C Y 39 N N Y 40 N C Y 41 N C N 42 N N Y 43 N N Y 44 N C Y 45 N N Y 46 N C N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N O N 62 N P N 63 N O N 64 N O N 65 N O N 66 N C N 67 R C N 68 N O N 69 S C N 70 N O N 71 N C N 72 R C N 73 N N N 74 N C N 75 N O N 76 N N N 77 N C N 78 N N N 79 N C N 80 N C N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N O N 96 N P N 97 N O N 98 N O N 99 N O N 100 N C N 101 R C N 102 N O N 103 S C N 104 N O N 105 N C N 106 R C Y 107 N N Y 108 N C Y 109 N N Y 110 N C N 111 N C N 112 N O N 113 N N N 114 N C N 115 N N N 116 N N Y 117 N C N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N O N 133 N P N 134 N O N 135 N O N 136 N O N 137 N C N 138 R C N 139 N O N 140 S C N 141 N O N 142 N C N 143 R C N 144 N N N 145 N C N 146 N O N 147 N N N 148 N C N 149 N O N 150 N C N 151 N C N 152 N C N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N O N 169 N H N 170 N H N 1 N sing N 2 N doub 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 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 sing N 32 N sing N 33 N sing 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 sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing Y 48 N sing Y 49 N sing Y 50 N doub N 51 N sing Y 52 N sing Y 53 N sing Y 54 N doub N 55 N sing Y 56 N doub N 57 N sing N 58 N sing Y 59 N sing Y 60 N doub N 61 N sing Y 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing 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 doub N 89 N sing N 90 N doub N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N doub N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing Y 121 N sing Y 122 N sing Y 123 N doub N 124 N sing Y 125 N sing N 126 N sing Y 127 N doub N 128 N doub N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N doub N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N doub N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing 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 sing 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 sing N 160 N sing N 161 N sing N 162 N doub N 163 N sing N 164 N sing N 165 N sing N 166 N doub N 167 N sing N 168 N sing N 169 N doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing US J.Biol.Chem. JBCHA3 0071 0021-9258 273 15565 15573 10.1074/jbc.273.25.15565 9624147 Structures of apurinic and apyrimidinic sites in duplex DNAs. 1998 10.2210/pdb1a9j/pdb pdb_00001a9j 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3211.077 DNA (5'-D(*CP*GP*CP*GP*AP*AABP*AP*CP*GP*CP*C)-3') 1 syn polymer 3390.209 DNA (5'-D(*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3') 1 syn polymer 18.015 water 1 nat water no yes (DC)(DG)(DC)(DG)(DA)(AAB)(DA)(DC)(DG)(DC)(DC) CGCGAXACGCC A polydeoxyribonucleotide no no (DG)(DG)(DC)(DG)(DT)(DA)(DT)(DC)(DG)(DC)(DG) GGCGTATCGCG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -4.550 1 19 A 1 B 22 1.380 A_DC1:DG22_B 1 -6.800 0.656 0.293 -0.340 -2.412 1 19 A 2 B 21 -1.676 A_DG2:DC21_B 2 -1.357 -0.575 -0.003 -0.396 -10.122 1 19 A 3 B 20 0.613 A_DC3:DG20_B 3 -2.231 0.530 0.508 -0.377 7.739 1 19 A 4 B 19 -0.357 A_DG4:DC19_B 4 -2.184 -0.488 0.141 -0.306 1.680 1 20 A 5 B 18 -5.544 A_DA5:DT18_B 5 -18.341 0.050 -0.084 -0.204 8.371 1 20 A 7 B 16 -7.168 A_DA7:DT16_B 6 -21.806 0.132 0.283 -0.200 9.592 1 19 A 8 B 15 -1.028 A_DC8:DG15_B 7 -1.698 0.575 0.001 -0.312 8.141 1 19 A 9 B 14 -0.779 A_DG9:DC14_B 8 -4.529 -0.562 0.266 -0.366 2.561 1 19 A 10 B 13 0.170 A_DC10:DG13_B 9 -8.335 0.580 0.238 -0.371 4.417 1 19 A 11 B 12 -0.649 A_DC11:DG12_B 10 -1.399 0.523 0.171 -0.346 2.091 28.270 A A 1 2 24.271 B B 22 21 2.886 11.516 -0.082 -1.356 AA_DC1DG2:DC21DG22_BB 1 1.641 -3.459 25.811 -4.908 0.472 3.476 46.146 A A 2 3 -2.668 B B 21 20 3.448 -2.090 0.007 -0.900 AA_DG2DC3:DG20DC21_BB 2 -2.946 3.762 46.012 -0.959 -0.276 2.699 29.536 A A 3 4 -0.088 B B 20 19 2.700 -0.045 0.157 -0.493 AA_DC3DG4:DC19DG20_BB 3 3.719 -7.314 29.306 -0.959 0.346 3.361 48.922 A A 4 5 -0.756 B B 19 18 3.371 -0.626 -0.751 0.471 AA_DG4DA5:DT18DC19_BB 4 0.257 -0.311 48.917 0.617 0.927 5.961 83.556 A A 5 7 3.823 B B 18 16 5.920 5.087 -0.080 1.171 AA_DA5DA7:DT16DT18_BB 5 -7.698 5.785 83.138 0.656 -0.276 3.379 40.122 A A 7 8 -7.127 B B 16 15 3.341 -4.877 1.133 -0.108 AA_DA7DC8:DG15DT16_BB 6 1.918 -2.803 39.792 0.416 -1.425 3.616 31.684 A A 8 9 -9.418 B B 15 14 3.445 -5.120 0.243 -1.427 AA_DC8DG9:DC14DG15_BB 7 -1.171 2.154 31.257 -1.589 -0.680 3.325 49.959 A A 9 10 -5.948 B B 14 13 3.282 -5.016 -0.028 -0.606 AA_DG9DC10:DG13DC14_BB 8 -0.105 0.124 49.723 -0.349 0.026 3.265 37.617 A A 10 11 -4.823 B B 13 12 3.189 -3.106 -0.110 -1.060 AA_DC10DC11:DG12DG13_BB 9 -1.230 1.910 37.474 -1.245 0.012 chem_comp_atom chem_comp_bond database_2 pdbx_database_status struct_conn repository Initial release Version format compliance Version format compliance Structure summary Data collection Database references Derived calculations Other 1 0 1998-07-15 1 1 2008-03-24 1 2 2011-07-13 1 3 2014-07-09 1 4 2024-04-10 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _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 1998-04-06 REL HOH water 100MS NOESY, 250MS NOESY 250MS QUIETNOESY 70MS BAND-SELECTIVE J TOCSY FOR PHOSPHOROUS "J SCALE" SET TO 2 AND 3 AVERAGE OF 5 STRUCTURES THAT THE NOESY BACK CALCULATION AGREES WITH EXPERIMENTAL NOESY 100 1 NOESY PECOSY TOCSY ROESY QUIET-NOESY 50 mM KCL 7.0 1 atm 300 K matrix relaxation TRIS BRUNGER refinement X-PLOR 3.1 structure solution VNMR 400 Varian UNITY 500 Varian INOVA HOH 23 3 HOH HOH 23 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A AAB 6 n 6 AAB 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A G 9 n 9 DG 9 A C 10 n 10 DC 10 A C 11 n 11 DC 11 A G 12 n 1 DG 12 B G 13 n 2 DG 13 B C 14 n 3 DC 14 B G 15 n 4 DG 15 B T 16 n 5 DT 16 B A 17 n 6 DA 17 B T 18 n 7 DT 18 B C 19 n 8 DC 19 B G 20 n 9 DG 20 B C 21 n 10 DC 21 B G 22 n 11 DG 22 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 A O1' H1 AAB HOH 6 23 1.59 1 -4.61 0.70 121.90 117.29 A A A N3 C2 O2 DC DC DC 1 1 1 N 1 -5.80 0.80 105.90 100.10 A A A O4' C1' C2' DG DG DG 2 2 2 N 1 4.10 0.30 108.30 112.40 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 7.24 1.20 119.70 126.94 A A A C3' O3' P DC DC DG 3 3 4 Y 1 1.97 0.30 108.30 110.27 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 7.74 1.20 119.70 127.44 A A A C3' O3' P DA DA AAB 5 5 6 Y 1 2.81 0.30 108.30 111.11 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 13.69 1.20 119.70 133.39 A A A C3' O3' P DC DC DG 8 8 9 Y 1 3.25 0.30 108.30 111.55 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 3.66 0.30 108.30 111.96 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 3.70 0.30 108.30 112.00 B B B O4' C1' N9 DG DG DG 13 13 13 N 1 8.77 1.20 119.70 128.47 B B B C3' O3' P DG DG DT 15 15 16 Y 1 2.93 0.30 108.30 111.23 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 2.91 0.30 108.30 111.21 B B B O4' C1' N1 DT DT DT 18 18 18 N 1 7.20 1.20 119.70 126.90 B B B C3' O3' P DT DT DC 18 18 19 Y 1 11.62 1.20 119.70 131.32 B B B C3' O3' P DG DG DC 20 20 21 Y 1 -4.99 0.70 102.20 97.21 B B B C4' C3' C2' DG DG DG 22 22 22 N 1 3.29 0.30 108.30 111.59 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 A A C4' C3' DC DC 1 1 -0.080 0.010 1.521 1.441 N 1 A A C3' C2' DC DC 1 1 -0.073 0.008 1.516 1.443 N 1 A A O3' C3' DC DC 1 1 -0.087 0.006 1.419 1.332 N 1 A A C2 O2 DC DC 1 1 -0.060 0.009 1.240 1.180 N 1 A A N1 C6 DC DC 1 1 -0.051 0.006 1.367 1.316 N 1 A A N3 C4 DC DC 1 1 -0.055 0.007 1.335 1.280 N 1 A A O3' P DC DG 1 2 -0.112 0.012 1.607 1.495 Y 1 A A P OP1 DG DG 2 2 -0.244 0.017 1.485 1.241 N 1 A A P OP2 DG DG 2 2 -0.229 0.017 1.485 1.256 N 1 A A P O5' DG DG 2 2 -0.091 0.010 1.593 1.502 N 1 A A P OP1 DC DC 8 8 -0.129 0.017 1.485 1.356 N 1 A A P OP2 DC DC 8 8 -0.113 0.017 1.485 1.372 N 1 A A P O5' DC DC 8 8 -0.075 0.010 1.593 1.518 N 1 A A C3' C2' DC DC 8 8 -0.050 0.008 1.516 1.466 N 1 A A O3' P DC DG 8 9 -0.092 0.012 1.607 1.515 Y 1 B B C3' C2' DC DC 21 21 -0.056 0.008 1.516 1.460 N 1 B B P OP2 DG DG 22 22 -0.156 0.017 1.485 1.329 N 1 B B P O5' DG DG 22 22 -0.141 0.010 1.593 1.452 N 1 B B O3' C3' DG DG 22 22 -0.042 0.006 1.419 1.377 N 1 B B C6 N1 DG DG 22 22 -0.046 0.007 1.391 1.345 N model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM, NMR, 1 STRUCTURE 1 N N 2 N N 3 N N covale 1.561 one A DA 5 A O3' DA 5 1_555 A AAB 6 A P AAB 6 1_555 covale 1.597 one A AAB 6 A O3' AAB 6 1_555 A DA 7 A P DA 7 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 22 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 22 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 22 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 21 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 21 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 21 B N4 DC 10 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 20 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 20 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 20 B N2 DG 9 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 19 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 19 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 19 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 18 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 18 B O4 DT 7 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 16 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 16 B O4 DT 5 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 15 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 15 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 15 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 14 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 14 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 14 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 13 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 13 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 13 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 12 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 12 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 12 B N2 DG 1 1_555 DNA DAMAGED DNA, APYRIMIDINIC DNA, WATER, DNA 1A9J PDB 1 1A9J 1A9J PDB 2 1A9J 1 11 1A9J 1 11 1A9J A 1 1 11 12 22 1A9J 12 22 1A9J B 2 1 11 1 P 1