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 (R)-(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 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/pdb1k5e/pdb pdb_00001k5e 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*(ABR)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)(ABR)(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 -8.032 1 19 A 1 B 22 -2.802 A_DC1:DG22_B 1 -10.320 0.115 0.324 -0.122 -10.951 1 19 A 2 B 21 1.042 A_DG2:DC21_B 2 -9.208 -0.223 -0.232 -0.095 -10.182 1 19 A 3 B 20 0.655 A_DG3:DC20_B 3 -10.098 -0.195 -0.209 -0.105 -10.001 1 20 A 4 B 19 1.895 A_DA4:DT19_B 4 -2.904 0.101 0.399 -0.196 -6.305 1 19 A 5 B 18 1.607 A_DC5:DG18_B 5 7.304 0.318 0.119 -0.083 6.967 1 20 A 6 B 17 -1.586 A_ABR6:DT17_B 6 -12.813 -0.039 -0.300 -0.147 1.649 1 20 A 7 B 16 4.197 A_DA7:DT16_B 7 -11.783 -0.049 0.160 -0.170 -2.161 1 19 A 8 B 15 -3.323 A_DG8:DC15_B 8 -13.492 -0.065 -0.176 -0.179 -0.962 1 20 A 9 B 14 0.142 A_DA9:DT14_B 9 -2.256 -0.055 0.164 -0.123 3.950 1 20 A 10 B 13 2.190 A_DA10:DT13_B 10 -7.185 -0.031 -0.064 -0.118 1.145 1 19 A 11 B 12 -3.004 A_DG11:DC12_B 11 -14.343 -0.095 0.160 -0.162 2.656 31.342 A A 1 2 22.167 B B 22 21 3.098 11.695 0.047 -0.621 AA_DC1DG2:DC21DG22_BB 1 1.345 -2.549 29.098 -3.165 0.144 3.179 33.302 A A 2 3 7.718 B B 21 20 3.301 4.403 -0.039 -0.637 AA_DG2DG3:DC20DC21_BB 2 -3.411 5.979 32.846 -1.844 -0.499 3.135 33.931 A A 3 4 0.238 B B 20 19 3.262 0.138 0.353 -0.829 AA_DG3DA4:DT19DC20_BB 3 -6.529 11.254 33.315 -1.443 -1.639 3.085 32.409 A A 4 5 3.348 B B 19 18 3.180 1.862 -0.021 -1.079 AA_DA4DC5:DG18DT19_BB 4 4.330 -7.784 32.073 -2.249 0.771 2.462 31.192 A A 5 6 6.960 B B 18 17 2.745 3.705 -0.532 -0.755 AA_DC5ABR6:DT17DG18_BB 5 6.820 -12.812 30.234 -1.974 2.040 3.594 41.772 A A 6 7 6.535 B B 17 16 3.507 4.643 -0.383 0.807 AA_ABR6DA7:DT16DT17_BB 6 -4.363 6.141 41.305 0.600 0.037 3.213 33.775 A A 7 8 8.719 B B 16 15 3.291 5.042 -0.687 -0.595 AA_DA7DG8:DC15DT16_BB 7 -2.651 4.584 33.304 -1.841 0.753 2.575 35.531 A A 8 9 6.152 B B 15 14 2.744 3.729 0.179 -0.820 AA_DG8DA9:DT14DC15_BB 8 -6.287 10.371 34.795 -1.792 -1.048 3.256 35.053 A A 9 10 -4.505 B B 14 13 3.215 -2.710 -0.226 -0.776 AA_DA9DA10:DT13DT14_BB 9 1.092 -1.814 34.935 -0.886 0.538 3.545 30.469 A A 10 11 -10.217 B B 13 12 3.486 -5.343 -0.387 -0.692 AA_DA10DG11:DC12DT13_BB 10 0.539 -1.031 30.003 -0.161 0.854 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-01-23 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag 1K5F is the SAME STRUCTURE WITH (S)-(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 293 K simulated annealing, molecular dynamics, matrix relaxation 1 minimized average structure 130 OD260 of double stranded oligodeoxynucleotide are 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 ABR 6 n 6 ABR 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 ABR 6 A ABR 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 A B HA O4 ABR DT 6 16 1.43 1 B B H2'' O5' DC DT 15 16 1.48 1 A B CA O4 ABR DT 6 16 2.15 1 2.56 0.30 108.30 110.86 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 2.55 0.30 108.30 110.85 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.48 0.50 113.10 117.58 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.42 0.40 106.40 103.98 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 2.80 0.30 108.30 111.10 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 -2.51 0.40 106.40 103.89 A A A C8 N9 C4 DG DG DG 3 3 3 N 1 3.83 0.50 113.80 117.63 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 2.47 0.30 108.30 110.77 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 1.83 0.30 108.30 110.13 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 3.85 0.50 113.80 117.65 A A A N7 C8 N9 DA DA DA 7 7 7 N 1 2.00 0.30 108.30 110.30 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.68 0.50 113.10 117.78 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 DG DG DG 8 8 8 N 1 3.66 0.50 113.80 117.46 A A A N7 C8 N9 DA DA DA 9 9 9 N 1 2.42 0.30 108.30 110.72 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 3.85 0.50 113.80 117.65 A A A N7 C8 N9 DA DA DA 10 10 10 N 1 2.09 0.30 108.30 110.39 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.57 0.50 113.10 117.67 A A A N7 C8 N9 DG DG DG 11 11 11 N 1 -2.52 0.40 106.40 103.88 A A A C8 N9 C4 DG DG DG 11 11 11 N 1 2.03 0.30 108.30 110.33 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 2.65 0.30 108.30 110.95 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 2.80 0.30 108.30 111.10 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 2.55 0.30 108.30 110.85 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 2.24 0.30 108.30 110.54 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 2.24 0.30 108.30 110.54 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 2.59 0.30 108.30 110.89 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.49 0.50 113.10 117.59 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -2.60 0.40 106.40 103.80 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 2.47 0.30 108.30 110.77 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 2.89 0.30 108.30 111.19 B B B O4' C1' N1 DC DC DC 20 20 20 N 1 2.72 0.30 108.30 111.02 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 2.87 0.30 108.30 111.17 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.53 0.50 113.10 117.63 B B B N7 C8 N9 DG DG DG 22 22 22 N 1 -2.61 0.40 106.40 103.79 B B B C8 N9 C4 DG DG DG 22 22 22 N minimized average Solution Structure of R-styrene Adduct in the Ras61 Sequence 1 N N 2 N N covale 1.611 both A DC 5 A O3' DC 5 1_555 A ABR 6 A P ABR 6 1_555 covale 1.613 both A ABR 6 A O3' ABR 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 ABR 6 A N1 ABR 6 1_555 B DT 17 B N3 DT 6 1_555 hydrog WATSON-CRICK A ABR 6 A N6 ABR 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 1K5E PDB 1 1K5E 1K5E PDB 2 1K5E 1 11 1K5E 1 11 1K5E A 1 1 11 12 22 1K5E 12 22 1K5E B 2 1 11