1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Weisenseel, J.P. Reddy, G.R. Marnett, L.J. Stone, M.P. 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 US Chem.Res.Toxicol. CRTOEC 2140 0893-228X 15 127 139 10.1021/tx0101090 11849038 Structure of an oligodeoxynucleotide containing a 1,N(2)-propanodeoxyguanosine adduct positioned in a palindrome derived from the Salmonella typhimurium hisD3052 gene: Hoogsteen pairing at pH 5.2. 2002 10.2210/pdb1lai/pdb pdb_00001lai 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 3984.572 5'-D(*CP*GP*CP*GP*GP*TP*GP*TP*CP*CP*GP*CP*G)-3' 1 syn polymer 3962.576 5'-D(*CP*GP*CP*GP*GP*AP*CP*AP*CP*CP*GP*CP*G)-3' 1 syn polymer no no (DC)(DG)(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DC)(DG)(DC)(DG) CGCGGTGTCCGCG A polydeoxyribonucleotide no no (DC)(DG)(DC)(DG)(DG)(DA)(DC)(DA)(DC)(DC)(DG)(DC)(DG) CGCGGACACCGCG 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 -18.025 1 19 A 1 B 26 -3.843 A_DC1:DG26_B 1 -6.776 0.077 0.636 -0.120 -10.488 1 19 A 2 B 25 -1.630 A_DG2:DC25_B 2 -8.001 -0.177 -0.005 -0.078 -1.920 1 19 A 3 B 24 -2.239 A_DC3:DG24_B 3 -4.168 0.125 0.197 -0.132 9.750 1 19 A 4 B 23 -4.046 A_DG4:DC23_B 4 -10.318 -0.057 0.479 -0.148 1.534 1 19 A 5 B 22 -2.206 A_DG5:DC22_B 5 -9.851 -0.169 0.245 -0.084 -3.220 1 20 A 6 B 21 -4.993 A_DT6:DA21_B 6 -18.249 -0.133 0.438 -0.179 -6.806 1 19 A 7 B 20 -2.032 A_DG7:DC20_B 7 -13.833 -0.171 0.141 -0.090 -8.577 1 20 A 8 B 19 -1.106 A_DT8:DA19_B 8 -10.264 -0.124 0.139 -0.092 -16.628 1 19 A 9 B 18 -2.574 A_DC9:DG18_B 9 -4.385 0.118 0.569 -0.098 -8.519 1 19 A 10 B 17 -3.229 A_DC10:DG17_B 10 -10.283 0.085 0.492 -0.144 0.330 1 19 A 11 B 16 -3.011 A_DG11:DC16_B 11 -5.188 -0.130 0.249 -0.126 8.497 1 19 A 12 B 15 -2.397 A_DC12:DG15_B 12 -8.457 0.161 0.083 -0.091 16.715 1 19 A 13 B 14 -3.739 A_DG13:DC14_B 13 -4.129 -0.110 0.654 -0.120 2.891 40.612 A A 1 2 4.738 B B 26 25 2.826 3.269 0.584 0.199 AA_DC1DG2:DC25DG26_BB 1 7.268 -10.535 39.854 -0.035 -0.128 2.930 37.921 A A 2 3 -2.440 B B 25 24 2.942 -1.583 -0.174 0.367 AA_DG2DC3:DG24DC25_BB 2 -2.921 4.501 37.780 0.747 -0.069 2.831 37.406 A A 3 4 3.292 B B 24 23 2.836 2.110 0.156 -0.058 AA_DC3DG4:DC23DG24_BB 3 0.569 -0.888 37.344 -0.332 -0.179 3.258 39.066 A A 4 5 5.991 B B 23 22 3.294 3.998 0.417 -0.361 AA_DG4DG5:DC22DC23_BB 4 1.845 -2.765 38.826 -1.023 -0.400 3.317 35.962 A A 5 6 -6.860 B B 22 21 3.267 -4.226 -0.445 -0.548 AA_DG5DT6:DA21DC22_BB 5 -0.882 1.431 35.710 -0.279 0.593 3.193 40.388 A A 6 7 5.704 B B 21 20 3.204 3.926 0.470 -0.286 AA_DT6DG7:DC20DA21_BB 6 4.066 -5.908 40.007 -0.848 -0.232 3.267 36.427 A A 7 8 -2.630 B B 20 19 3.266 -1.644 0.258 -0.108 AA_DG7DT8:DA19DC20_BB 7 0.025 -0.040 36.391 0.056 -0.410 3.483 43.495 A A 8 9 7.351 B B 19 18 3.484 5.431 -0.219 0.138 AA_DT8DC9:DG18DA19_BB 8 -2.842 3.847 43.082 -0.375 0.002 3.012 36.515 A A 9 10 -3.407 B B 18 17 3.009 -2.132 -0.587 0.406 AA_DC9DC10:DG17DG18_BB 9 -2.378 3.800 36.380 0.920 0.634 2.835 40.289 A A 10 11 2.704 B B 17 16 2.829 1.861 0.217 0.069 AA_DC10DG11:DC16DG17_BB 10 1.471 -2.137 40.222 -0.082 -0.171 2.921 37.603 A A 11 12 -8.110 B B 16 15 2.974 -5.210 0.086 0.196 AA_DG11DC12:DG15DC16_BB 11 2.030 -3.160 37.200 0.918 0.106 2.822 41.199 A A 12 13 1.539 B B 15 14 2.808 1.079 -0.285 0.126 AA_DC12DG13:DC14DG15_BB 12 -6.182 8.816 40.739 0.078 -0.172 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-04-17 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name 1la8 is the Solution structure of the DNA 13-mer hairpin CGCGGTGTCCGCG. 1lae is the Solution structure of the DNA 13-mer hairpin CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanodeoxyguanosine adduct at the seventh positon. 1laq is the Solution structure of the B-DNA duplex CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanogeoxyguanosine adduct with the deoxyribose at C20 opposite PdG in the C2' endo conformation. 1LAS IS THE Solution structure of the B-DNA duplex CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanogeoxyguanosine adduct with the deoxyribose at C20 opposite PdG in the C3' endo conformation. RCSB Y RCSB 2002-03-28 REL REL This Synthetic DNA sequence was derived from the hisD3052 gene of salmonella typhimurium. sample This Synthetic DNA sequence was derived from the hisD3052 gene of salmonella typhimurium. sample 1 2D NOESY DQF-COSY 31P-1H COSY 2D NOESY 100 mM NaCl 6.8 ambient 303 K 100 mM NaCl 6.8 ambient 278 K Molecular dynamics using a simulated annealing protocol. 1 minimized average structure 1.8 mM DNA strand, 10 mM sodium phosphate, 100 mM NaCl, 50 uM EDTA D2O 1.8 mM DNA strand, 1 mM sodium phosphate, 100 mM NaCl, 50 uM EDTA H2O/D2O Bruker collection UXNMR 3.0 Hare, D. data analysis Felix 97.0, 2000 Borgias & James iterative matrix relaxation MARDIGRAS 3.2 Brunger, A. refinement X-PLOR 3.8 500 Bruker DRX C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A G 5 n 5 DG 5 A T 6 n 6 DT 6 A G 7 n 7 DG 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A C 10 n 10 DC 10 A G 11 n 11 DG 11 A C 12 n 12 DC 12 A G 13 n 13 DG 13 A C 14 n 1 DC 14 B G 15 n 2 DG 15 B C 16 n 3 DC 16 B G 17 n 4 DG 17 B G 18 n 5 DG 18 B A 19 n 6 DA 19 B C 20 n 7 DC 20 B A 21 n 8 DA 21 B C 22 n 9 DC 22 B C 23 n 10 DC 23 B G 24 n 11 DG 24 B C 25 n 12 DC 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 3.06 0.30 108.30 111.36 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.04 0.30 108.30 111.34 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.71 0.50 113.10 117.81 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 2.56 0.30 108.30 110.86 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 2.95 0.30 108.30 111.25 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 -2.78 0.40 106.40 103.62 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 3.17 0.30 108.30 111.47 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 4.60 0.50 113.10 117.70 A A A N7 C8 N9 DG DG DG 5 5 5 N 1 -2.75 0.40 106.40 103.65 A A A C8 N9 C4 DG DG DG 5 5 5 N 1 3.36 0.30 108.30 111.66 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 -4.03 0.60 122.90 118.87 A A A C6 C5 C7 DT DT DT 6 6 6 N 1 3.18 0.30 108.30 111.48 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 4.55 0.50 113.10 117.65 A A A N7 C8 N9 DG DG DG 7 7 7 N 1 -2.75 0.40 106.40 103.65 A A A C8 N9 C4 DG DG DG 7 7 7 N 1 3.49 0.30 108.30 111.79 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -4.18 0.60 122.90 118.72 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 3.38 0.30 108.30 111.68 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.00 0.30 108.30 111.30 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 2.77 0.30 108.30 111.07 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 DG DG DG 11 11 11 N 1 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 DG DG DG 11 11 11 N 1 2.80 0.30 108.30 111.10 A A A O4' C1' N1 DC DC DC 12 12 12 N 1 2.57 0.30 108.30 110.87 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 4.61 0.50 113.10 117.71 A A A N7 C8 N9 DG DG DG 13 13 13 N 1 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 DG DG DG 13 13 13 N 1 3.27 0.30 108.30 111.57 B B B O4' C1' N1 DC DC DC 14 14 14 N 1 2.84 0.30 108.30 111.14 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 4.49 0.50 113.10 117.59 B B B N7 C8 N9 DG DG DG 15 15 15 N 1 -2.66 0.40 106.40 103.74 B B B C8 N9 C4 DG DG DG 15 15 15 N 1 2.83 0.30 108.30 111.13 B B B O4' C1' N1 DC DC DC 16 16 16 N 1 2.79 0.30 108.30 111.09 B B B O4' C1' N9 DG DG DG 17 17 17 N 1 4.55 0.50 113.10 117.65 B B B N7 C8 N9 DG DG DG 17 17 17 N 1 -2.67 0.40 106.40 103.73 B B B C8 N9 C4 DG DG DG 17 17 17 N 1 3.25 0.30 108.30 111.55 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.52 0.50 113.10 117.62 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -2.73 0.40 106.40 103.67 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 2.36 0.30 108.30 110.66 B B B O4' C1' N9 DA DA DA 19 19 19 N 1 3.90 0.50 113.80 117.70 B B B N7 C8 N9 DA DA DA 19 19 19 N 1 3.22 0.30 108.30 111.52 B B B O4' C1' N1 DC DC DC 20 20 20 N 1 2.16 0.30 108.30 110.46 B B B O4' C1' N9 DA DA DA 21 21 21 N 1 3.91 0.50 113.80 117.71 B B B N7 C8 N9 DA DA DA 21 21 21 N 1 3.22 0.30 108.30 111.52 B B B O4' C1' N1 DC DC DC 22 22 22 N 1 2.95 0.30 108.30 111.25 B B B O4' C1' N1 DC DC DC 23 23 23 N 1 2.72 0.30 108.30 111.02 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 4.48 0.50 113.10 117.58 B B B N7 C8 N9 DG DG DG 24 24 24 N 1 -2.50 0.40 106.40 103.90 B B B C8 N9 C4 DG DG DG 24 24 24 N 1 2.62 0.30 108.30 110.92 B B B O4' C1' N1 DC DC DC 25 25 25 N 1 2.54 0.30 108.30 110.84 B B B O4' C1' N9 DG DG DG 26 26 26 N 1 4.64 0.50 113.10 117.74 B B B N7 C8 N9 DG DG DG 26 26 26 N 1 -2.74 0.40 106.40 103.66 B B B C8 N9 C4 DG DG DG 26 26 26 N minimized average Solution Structure of the B-DNA Duplex CGCGGTGTCCGCG. 1 N N 2 N N 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 DG 2 A N1 DG 2 1_555 B DC 25 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 25 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 25 B N4 DC 12 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 24 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 24 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 24 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 23 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 23 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 23 B N4 DC 10 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 22 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 22 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 22 B N4 DC 9 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 21 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 21 B N6 DA 8 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 20 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 20 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 20 B N4 DC 7 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 19 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 19 B N6 DA 6 1_555 hydrog DC-DG PAIR A DC 9 A N4 DC 9 1_555 B DG 17 B O6 DG 4 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 DC 10 A N3 DC 10 1_555 B DG 17 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 17 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 17 B N2 DG 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 DC 12 A N3 DC 12 1_555 B DG 15 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 15 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 15 B N2 DG 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 DNA, B-type 1LAI PDB 1 1LAI 1LAI PDB 2 1LAI 1 13 1LAI 1 13 1LAI A 1 1 13 14 26 1LAI 14 26 1LAI B 2 1 13