1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Hoehn, S.T. Turner, C.J. Stubbe, J. 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 C5 H11 O7 P 214.110 2-DEOXY-5-PHOSPHONO-RIBOSE saccharide 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 S C N 145 N O N 146 N C N 147 S C N 148 N O N 149 R C N 150 N O N 151 N C N 152 N O N 153 N P N 154 N O N 155 N O N 156 N O 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 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 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 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 doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 29 3413 3423 10.1093/nar/29.16.3413 11504879 Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation. 2001 10.2210/pdb1giz/pdb pdb_00001giz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3892.526 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3' 1 syn polymer 3942.572 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' 1 syn polymer no yes (DC)(DC)(DA)(DA)(DA)(DG)(ORP)(DA)(DC)(DT)(DG)(DG)(DG) CCAAAGXACTGGG A polydeoxyribonucleotide no no (DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG) CCCAGTACTTTGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n 40.798 1 19 A 1 B 26 -0.782 A_DC1:DG26_B 1 -27.508 0.621 -0.502 -0.098 28.216 1 19 A 2 B 25 -1.766 A_DC2:DG25_B 2 -23.394 0.469 -0.326 -0.189 -20.727 1 20 A 3 B 24 0.238 A_DA3:DT24_B 3 -14.346 0.101 -0.227 -0.169 -15.997 1 20 A 4 B 23 -0.183 A_DA4:DT23_B 4 -5.372 -0.015 -0.011 -0.193 -11.401 1 20 A 5 B 22 -6.700 A_DA5:DT22_B 5 2.688 -0.093 0.166 -0.221 0.344 1 19 A 6 B 21 -4.072 A_DG6:DC21_B 6 -13.304 -0.637 0.409 -0.398 11.631 1 20 A 8 B 19 -11.575 A_DA8:DT19_B 7 -7.915 0.009 0.319 -0.133 15.359 1 19 A 9 B 18 2.689 A_DC9:DG18_B 8 -6.953 0.431 -0.043 -0.071 13.126 1 20 A 10 B 17 0.344 A_DT10:DA17_B 9 -10.034 -0.017 -0.170 -0.177 -16.905 1 19 A 11 B 16 -2.666 A_DG11:DC16_B 10 -18.127 -0.277 0.069 -0.267 -28.869 1 19 A 12 B 15 -0.635 A_DG12:DC15_B 11 -23.858 -0.490 -0.128 -0.174 -27.054 1 19 A 13 B 14 -2.827 A_DG13:DC14_B 12 -12.701 -0.701 0.133 -0.258 3.682 38.965 A A 1 2 2.636 B B 26 25 3.700 1.757 0.698 -0.341 AA_DC1DC2:DG25DG26_BB 1 0.006 -0.009 38.927 -0.752 -1.045 3.834 46.045 A A 2 3 17.202 B B 25 24 4.190 13.279 0.251 -0.739 AA_DC2DA3:DT24DG25_BB 2 2.101 -2.721 44.140 -2.378 -0.094 3.119 36.896 A A 3 4 -6.200 B B 24 23 3.084 -3.916 -0.259 -0.433 AA_DA3DA4:DT23DT24_BB 3 -1.304 2.065 36.672 -0.180 0.241 3.176 32.857 A A 4 5 -1.490 B B 23 22 3.115 -0.842 -0.687 -0.513 AA_DA4DA5:DT22DT23_BB 4 -3.002 5.314 32.712 -0.767 0.720 3.145 35.865 A A 5 6 -12.739 B B 22 21 3.082 -7.786 -0.361 -0.599 AA_DA5DG6:DC21DT22_BB 5 -0.562 0.920 35.033 0.102 0.508 6.383 80.681 A A 6 8 -13.802 B B 21 19 6.542 -17.766 0.394 0.209 AA_DG6DA8:DT19DC21_BB 6 -1.940 1.507 79.009 1.088 -0.405 3.275 35.372 A A 8 9 -5.728 B B 19 18 3.272 -3.473 0.651 0.196 AA_DA8DC9:DG18DT19_BB 7 2.473 -4.079 35.123 0.836 -0.706 3.311 36.620 A A 9 10 -2.129 B B 18 17 3.286 -1.337 0.181 -0.644 AA_DC9DT10:DA17DG18_BB 8 1.141 -1.817 36.579 -0.839 -0.129 3.754 41.726 A A 10 11 7.312 B B 17 16 3.885 5.181 -0.215 -0.829 AA_DT10DG11:DC16DA17_BB 9 -5.627 7.941 41.050 -1.806 -0.395 3.316 39.252 A A 11 12 7.214 B B 16 15 3.470 4.829 -0.109 -0.915 AA_DG11DG12:DC15DC16_BB 10 3.334 -4.980 38.828 -1.963 0.577 3.225 38.702 A A 12 13 -1.140 B B 15 14 3.184 -0.755 -0.644 -0.286 AA_DG12DG13:DC14DC15_BB 11 -2.745 4.146 38.601 -0.341 0.642 database_2 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 Data collection 1 0 2001-08-22 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-02-23 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag Apyrimidinic Dna With Bound Water At The Damaged Site, Alpha Form, Nmr, 1 Structure Apyrimidinic Dna With Bound Water At The Damaged Site, Beta Form, Nmr, 1 Structure Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha Anomer Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer Minimized average structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer RCSB Y RCSB 2000-10-31 REL THE ABASIC SITE DEOXYRIBOSE 1H-1H COUPLING CONSTANTS AND THE DNA 31P-H3' COUPLING CONSTANTS WERE EXPERIMENTALLY DETERMINED. THIS INFORMATION WAS USED IN THE MODELING PROTOCOL. 1 NOESY PE-COSY watergate-NOESY 31P-HCOSY 31P-decoupled-PE-COSY 31P-decoupled-J-scaled-DQCOSY 10 mM sodium phosphate buffer 6.8 ambient 293 K 10 mM sodium phosphate buffer 6.8 ambient 278 K 10 mM sodium phosphate buffer 6.8 ambient 298 K THE STRUCTURE IS BASED ON 475 NOE-DERIVED DISTANCE CONSTRAINTS AND 101 DIHEDRAL ANGLE RESTRAINTS. molecular dynamics 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer D2O 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer 10% D2O, 90% H2O 3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer D2O Brunger structure solution X-PLOR 3.851 MSI processing Felix 95.0 MSI data analysis Felix 95.0 Brunger refinement X-PLOR 3.851 750 Home-built HOME-BUILT 600 Home-built HOME-BUILT C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A A 4 n 4 DA 4 A A 5 n 5 DA 5 A G 6 n 6 DG 6 A D1P 7 n 7 ORP 7 A A 8 n 8 DA 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A G 11 n 11 DG 11 A G 12 n 12 DG 12 A G 13 n 13 DG 13 A C 14 n 1 DC 14 B C 15 n 2 DC 15 B C 16 n 3 DC 16 B A 17 n 4 DA 17 B G 18 n 5 DG 18 B T 19 n 6 DT 19 B A 20 n 7 DA 20 B C 21 n 8 DC 21 B T 22 n 9 DT 22 B T 23 n 10 DT 23 B T 24 n 11 DT 24 B G 25 n 12 DG 25 B G 26 n 13 DG 26 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 DA 8 0.070 SIDE CHAIN 1 A DG 11 0.087 SIDE CHAIN 1 B DT 22 0.077 SIDE CHAIN 1 B DG 25 0.065 SIDE CHAIN 1 4.02 0.60 118.60 122.62 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 5.80 0.60 118.60 124.40 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 -5.24 0.80 123.70 118.46 A A A C5 C6 N6 DA DA DA 5 5 5 N 1 5.16 0.70 119.90 125.06 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 5.01 0.60 118.60 123.61 A A A N1 C6 N6 DA DA DA 8 8 8 N 1 -4.89 0.80 123.70 118.81 A A A C5 C6 N6 DA DA DA 8 8 8 N 1 5.34 0.70 119.90 125.24 A A A N3 C2 N2 DG DG DG 12 12 12 N 1 4.65 0.70 119.90 124.55 A A A N3 C2 N2 DG DG DG 13 13 13 N 1 3.94 0.60 118.60 122.54 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 8.05 1.20 119.70 127.75 B B B C3' O3' P DC DC DT 21 21 22 Y 1 7.65 1.20 119.70 127.35 B B B C3' O3' P DT DT DT 22 22 23 Y 1 4.50 0.70 119.90 124.40 B B B N3 C2 N2 DG DG DG 25 25 25 N 1 4.86 0.70 119.90 124.76 B B B N3 C2 N2 DG DG DG 26 26 26 N 1 A A N9 C4 DA DA 4 4 0.037 0.006 1.374 1.411 N 1 A A N9 C4 DA DA 8 8 0.038 0.006 1.374 1.412 N 1 B B C8 N9 DG DG 25 25 -0.042 0.007 1.374 1.332 N NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER 1 N N 2 N N covale 1.577 both A DG 6 A O3' DG 6 1_555 A ORP 7 A P ORP 7 1_555 covale 1.581 one A ORP 7 A O3 ORP 7 1_555 A DA 8 A P DA 8 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 26 B N1 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 26 B O6 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 26 B N2 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 25 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 25 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 25 B N2 DG 12 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 24 B N3 DT 11 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 24 B O4 DT 11 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 23 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 23 B O4 DT 10 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 22 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 22 B O4 DT 9 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 21 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 21 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 21 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 19 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 19 B O4 DT 6 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 18 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 18 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 18 B N2 DG 5 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 17 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 17 B N6 DA 4 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 16 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 16 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 16 B N4 DC 3 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 15 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 15 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 15 B N4 DC 2 1_555 hydrog WATSON-CRICK A DG 13 A N1 DG 13 1_555 B DC 14 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 13 A N2 DG 13 1_555 B DC 14 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 13 A O6 DG 13 1_555 B DC 14 B N4 DC 1 1_555 DNA DAMAGED DNA, APYRIMIDINIC SITE, DNA 1GIZ PDB 1 1GIZ 1GIZ PDB 2 1GIZ 1 13 1GIZ 1 13 1GIZ A 1 1 13 14 26 1GIZ 14 26 1GIZ B 2 1 13 1 P 1