1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Hennard, C. Finneman, J. Harris, C.M. Harris, T.M. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C18 H22 N5 O7 P 451.370 n (S)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-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 N 1 N P N 2 N O N 3 N O N 4 N O N 5 N C N 6 R C N 7 N O N 8 R C Y 9 N N Y 10 N C Y 11 N N Y 12 N C Y 13 N N Y 14 N C N 15 N N N 16 S C N 17 N O N 18 N C Y 19 N C Y 20 N C Y 21 N C Y 22 N C Y 23 N C Y 24 N C Y 25 N C Y 26 N N Y 27 N C N 28 N C N 29 S C N 30 N O N 31 N O 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 H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H 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 O N 55 N P N 56 N O N 57 N O N 58 N O N 59 N C N 60 R C N 61 N O N 62 S C N 63 N O N 64 N C N 65 R C Y 66 N N Y 67 N C Y 68 N N Y 69 N C Y 70 N C N 71 N N Y 72 N N Y 73 N C Y 74 N N Y 75 N C N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H 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 O N 91 N P N 92 N O N 93 N O N 94 N O N 95 N C N 96 R C N 97 N O N 98 S C N 99 N O N 100 N C N 101 R C N 102 N N N 103 N C N 104 N O N 105 N N N 106 N C N 107 N N N 108 N C N 109 N C N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H 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 O N 125 N P N 126 N O N 127 N O N 128 N O N 129 N C N 130 R C N 131 N O N 132 S C N 133 N O N 134 N C N 135 R C Y 136 N N Y 137 N C Y 138 N N Y 139 N C N 140 N C N 141 N O N 142 N N N 143 N C N 144 N N N 145 N N Y 146 N C N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H 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 O N 162 N P N 163 N O N 164 N O N 165 N O N 166 N C N 167 R C N 168 N O N 169 S C N 170 N O N 171 N C N 172 R C N 173 N N N 174 N C N 175 N O N 176 N N N 177 N C N 178 N O N 179 N C N 180 N C N 181 N C N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 1 N doub N 2 N sing 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 Y 17 N sing Y 18 N sing Y 19 N doub Y 20 N sing Y 21 N sing Y 22 N doub N 23 N sing Y 24 N sing N 25 N sing Y 26 N doub N 27 N sing 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 Y 36 N doub Y 37 N sing Y 38 N sing N 39 N sing Y 40 N doub N 41 N sing Y 42 N doub N 43 N sing Y 44 N sing N 45 N sing N 46 N sing Y 47 N sing Y 48 N doub 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 doub N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing 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 Y 80 N sing Y 81 N sing Y 82 N doub N 83 N sing Y 84 N sing Y 85 N sing Y 86 N doub N 87 N sing Y 88 N doub N 89 N sing N 90 N sing Y 91 N sing Y 92 N doub N 93 N sing Y 94 N sing N 95 N sing N 96 N sing N 97 N doub 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 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 doub N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N doub N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing 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 Y 153 N sing Y 154 N sing Y 155 N doub N 156 N sing Y 157 N sing N 158 N sing Y 159 N doub N 160 N doub N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub 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 sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N doub N 195 N sing N 196 N sing N 197 N sing N 198 N doub N 199 N sing N 200 N sing N 201 N doub N 202 N sing N 203 N sing N 204 N sing N 205 N sing US Biochemistry BICHAW 0033 0006-2960 40 9780 9791 10.1021/bi010564v 11502171 The nonmutagenic (R)- and (S)-beta-(N(6)-adenyl)styrene oxide adducts are oriented in the major groove and show little perturbation to DNA structure. 2001 10.2210/pdb1k5f/pdb pdb_00001k5f 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 N-RAS PROTOONCOGENE 3536.411 5'-D(*CP*GP*GP*AP*CP*(ABS)P*AP*GP*AP*AP*G)-3' 1 syn polymer N-RAS PROTOONCOGENE 3291.145 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3' 1 syn polymer no yes (DC)(DG)(DG)(DA)(DC)(ABS)(DA)(DG)(DA)(DA)(DG) CGGACAAGAAG A polydeoxyribonucleotide no no (DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG) CTTCTTGTCCG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n 3.639 1 19 A 1 B 22 -4.564 A_DC1:DG22_B 1 -11.299 0.111 0.058 -0.139 0.404 1 19 A 2 B 21 0.867 A_DG2:DC21_B 2 -7.442 -0.259 -0.111 -0.114 1.287 1 19 A 3 B 20 -0.647 A_DG3:DC20_B 3 -8.346 -0.236 -0.026 -0.089 -7.511 1 20 A 4 B 19 -3.997 A_DA4:DT19_B 4 -2.359 0.049 0.541 -0.156 4.096 1 19 A 5 B 18 1.312 A_DC5:DG18_B 5 -1.797 0.330 0.183 -0.125 7.038 1 20 A 6 B 17 0.416 A_ABS6:DT17_B 6 -4.866 -0.066 0.188 -0.173 6.391 1 20 A 7 B 16 0.050 A_DA7:DT16_B 7 -12.408 -0.046 -0.006 -0.102 8.888 1 19 A 8 B 15 -0.808 A_DG8:DC15_B 8 -11.468 -0.040 0.088 -0.164 0.839 1 20 A 9 B 14 0.910 A_DA9:DT14_B 9 -10.906 -0.114 0.190 -0.153 -6.171 1 20 A 10 B 13 -1.582 A_DA10:DT13_B 10 -6.885 0.102 0.035 -0.095 -17.177 1 19 A 11 B 12 -3.894 A_DG11:DC12_B 11 -8.300 0.024 -0.526 -0.095 3.112 39.190 A A 1 2 23.837 B B 22 21 3.329 15.561 0.184 0.093 AA_DC1DG2:DC21DG22_BB 1 3.226 -4.942 35.939 -1.782 0.123 3.049 32.814 A A 2 3 7.724 B B 21 20 3.182 4.334 0.057 -0.470 AA_DG2DG3:DC20DC21_BB 2 -5.146 9.171 32.135 -1.549 -0.952 3.153 37.212 A A 3 4 3.056 B B 20 19 3.173 1.942 -0.422 -0.863 AA_DG3DA4:DT19DC20_BB 3 -5.851 9.208 36.716 -1.603 -0.097 2.912 34.003 A A 4 5 1.993 B B 19 18 2.901 1.164 0.488 -0.505 AA_DA4DC5:DG18DT19_BB 4 2.805 -4.802 33.871 -1.029 -0.436 2.974 37.204 A A 5 6 -5.820 B B 18 17 2.928 -3.707 0.059 -0.611 AA_DC5ABS6:DT17DG18_BB 5 0.723 -1.134 37.019 -0.512 -0.006 3.174 37.931 A A 6 7 1.430 B B 17 16 3.179 0.929 -0.523 -0.212 AA_ABS6DA7:DT16DT17_BB 6 -0.025 0.038 37.920 -0.441 0.802 2.671 35.661 A A 7 8 18.371 B B 16 15 2.939 11.066 -0.154 -0.447 AA_DA7DG8:DC15DT16_BB 7 -2.623 4.354 33.855 -2.144 -0.083 2.993 38.365 A A 8 9 1.644 B B 15 14 3.016 1.080 0.082 -0.670 AA_DG8DA9:DT14DC15_BB 8 -1.085 1.652 38.335 -1.144 -0.250 3.442 37.041 A A 9 10 -13.195 B B 14 13 3.357 -8.315 0.052 -0.761 AA_DA9DA10:DT13DT14_BB 9 1.283 -2.036 36.106 -0.022 0.099 3.455 38.681 A A 10 11 11.205 B B 13 12 3.491 7.378 -0.924 -0.059 AA_DA10DG11:DC12DT13_BB 10 -1.632 2.479 37.963 -1.061 1.180 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 2002-01-23 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag 1k5e is the same structure with (R)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-5'-MONOPHOSPHATE. RCSB Y RCSB 2001-10-10 REL This sequence was generated by an oligonucleotide synthesizer sample This sequence was generated by an oligonucleotide synthesizer sample NOESY at 100, 150 and 200 ms mixing time back calculated data agree with experimental NOESY spectrum 50 1 Noesy DQF-COSY 10mM phosphate buffer 6.9 1 atm 283 K simulated annealing, molecular dynamics, matrix relaxation 1 minimized average structure 130 OD260 of double stranded oligodeoxynucleotide dissolved in 0.5 ml nmr buffer containing 99.996% D2O The buffer is 10mM sodium phosphate pH 6.9 containing 100mM NaCl and 0.05mM Na2EDTA Molecular Simulations collection Felix 97 James, TL refinement MARDIGRAS 3.0 Brunger iterative matrix relaxation X-PLOR 3.85 James data analysis CORMA 4.0 500 Bruker DRX C 1 n 1 DC 1 A G 2 n 2 DG 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A ABS 6 n 6 ABS 6 A A 7 n 7 DA 7 A G 8 n 8 DG 8 A A 9 n 9 DA 9 A A 10 n 10 DA 10 A G 11 n 11 DG 11 A C 12 n 1 DC 12 B T 13 n 2 DT 13 B T 14 n 3 DT 14 B C 15 n 4 DC 15 B T 16 n 5 DT 16 B T 17 n 6 DT 17 B G 18 n 7 DG 18 B T 19 n 8 DT 19 B C 20 n 9 DC 20 B C 21 n 10 DC 21 B G 22 n 11 DG 22 B author_defined_assembly 2 dimeric A ABS 6 A ABS 6 DA 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 2.60 0.30 108.30 110.90 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.60 0.50 113.10 117.70 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 2.11 0.30 108.30 110.41 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 3.82 0.50 113.80 117.62 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 2.50 0.30 108.30 110.80 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 4.28 0.50 113.80 118.08 A A A N7 C8 N9 DA DA DA 7 7 7 N 1 2.91 0.30 108.30 111.21 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.55 0.50 113.10 117.65 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -2.80 0.40 106.40 103.60 A A A C8 N9 C4 DG DG DG 8 8 8 N 1 2.33 0.30 108.30 110.63 A A A O4' C1' N9 DA DA DA 9 9 9 N 1 3.77 0.50 113.80 117.57 A A A N7 C8 N9 DA DA DA 9 9 9 N 1 2.53 0.30 108.30 110.83 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 3.79 0.50 113.80 117.59 A A A N7 C8 N9 DA DA DA 10 10 10 N 1 2.56 0.30 108.30 110.86 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.50 0.50 113.10 117.60 A A A N7 C8 N9 DG DG DG 11 11 11 N 1 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 DG DG DG 11 11 11 N 1 2.23 0.30 108.30 110.53 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 2.23 0.30 108.30 110.53 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 3.79 0.30 108.30 112.09 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 2.86 0.30 108.30 111.16 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 3.45 0.30 108.30 111.75 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 2.69 0.30 108.30 110.99 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.63 0.50 113.10 117.73 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -2.48 0.40 106.40 103.92 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 1.81 0.30 108.30 110.11 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 -3.82 0.60 122.90 119.08 B B B C6 C5 C7 DT DT DT 19 19 19 N 1 2.93 0.30 108.30 111.23 B B B O4' C1' N1 DC DC DC 20 20 20 N 1 2.85 0.30 108.30 111.15 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.68 0.50 113.10 117.78 B B B N7 C8 N9 DG DG DG 22 22 22 N 1 -2.75 0.40 106.40 103.65 B B B C8 N9 C4 DG DG DG 22 22 22 N 1 B B C5 C7 DT DT 13 13 0.038 0.006 1.496 1.534 N minimized average SOLUTION STRUCTURE OF THE S-STYRENE ADDUCT IN THE RAS61 SEQUENCE 1 N N 2 N N covale 1.613 both A DC 5 A O3' DC 5 1_555 A ABS 6 A P ABS 6 1_555 covale 1.610 both A ABS 6 A O3' ABS 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 DG 3 A N1 DG 3 1_555 B DC 20 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 20 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 20 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 19 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 19 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 18 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 18 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 18 B N2 DG 7 1_555 hydrog WATSON-CRICK A ABS 6 A N1 ABS 6 1_555 B DT 17 B N3 DT 6 1_555 hydrog WATSON-CRICK A ABS 6 A N6 ABS 6 1_555 B DT 17 B O4 DT 6 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 DG 8 A N1 DG 8 1_555 B DC 15 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 15 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 15 B N4 DC 4 1_555 hydrog WATSON-CRICK A DA 9 A N1 DA 9 1_555 B DT 14 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 9 A N6 DA 9 1_555 B DT 14 B O4 DT 3 1_555 hydrog WATSON-CRICK A DA 10 A N1 DA 10 1_555 B DT 13 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 13 B O4 DT 2 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 12 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 12 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 12 B N4 DC 1 1_555 DNA Styrene, DNA adduct, solution structure of DNA, DNA 1K5F PDB 1 1K5F 1K5F PDB 2 1K5F 1 11 1K5F 1 11 1K5F A 1 1 11 12 22 1K5F 12 22 1K5F B 2 1 11