1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Junker, H.-D. Hoehn, S.T. Bunt, R.C. Marathius, V. Chen, J. Turner, C.J. Stubbe, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C2 H5 O6 P 156.031 2-PHOSPHOGLYCOLIC ACID 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 P N 145 N O N 146 N O N 147 N O N 148 N O N 149 N C N 150 N C N 151 N O N 152 N O N 153 N H N 154 N H N 155 N H N 156 N H N 157 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 doub 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 doub N 161 N sing N 162 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 30 5497 5508 10.1093/nar/gkf681 12490718 Synthesis, Characterization and Solution Structure of Tethered Oligonucleotides Containing an Internal 3'-Phosphoglycolate, 5'-Phosphate Gapped Lesion 2002 10.2210/pdb1g5k/pdb pdb_00001g5k 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 1802.232 5'-D(*CP*CP*AP*AP*AP*G)-3' 1 syn polymer 1849.241 5'-D(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 156.031 2-PHOSPHOGLYCOLIC ACID 1 man non-polymer no no (DC)(DC)(DA)(DA)(DA)(DG) CCAAAG A polydeoxyribonucleotide no no (DA)(DC)(DT)(DG)(DG)(DG) ACTGGG B polydeoxyribonucleotide no no (DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG) CCCAGTACTTTGG C 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 34.031 1 19 A 1 C 26 -1.125 A_DC1:DG26_C 1 -21.216 0.741 -0.282 -0.164 13.149 1 19 A 2 C 25 -5.105 A_DC2:DG25_C 2 -15.557 0.662 0.243 -0.383 -0.474 1 20 A 3 C 24 2.678 A_DA3:DT24_C 3 3.651 -0.012 0.484 -0.193 7.468 1 20 A 4 C 23 2.520 A_DA4:DT23_C 4 -4.579 0.040 0.824 -0.267 9.468 1 20 A 5 C 22 -4.115 A_DA5:DT22_C 5 -4.671 -0.180 0.655 -0.336 18.521 1 19 A 6 C 21 -2.836 A_DG6:DC21_C 6 -0.796 -0.906 0.945 -0.450 -8.449 1 20 B 8 C 19 5.930 B_DA8:DT19_C 7 4.043 -0.040 0.526 -0.247 -1.600 1 19 B 9 C 18 9.270 B_DC9:DG18_C 8 16.476 0.789 0.884 -0.359 6.801 1 20 B 10 C 17 2.400 B_DT10:DA17_C 9 6.494 0.005 0.425 -0.207 -12.553 1 19 B 11 C 16 1.238 B_DG11:DC16_C 10 -18.197 -0.866 -0.378 -0.339 -32.475 1 19 B 12 C 15 -6.156 B_DG12:DC15_C 11 -19.897 -0.657 -0.114 -0.227 -18.467 1 19 B 13 C 14 -9.319 B_DG13:DC14_C 12 -9.203 -0.612 0.034 -0.347 3.737 40.759 A A 1 2 11.862 C C 26 25 3.931 8.207 0.346 -0.515 AA_DC1DC2:DG25DG26_CC 1 -1.978 2.859 39.911 -1.813 -0.756 3.978 37.584 A A 2 3 -17.424 C C 25 24 3.817 -11.061 0.580 -1.306 AA_DC2DA3:DT24DG25_CC 2 -2.789 4.393 35.871 -0.266 -1.343 2.989 35.218 A A 3 4 5.705 C C 24 23 3.073 3.432 -0.420 -1.027 AA_DA3DA4:DT23DT24_CC 3 -5.789 9.624 34.589 -2.174 -0.112 3.140 35.463 A A 4 5 0.176 C C 23 22 3.121 0.107 -0.636 -0.989 AA_DA4DA5:DT22DT23_CC 4 -1.382 2.270 35.436 -1.638 0.850 2.906 36.326 A A 5 6 -2.935 C C 22 21 2.876 -1.827 -0.075 -0.776 AA_DA5DG6:DC21DT22_CC 5 -3.262 5.240 36.140 -1.019 -0.284 6.468 91.225 A B 6 8 -4.485 C C 21 19 6.571 -6.390 0.487 -0.315 AB_DG6DA8:DT19DC21_CC 6 -14.333 10.059 90.160 0.031 -0.905 3.561 39.975 B B 8 9 -2.275 C C 19 18 3.532 -1.555 -0.045 -0.853 BB_DA8DC9:DG18DT19_CC 7 -1.106 1.618 39.931 -1.054 -0.071 3.345 28.835 B B 9 10 -11.991 C C 18 17 3.234 -5.914 -0.201 -1.136 BB_DC9DT10:DA17DG18_CC 8 3.712 -7.526 27.994 -0.934 1.250 3.884 36.281 B B 10 11 -2.760 C C 17 16 3.917 -1.711 -0.207 -1.158 BB_DT10DG11:DC16DA17_CC 9 5.946 -9.593 35.767 -1.572 1.332 3.953 42.874 B B 11 12 -0.648 C C 16 15 3.863 -0.473 -0.963 -0.189 BB_DG11DG12:DC15DC16_CC 10 -5.453 7.479 42.539 -0.202 0.667 3.042 39.151 B B 12 13 -5.225 C C 15 14 3.021 -3.494 -0.825 0.205 BB_DG12DG13:DC14DC15_CC 11 -2.788 4.169 38.904 0.696 0.920 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection 1 0 2003-01-07 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id ensemble model OF PDB ENTRY 1N0K MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1N0O MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1G5K RCSB Y RCSB 2002-10-14 REL PGA 2-PHOSPHOGLYCOLIC ACID minimum rmsd and nmr constraints violation 10 10 PECOSY TOCSY NOESY HSQC GE-HSQC % 40 mM NaHPO4 6.9 1.0 atm 293.15 K CONJUGATE GRADIENT MINIMIZATION Brunger refinement XPLOR 3.851 Brunger structure solution XPLOR 3.851 500 custom build 600 custom build 750 custom build T 7 4 PGA PGA 7 A 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 T 7 n 1 DA 8 B C 9 n 2 DC 9 B T 10 n 3 DT 10 B G 11 n 4 DG 11 B G 12 n 5 DG 12 B G 13 n 6 DG 13 B C 14 n 1 DC 14 C C 15 n 2 DC 15 C C 16 n 3 DC 16 C A 17 n 4 DA 17 C G 18 n 5 DG 18 C T 19 n 6 DT 19 C A 20 n 7 DA 20 C C 21 n 8 DC 21 C T 22 n 9 DT 22 C T 23 n 10 DT 23 C T 24 n 11 DT 24 C G 25 n 12 DG 25 C G 26 n 13 DG 26 C author_defined_assembly 3 trimeric 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 DG 6 0.056 SIDE CHAIN 1 B DC 9 0.095 SIDE CHAIN 1 B DG 13 0.093 SIDE CHAIN 1 C DA 20 0.053 SIDE CHAIN 1 C DT 22 0.094 SIDE CHAIN 1 C DT 23 0.096 SIDE CHAIN 1 C DG 25 0.074 SIDE CHAIN 2 A DC 2 0.075 SIDE CHAIN 2 B DT 10 0.072 SIDE CHAIN 2 B DG 11 0.078 SIDE CHAIN 2 B DG 13 0.059 SIDE CHAIN 2 C DC 14 0.082 SIDE CHAIN 2 C DC 16 0.094 SIDE CHAIN 2 C DG 18 0.081 SIDE CHAIN 2 C DT 19 0.074 SIDE CHAIN 2 C DA 20 0.073 SIDE CHAIN 2 C DC 21 0.063 SIDE CHAIN 2 C DT 22 0.092 SIDE CHAIN 2 C DT 23 0.100 SIDE CHAIN 2 C DG 25 0.054 SIDE CHAIN 2 C DG 26 0.060 SIDE CHAIN 3 A DG 6 0.067 SIDE CHAIN 3 B DG 11 0.054 SIDE CHAIN 3 C DC 14 0.059 SIDE CHAIN 3 C DC 15 0.065 SIDE CHAIN 3 C DC 16 0.102 SIDE CHAIN 3 C DT 23 0.080 SIDE CHAIN 3 C DG 25 0.065 SIDE CHAIN 4 A DC 1 0.090 SIDE CHAIN 4 A DA 5 0.062 SIDE CHAIN 4 B DG 11 0.075 SIDE CHAIN 4 C DC 14 0.092 SIDE CHAIN 4 C DC 16 0.100 SIDE CHAIN 4 C DC 21 0.068 SIDE CHAIN 4 C DT 23 0.126 SIDE CHAIN 5 A DG 6 0.053 SIDE CHAIN 5 B DG 11 0.072 SIDE CHAIN 5 C DC 14 0.106 SIDE CHAIN 5 C DC 16 0.095 SIDE CHAIN 5 C DA 20 0.062 SIDE CHAIN 5 C DT 22 0.063 SIDE CHAIN 5 C DT 23 0.097 SIDE CHAIN 5 C DG 25 0.062 SIDE CHAIN 6 A DC 1 0.101 SIDE CHAIN 6 A DG 6 0.051 SIDE CHAIN 6 B DT 10 0.063 SIDE CHAIN 6 B DG 11 0.080 SIDE CHAIN 6 C DC 14 0.092 SIDE CHAIN 6 C DC 16 0.103 SIDE CHAIN 6 C DA 20 0.063 SIDE CHAIN 6 C DT 23 0.098 SIDE CHAIN 6 C DG 25 0.104 SIDE CHAIN 6 C DG 26 0.089 SIDE CHAIN 7 A DC 1 0.080 SIDE CHAIN 7 A DA 5 0.061 SIDE CHAIN 7 B DG 11 0.062 SIDE CHAIN 7 C DC 14 0.092 SIDE CHAIN 7 C DC 16 0.100 SIDE CHAIN 7 C DA 20 0.058 SIDE CHAIN 7 C DC 21 0.080 SIDE CHAIN 7 C DT 23 0.085 SIDE CHAIN 7 C DG 26 0.074 SIDE CHAIN 8 B DG 11 0.054 SIDE CHAIN 8 B DG 12 0.052 SIDE CHAIN 8 C DC 14 0.090 SIDE CHAIN 8 C DT 22 0.066 SIDE CHAIN 8 C DT 23 0.101 SIDE CHAIN 8 C DT 24 0.059 SIDE CHAIN 8 C DG 25 0.066 SIDE CHAIN 9 A DC 1 0.074 SIDE CHAIN 9 A DA 5 0.053 SIDE CHAIN 9 B DG 11 0.074 SIDE CHAIN 9 C DC 14 0.094 SIDE CHAIN 9 C DC 16 0.099 SIDE CHAIN 9 C DT 23 0.125 SIDE CHAIN 10 A DG 6 0.052 SIDE CHAIN 10 B DT 10 0.065 SIDE CHAIN 10 B DG 11 0.079 SIDE CHAIN 10 C DC 14 0.103 SIDE CHAIN 10 C DC 16 0.091 SIDE CHAIN 10 C DA 20 0.058 SIDE CHAIN 10 C DT 22 0.062 SIDE CHAIN 10 C DT 23 0.090 SIDE CHAIN 10 C DG 25 0.075 SIDE CHAIN 1 8.47 1.20 119.70 128.17 A A A C3' O3' P DC DC DA 2 2 3 Y 1 4.82 0.60 118.60 123.42 A A A N1 C6 N6 DA DA DA 4 4 4 N 1 4.85 0.60 118.60 123.45 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 5.79 0.70 119.90 125.69 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 3.67 0.60 118.60 122.27 B B B N1 C6 N6 DA DA DA 8 8 8 N 1 11.15 1.20 119.70 130.85 B B B C3' O3' P DT DT DG 10 10 11 Y 1 5.23 0.70 119.90 125.13 B B B N3 C2 N2 DG DG DG 11 11 11 N 1 5.88 0.70 119.90 125.78 B B B N3 C2 N2 DG DG DG 12 12 12 N 1 5.12 0.70 119.90 125.02 B B B N3 C2 N2 DG DG DG 13 13 13 N 1 3.66 0.60 118.90 122.56 C C C N1 C2 O2 DC DC DC 14 14 14 N 1 8.54 1.20 119.70 128.24 C C C C3' O3' P DC DC DT 21 21 22 Y 1 7.42 1.20 119.70 127.12 C C C C3' O3' P DT DT DG 24 24 25 Y 1 4.91 0.70 119.90 124.81 C C C N3 C2 N2 DG DG DG 26 26 26 N 2 8.06 1.20 119.70 127.76 A A A C3' O3' P DC DC DA 2 2 3 Y 2 4.36 0.60 118.60 122.96 A A A N1 C6 N6 DA DA DA 4 4 4 N 2 4.79 0.60 118.60 123.39 A A A N1 C6 N6 DA DA DA 5 5 5 N 2 5.48 0.70 119.90 125.38 A A A N3 C2 N2 DG DG DG 6 6 6 N 2 2.00 0.30 108.30 110.30 B B B O4' C1' N9 DA DA DA 8 8 8 N 2 4.43 0.70 118.00 122.43 B B B N3 C4 N4 DC DC DC 9 9 9 N 2 7.21 0.70 119.90 127.11 B B B N3 C2 N2 DG DG DG 11 11 11 N 2 5.65 0.70 119.90 125.55 B B B N3 C2 N2 DG DG DG 12 12 12 N 2 4.80 0.70 119.90 124.70 B B B N3 C2 N2 DG DG DG 13 13 13 N 2 3.68 0.60 118.60 122.28 C C C N1 C6 N6 DA DA DA 17 17 17 N 2 3.45 0.50 111.90 115.35 C C C C2 N3 C4 DG DG DG 18 18 18 N 2 7.87 1.20 119.70 127.57 C C C C3' O3' P DC DC DT 21 21 22 Y 2 6.58 0.70 119.90 126.48 C C C N3 C2 N2 DG DG DG 25 25 25 N 2 4.98 0.70 119.90 124.88 C C C N3 C2 N2 DG DG DG 26 26 26 N 3 3.60 0.60 118.90 122.50 A A A N1 C2 O2 DC DC DC 2 2 2 N 3 4.95 0.60 118.60 123.55 A A A N1 C6 N6 DA DA DA 4 4 4 N 3 4.99 0.60 118.60 123.59 A A A N1 C6 N6 DA DA DA 5 5 5 N 3 5.85 0.70 119.90 125.75 A A A N3 C2 N2 DG DG DG 6 6 6 N 3 4.53 0.60 118.60 123.13 B B B N1 C6 N6 DA DA DA 8 8 8 N 3 8.64 1.20 119.70 128.34 B B B C3' O3' P DT DT DG 10 10 11 Y 3 4.45 0.70 119.90 124.35 B B B N3 C2 N2 DG DG DG 11 11 11 N 3 6.18 0.70 119.90 126.08 B B B N3 C2 N2 DG DG DG 12 12 12 N 3 4.82 0.70 119.90 124.72 B B B N3 C2 N2 DG DG DG 13 13 13 N 3 4.98 0.70 119.90 124.88 C C C N3 C2 N2 DG DG DG 18 18 18 N 3 8.60 1.20 119.70 128.30 C C C C3' O3' P DT DT DT 22 22 23 Y 3 -3.93 0.60 122.90 118.97 C C C C6 C5 C7 DT DT DT 23 23 23 N 3 4.45 0.70 119.90 124.35 C C C N3 C2 N2 DG DG DG 26 26 26 N 4 3.72 0.60 118.60 122.32 A A A N1 C6 N6 DA DA DA 3 3 3 N 4 4.54 0.60 118.60 123.14 A A A N1 C6 N6 DA DA DA 4 4 4 N 4 5.74 0.60 118.60 124.34 A A A N1 C6 N6 DA DA DA 5 5 5 N 4 -4.93 0.80 123.70 118.77 A A A C5 C6 N6 DA DA DA 5 5 5 N 4 7.04 0.70 119.90 126.94 A A A N3 C2 N2 DG DG DG 6 6 6 N 4 3.70 0.60 118.60 122.30 B B B N1 C6 N6 DA DA DA 8 8 8 N 4 5.80 0.70 119.90 125.70 B B B N3 C2 N2 DG DG DG 12 12 12 N 4 4.88 0.70 119.90 124.78 B B B N3 C2 N2 DG DG DG 13 13 13 N 4 4.72 0.60 118.60 123.32 C C C N1 C6 N6 DA DA DA 17 17 17 N 4 5.20 0.70 119.90 125.10 C C C N3 C2 N2 DG DG DG 18 18 18 N 4 -3.97 0.60 122.90 118.93 C C C C6 C5 C7 DT DT DT 23 23 23 N 4 7.47 1.20 119.70 127.17 C C C C3' O3' P DT DT DG 24 24 25 Y 4 8.29 1.20 119.70 127.99 C C C C3' O3' P DG DG DG 25 25 26 Y 5 3.68 0.60 118.90 122.58 A A A N1 C2 O2 DC DC DC 2 2 2 N 5 8.21 1.20 119.70 127.91 A A A C3' O3' P DC DC DA 2 2 3 Y 5 4.69 0.60 118.60 123.29 A A A N1 C6 N6 DA DA DA 4 4 4 N 5 4.69 0.60 118.60 123.29 A A A N1 C6 N6 DA DA DA 5 5 5 N 5 4.93 0.70 119.90 124.83 A A A N3 C2 N2 DG DG DG 6 6 6 N 5 4.66 0.60 118.60 123.26 B B B N1 C6 N6 DA DA DA 8 8 8 N 5 4.26 0.70 119.90 124.16 B B B N3 C2 N2 DG DG DG 11 11 11 N 5 5.85 0.70 119.90 125.75 B B B N3 C2 N2 DG DG DG 12 12 12 N 5 4.96 0.70 119.90 124.86 B B B N3 C2 N2 DG DG DG 13 13 13 N 5 4.31 0.60 118.60 122.91 C C C N1 C6 N6 DA DA DA 17 17 17 N 5 -3.75 0.60 122.90 119.15 C C C C6 C5 C7 DT DT DT 23 23 23 N 5 4.91 0.70 119.90 124.81 C C C N3 C2 N2 DG DG DG 26 26 26 N 6 4.03 0.60 118.60 122.63 A A A N1 C6 N6 DA DA DA 3 3 3 N 6 4.68 0.60 118.60 123.28 A A A N1 C6 N6 DA DA DA 4 4 4 N 6 4.79 0.60 118.60 123.39 A A A N1 C6 N6 DA DA DA 5 5 5 N 6 4.44 0.70 119.90 124.34 A A A N3 C2 N2 DG DG DG 6 6 6 N 6 5.84 0.60 118.60 124.44 B B B N1 C6 N6 DA DA DA 8 8 8 N 6 -5.10 0.80 123.70 118.60 B B B C5 C6 N6 DA DA DA 8 8 8 N 6 6.08 0.70 119.90 125.98 B B B N3 C2 N2 DG DG DG 12 12 12 N 6 4.96 0.70 119.90 124.86 B B B N3 C2 N2 DG DG DG 13 13 13 N 6 3.95 0.60 118.60 122.55 C C C N1 C6 N6 DA DA DA 17 17 17 N 6 4.99 0.70 119.90 124.89 C C C N3 C2 N2 DG DG DG 18 18 18 N 6 -4.34 0.60 122.90 118.56 C C C C6 C5 C7 DT DT DT 23 23 23 N 6 5.31 0.70 119.90 125.21 C C C N3 C2 N2 DG DG DG 25 25 25 N 6 10.84 1.20 119.70 130.54 C C C C3' O3' P DG DG DG 25 25 26 Y 7 3.70 0.60 118.60 122.30 A A A N1 C6 N6 DA DA DA 3 3 3 N 7 4.08 0.60 118.60 122.68 A A A N1 C6 N6 DA DA DA 4 4 4 N 7 5.45 0.60 118.60 124.05 A A A N1 C6 N6 DA DA DA 5 5 5 N 7 5.82 0.70 119.90 125.72 A A A N3 C2 N2 DG DG DG 6 6 6 N 7 3.73 0.60 118.60 122.33 B B B N1 C6 N6 DA DA DA 8 8 8 N 7 5.84 0.70 119.90 125.74 B B B N3 C2 N2 DG DG DG 12 12 12 N 7 4.93 0.70 119.90 124.83 B B B N3 C2 N2 DG DG DG 13 13 13 N 7 4.04 0.60 118.60 122.64 C C C N1 C6 N6 DA DA DA 17 17 17 N 7 5.37 0.70 119.90 125.27 C C C N3 C2 N2 DG DG DG 18 18 18 N 7 8.20 1.20 119.70 127.90 C C C C3' O3' P DC DC DT 21 21 22 Y 7 -3.88 0.60 122.90 119.02 C C C C6 C5 C7 DT DT DT 23 23 23 N 7 4.42 0.70 119.90 124.32 C C C N3 C2 N2 DG DG DG 25 25 25 N 7 8.14 1.20 119.70 127.84 C C C C3' O3' P DG DG DG 25 25 26 Y 8 3.64 0.60 118.90 122.54 A A A N1 C2 O2 DC DC DC 2 2 2 N 8 5.12 0.60 118.60 123.72 A A A N1 C6 N6 DA DA DA 4 4 4 N 8 4.82 0.60 118.60 123.42 A A A N1 C6 N6 DA DA DA 5 5 5 N 8 5.72 0.70 119.90 125.62 A A A N3 C2 N2 DG DG DG 6 6 6 N 8 4.50 0.60 118.60 123.10 B B B N1 C6 N6 DA DA DA 8 8 8 N 8 7.40 1.20 119.70 127.10 B B B C3' O3' P DT DT DG 10 10 11 Y 8 4.86 0.70 119.90 124.76 B B B N3 C2 N2 DG DG DG 12 12 12 N 8 6.77 0.70 119.90 126.67 B B B N3 C2 N2 DG DG DG 13 13 13 N 8 9.14 1.20 119.70 128.84 C C C C3' O3' P DC DC DC 15 15 16 Y 8 3.99 0.60 118.60 122.59 C C C N1 C6 N6 DA DA DA 17 17 17 N 8 4.65 0.70 119.90 124.55 C C C N3 C2 N2 DG DG DG 18 18 18 N 8 4.72 0.70 119.90 124.62 C C C N3 C2 N2 DG DG DG 26 26 26 N 9 3.66 0.60 118.90 122.56 A A A N1 C2 O2 DC DC DC 2 2 2 N 9 3.85 0.60 118.60 122.45 A A A N1 C6 N6 DA DA DA 3 3 3 N 9 4.65 0.60 118.60 123.25 A A A N1 C6 N6 DA DA DA 4 4 4 N 9 6.26 0.60 118.60 124.86 A A A N1 C6 N6 DA DA DA 5 5 5 N 9 -5.50 0.80 123.70 118.20 A A A C5 C6 N6 DA DA DA 5 5 5 N 9 7.12 0.70 119.90 127.02 A A A N3 C2 N2 DG DG DG 6 6 6 N 9 5.83 0.70 119.90 125.73 B B B N3 C2 N2 DG DG DG 12 12 12 N 9 4.95 0.70 119.90 124.85 B B B N3 C2 N2 DG DG DG 13 13 13 N 9 4.81 0.60 118.60 123.41 C C C N1 C6 N6 DA DA DA 17 17 17 N 9 5.14 0.70 119.90 125.04 C C C N3 C2 N2 DG DG DG 18 18 18 N 9 3.74 0.60 118.90 122.64 C C C N1 C2 O2 DC DC DC 21 21 21 N 9 8.07 1.20 119.70 127.77 C C C C3' O3' P DT DT DG 24 24 25 Y 9 4.49 0.70 119.90 124.39 C C C N3 C2 N2 DG DG DG 26 26 26 N 10 3.66 0.60 118.90 122.56 A A A N1 C2 O2 DC DC DC 2 2 2 N 10 7.38 1.20 119.70 127.08 A A A C3' O3' P DC DC DA 2 2 3 Y 10 5.01 0.60 118.60 123.61 A A A N1 C6 N6 DA DA DA 4 4 4 N 10 4.78 0.60 118.60 123.38 A A A N1 C6 N6 DA DA DA 5 5 5 N 10 4.98 0.70 119.90 124.88 A A A N3 C2 N2 DG DG DG 6 6 6 N 10 4.81 0.60 118.60 123.41 B B B N1 C6 N6 DA DA DA 8 8 8 N 10 4.25 0.70 119.90 124.15 B B B N3 C2 N2 DG DG DG 11 11 11 N 10 5.86 0.70 119.90 125.76 B B B N3 C2 N2 DG DG DG 12 12 12 N 10 4.89 0.70 119.90 124.79 B B B N3 C2 N2 DG DG DG 13 13 13 N 10 4.51 0.60 118.60 123.11 C C C N1 C6 N6 DA DA DA 17 17 17 N 10 7.37 1.20 119.70 127.07 C C C C3' O3' P DA DA DG 17 17 18 Y 10 -3.84 0.60 122.90 119.06 C C C C6 C5 C7 DT DT DT 23 23 23 N 1 B B P OP3 DA DA 8 8 -0.124 0.012 1.607 1.483 N 1 C C C5' C4' DT DT 19 19 0.044 0.007 1.512 1.556 N 1 C C C5' C4' DA DA 20 20 0.046 0.007 1.512 1.558 N 1 C C C5' C4' DT DT 23 23 0.043 0.007 1.512 1.555 N 2 B B P OP3 DA DA 8 8 -0.124 0.012 1.607 1.483 N 2 B B C5' C4' DG DG 11 11 0.044 0.007 1.512 1.556 N 2 C C C5' C4' DA DA 20 20 0.052 0.007 1.512 1.564 N 2 C C C5' C4' DT DT 22 22 0.042 0.007 1.512 1.554 N 2 C C C5' C4' DT DT 23 23 0.044 0.007 1.512 1.556 N 3 B B P OP3 DA DA 8 8 -0.121 0.012 1.607 1.486 N 3 B B N1 C2 DT DT 10 10 0.049 0.008 1.376 1.425 N 3 C C C5' C4' DC DC 21 21 0.042 0.007 1.512 1.554 N 3 C C C5' C4' DT DT 22 22 0.044 0.007 1.512 1.556 N 4 A A C5' C4' DA DA 3 3 0.044 0.007 1.512 1.556 N 4 B B P OP3 DA DA 8 8 -0.124 0.012 1.607 1.483 N 4 B B C5' C4' DG DG 11 11 0.044 0.007 1.512 1.556 N 4 C C C5' C4' DT DT 19 19 0.046 0.007 1.512 1.558 N 4 C C C5' C4' DT DT 22 22 0.046 0.007 1.512 1.558 N 4 C C N1 C2 DT DT 22 22 0.052 0.008 1.376 1.428 N 5 B B P OP3 DA DA 8 8 -0.130 0.012 1.607 1.477 N 5 C C C5' C4' DC DC 21 21 0.042 0.007 1.512 1.554 N 5 C C C5' C4' DT DT 22 22 0.044 0.007 1.512 1.556 N 6 A A C5' C4' DA DA 3 3 0.045 0.007 1.512 1.557 N 6 A A C5' C4' DA DA 4 4 0.044 0.007 1.512 1.556 N 6 B B P OP3 DA DA 8 8 -0.124 0.012 1.607 1.483 N 6 C C N1 C2 DT DT 19 19 0.048 0.008 1.376 1.424 N 6 C C C5' C4' DT DT 22 22 0.042 0.007 1.512 1.554 N 7 A A C5' C4' DA DA 3 3 0.048 0.007 1.512 1.560 N 7 B B P OP3 DA DA 8 8 -0.122 0.012 1.607 1.485 N 7 B B C5' C4' DG DG 11 11 0.044 0.007 1.512 1.556 N 7 C C C5' C4' DT DT 19 19 0.045 0.007 1.512 1.557 N 7 C C C5' C4' DC DC 21 21 0.042 0.007 1.512 1.554 N 7 C C C5' C4' DT DT 22 22 0.051 0.007 1.512 1.563 N 7 C C N1 C2 DT DT 22 22 0.053 0.008 1.376 1.429 N 8 B B P OP3 DA DA 8 8 -0.124 0.012 1.607 1.483 N 8 C C C5' C4' DT DT 22 22 0.045 0.007 1.512 1.557 N 8 C C C5' C4' DT DT 23 23 0.044 0.007 1.512 1.556 N 9 B B P OP3 DA DA 8 8 -0.125 0.012 1.607 1.482 N 9 B B C5' C4' DG DG 11 11 0.043 0.007 1.512 1.555 N 9 C C C5' C4' DT DT 19 19 0.047 0.007 1.512 1.559 N 9 C C C5' C4' DA DA 20 20 0.042 0.007 1.512 1.554 N 9 C C C5' C4' DT DT 22 22 0.043 0.007 1.512 1.555 N 9 C C N1 C2 DT DT 22 22 0.051 0.008 1.376 1.427 N 10 B B P OP3 DA DA 8 8 -0.130 0.012 1.607 1.477 N 10 C C C5' C4' DC DC 21 21 0.044 0.007 1.512 1.556 N 10 C C C5' C4' DT DT 22 22 0.045 0.007 1.512 1.557 N 10 C C C5' C4' DT DT 23 23 0.042 0.007 1.512 1.554 N NMR Structrure of d(CCAAAGXACTGGG), X is a 3'-phosphoglycolate, 5'-phosphate gapped lesion, 10 structures 1 N N 2 N N 3 N N 4 N N covale 1.578 one A DG 6 A O3' DG 6 1_555 A PGA 7 D P PGA 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 C DG 26 C N1 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 C DG 26 C O6 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 C DG 26 C N2 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 C DG 25 C N1 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 C DG 25 C O6 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 C DG 25 C N2 DG 12 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 C DT 24 C N3 DT 11 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 C DT 24 C O4 DT 11 1_555 hydrog DA-DT PAIR A DA 4 A N6 DA 4 1_555 C DT 22 C O4 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 C DT 23 C N3 DT 10 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 C DT 23 C O4 DT 10 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 C DT 22 C N3 DT 9 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 C DT 22 C O4 DT 9 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 C DC 21 C N3 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 C DC 21 C O2 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 C DC 21 C N4 DC 8 1_555 hydrog WATSON-CRICK B DA 8 B N1 DA 1 1_555 C DT 19 C N3 DT 6 1_555 hydrog WATSON-CRICK B DA 8 B N6 DA 1 1_555 C DT 19 C O4 DT 6 1_555 hydrog WATSON-CRICK B DC 9 B N3 DC 2 1_555 C DG 18 C N1 DG 5 1_555 hydrog WATSON-CRICK B DC 9 B N4 DC 2 1_555 C DG 18 C O6 DG 5 1_555 hydrog WATSON-CRICK B DC 9 B O2 DC 2 1_555 C DG 18 C N2 DG 5 1_555 hydrog WATSON-CRICK B DT 10 B N3 DT 3 1_555 C DA 17 C N1 DA 4 1_555 hydrog WATSON-CRICK B DT 10 B O4 DT 3 1_555 C DA 17 C N6 DA 4 1_555 hydrog WATSON-CRICK B DG 11 B N1 DG 4 1_555 C DC 16 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B N2 DG 4 1_555 C DC 16 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B O6 DG 4 1_555 C DC 16 C N4 DC 3 1_555 hydrog WATSON-CRICK B DG 12 B N1 DG 5 1_555 C DC 15 C N3 DC 2 1_555 hydrog WATSON-CRICK B DG 12 B N2 DG 5 1_555 C DC 15 C O2 DC 2 1_555 hydrog WATSON-CRICK B DG 12 B O6 DG 5 1_555 C DC 15 C N4 DC 2 1_555 hydrog WATSON-CRICK B DG 13 B N1 DG 6 1_555 C DC 14 C N3 DC 1 1_555 hydrog WATSON-CRICK B DG 13 B N2 DG 6 1_555 C DC 14 C O2 DC 1 1_555 hydrog WATSON-CRICK B DG 13 B O6 DG 6 1_555 C DC 14 C N4 DC 1 1_555 DNA DNA, bleomycin, phosphoglycolate 1G5K PDB 1 1G5K 1G5K PDB 2 1G5K 1G5K PDB 3 1G5K 1 6 1G5K 1 6 1G5K A 1 1 6 8 13 1G5K 8 13 1G5K B 2 1 6 14 26 1G5K 14 26 1G5K C 3 1 13 BINDING SITE FOR RESIDUE PGA A 7 A PGA 7 Software 1 A DG 6 A DG 6 1 1_555