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 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 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 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 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/pdb1gj0/pdb pdb_00001gj0 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*(AAB)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)(AAB)(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 38.542 1 19 A 1 B 26 -0.227 A_DC1:DG26_B 1 -28.248 0.624 -0.434 -0.110 28.087 1 19 A 2 B 25 -1.851 A_DC2:DG25_B 2 -23.620 0.423 -0.277 -0.173 -17.364 1 20 A 3 B 24 1.364 A_DA3:DT24_B 3 -13.891 0.053 -0.085 -0.170 -16.265 1 20 A 4 B 23 0.710 A_DA4:DT23_B 4 -7.987 -0.069 0.099 -0.195 -13.970 1 20 A 5 B 22 -7.135 A_DA5:DT22_B 5 0.848 -0.037 0.189 -0.183 4.582 1 19 A 6 B 21 -5.540 A_DG6:DC21_B 6 -7.884 -0.766 0.433 -0.419 15.212 1 20 A 8 B 19 -12.776 A_DA8:DT19_B 7 -13.405 0.118 0.642 -0.180 11.427 1 19 A 9 B 18 -1.158 A_DC9:DG18_B 8 -9.862 0.387 0.347 -0.239 12.116 1 20 A 10 B 17 -1.371 A_DT10:DA17_B 9 -8.401 -0.073 -0.011 -0.168 -17.032 1 19 A 11 B 16 -2.798 A_DG11:DC16_B 10 -18.866 -0.148 0.040 -0.253 -30.101 1 19 A 12 B 15 -0.012 A_DG12:DC15_B 11 -24.057 -0.555 -0.088 -0.145 -25.713 1 19 A 13 B 14 -3.742 A_DG13:DC14_B 12 -13.889 -0.666 0.240 -0.258 3.602 38.731 A A 1 2 3.386 B B 26 25 3.622 2.244 0.684 -0.335 AA_DC1DC2:DG25DG26_BB 1 0.266 -0.402 38.668 -0.809 -0.996 3.815 45.347 A A 2 3 15.559 B B 25 24 4.126 11.868 0.358 -0.755 AA_DC2DA3:DT24DG25_BB 2 1.157 -1.516 43.831 -2.282 -0.337 3.219 36.937 A A 3 4 -5.108 B B 24 23 3.182 -3.232 -0.262 -0.479 AA_DA3DA4:DT23DT24_BB 3 -1.699 2.686 36.763 -0.329 0.189 3.211 33.261 A A 4 5 -1.490 B B 23 22 3.154 -0.852 -0.735 -0.575 AA_DA4DA5:DT22DT23_BB 4 -2.373 4.149 33.168 -0.866 0.898 2.969 32.557 A A 5 6 -14.223 B B 22 21 2.885 -7.898 -0.233 -0.728 AA_DA5DG6:DC21DT22_BB 5 0.762 -1.372 31.600 -0.046 0.536 6.056 85.039 A A 6 8 -8.018 B B 21 19 6.132 -10.814 0.044 0.343 AA_DG6DA8:DT19DC21_BB 6 -4.728 3.505 84.371 0.721 -0.237 3.376 38.338 A A 8 9 -9.412 B B 19 18 3.446 -6.156 0.606 0.279 AA_DA8DC9:DG18DT19_BB 7 0.975 -1.491 37.847 1.233 -0.795 3.320 37.508 A A 9 10 -5.620 B B 18 17 3.247 -3.604 0.358 -0.733 AA_DC9DT10:DA17DG18_BB 8 3.365 -5.248 37.194 -0.665 -0.112 3.716 42.039 A A 10 11 7.144 B B 17 16 3.839 5.109 -0.240 -0.899 AA_DT10DG11:DC16DA17_BB 9 -3.321 4.644 41.615 -1.867 -0.065 3.281 38.961 A A 11 12 7.065 B B 16 15 3.418 4.699 -0.110 -0.877 AA_DG11DG12:DC15DC16_BB 10 2.334 -3.509 38.619 -1.900 0.456 3.192 39.873 A A 12 13 -2.243 B B 15 14 3.142 -1.528 -0.647 -0.348 AA_DG12DG13:DC14DC15_BB 11 -3.073 4.511 39.731 -0.339 0.604 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: Beta Anomer Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha Anomer Minimized Average Structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha 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 AAB 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 0.079 SIDE CHAIN 1 A DG 11 0.090 SIDE CHAIN 1 B DT 22 0.075 SIDE CHAIN 1 B DG 25 0.065 SIDE CHAIN 1 4.18 0.60 118.60 122.78 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 5.48 0.60 118.60 124.08 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 -5.02 0.80 123.70 118.68 A A A C5 C6 N6 DA DA DA 5 5 5 N 1 4.66 0.70 119.90 124.56 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 5.69 0.60 118.60 124.29 A A A N1 C6 N6 DA DA DA 8 8 8 N 1 4.76 0.70 119.90 124.66 A A A N3 C2 N2 DG DG DG 12 12 12 N 1 5.31 0.70 119.90 125.21 A A A N3 C2 N2 DG DG DG 13 13 13 N 1 4.69 0.60 118.60 123.29 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 7.75 1.20 119.70 127.45 B B B C3' O3' P DA DA DG 17 17 18 Y 1 5.00 0.70 119.90 124.90 B B B N3 C2 N2 DG DG DG 18 18 18 N 1 4.33 0.60 118.60 122.93 B B B N1 C6 N6 DA DA DA 20 20 20 N 1 3.74 0.60 118.90 122.64 B B B N1 C2 O2 DC DC DC 21 21 21 N 1 9.30 1.20 119.70 129.00 B B B C3' O3' P DC DC DT 21 21 22 Y 1 7.61 1.20 119.70 127.31 B B B C3' O3' P DT DT DT 22 22 23 Y 1 4.46 0.70 119.90 124.36 B B B N3 C2 N2 DG DG DG 25 25 25 N 1 4.96 0.70 119.90 124.86 B B B N3 C2 N2 DG DG DG 26 26 26 N 1 A A N9 C4 DA DA 4 4 0.039 0.006 1.374 1.413 N 1 A A C5' C4' DT DT 10 10 0.043 0.007 1.512 1.555 N 1 B B N1 C2 DT DT 22 22 0.049 0.008 1.376 1.425 N NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BETA ANOMER 1 N N 2 N N covale 1.585 one A DG 6 A O3' DG 6 1_555 A AAB 7 A P AAB 7 1_555 covale 1.582 one A AAB 7 A O3' AAB 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 1GJ0 PDB 1 1GJ0 1GJ0 PDB 2 1GJ0 1 13 1GJ0 1 13 1GJ0 A 1 1 13 14 26 1GJ0 14 26 1GJ0 B 2 1 13 1 P 1