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 C9 H15 N3 O7 P 1 308.205 n 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C13 H18 N5 O7 P 387.285 n 2'-DEOXY-N1,N2-PROPANO GUANOSINE 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/pdb1laq/pdb pdb_00001laq 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 4024.636 5'-D(*CP*GP*CP*GP*GP*TP*(P)P*TP*CP*CP*GP*CP*G)-3' 1 syn polymer 3963.584 5'-D(*CP*GP*CP*GP*GP*AP*(DNR)P*AP*CP*CP*GP*CP*G)-3' 1 syn polymer no yes (DC)(DG)(DC)(DG)(DG)(DT)(P)(DT)(DC)(DC)(DG)(DC)(DG) CGCGGTGTCCGCG A polydeoxyribonucleotide no yes (DC)(DG)(DC)(DG)(DG)(DA)(DNR)(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 -30.048 1 19 A 1 B 26 -3.491 A_DC1:DG26_B 1 -1.048 0.100 0.723 -0.031 -13.398 1 19 A 2 B 25 -1.865 A_DG2:DC25_B 2 -4.093 -0.136 0.052 -0.120 2.805 1 19 A 3 B 24 -2.765 A_DC3:DG24_B 3 -3.186 0.144 -0.023 -0.109 12.524 1 19 A 4 B 23 -2.871 A_DG4:DC23_B 4 -2.128 -0.137 0.240 -0.090 20.089 1 19 A 5 B 22 -0.027 A_DG5:DC22_B 5 -4.374 -0.172 0.227 -0.045 22.926 1 20 A 6 B 21 3.193 A_DT6:DA21_B 6 -22.716 0.099 -0.504 -0.160 21.889 A 7 B 20 83.671 A_P7:DNR20_B 7 3.309 1.083 -1.328 -3.654 1.073 1 20 A 8 B 19 3.276 A_DT8:DA19_B 8 -9.660 -0.101 -0.116 -0.139 12.980 1 19 A 9 B 18 1.426 A_DC9:DG18_B 9 -21.400 0.192 -0.390 -0.121 5.087 1 19 A 10 B 17 -1.294 A_DC10:DG17_B 10 -17.385 0.164 0.004 -0.104 6.953 1 19 A 11 B 16 -2.033 A_DG11:DC16_B 11 -6.498 -0.153 0.402 -0.101 12.355 1 19 A 12 B 15 -3.014 A_DC12:DG15_B 12 -2.371 0.140 0.210 -0.121 26.636 1 19 A 13 B 14 -3.938 A_DG13:DC14_B 13 -8.039 -0.008 0.711 -0.088 2.834 38.737 A A 1 2 -6.076 B B 26 25 2.876 -4.021 -0.112 0.168 AA_DC1DG2:DC25DG26_BB 1 2.308 -3.488 38.469 0.684 0.417 2.763 36.490 A A 2 3 -5.316 B B 25 24 2.846 -3.325 -0.078 0.819 AA_DG2DC3:DG24DC25_BB 2 -0.002 0.004 36.343 1.703 0.125 2.767 35.804 A A 3 4 11.504 B B 24 23 2.857 7.029 0.487 -0.256 AA_DC3DG4:DC23DG24_BB 3 0.925 -1.515 35.118 -1.294 -0.677 3.005 37.403 A A 4 5 -0.342 B B 23 22 2.998 -0.219 0.307 0.120 AA_DG4DG5:DC22DC23_BB 4 1.053 -1.643 37.388 0.213 -0.351 3.040 39.803 A A 5 6 -6.931 B B 22 21 3.085 -4.667 0.484 0.479 AA_DG5DT6:DA21DC22_BB 5 9.375 -13.921 38.455 1.220 0.325 0.501 -174.226 A A 6 7 -2.825 B B 21 20 -1.351 5.587 -2.825 3.907 AA_DT6P7:DNR20DA21_BB 6 170.145 86.016 -107.421 -1.951 -1.553 -0.378 -175.122 A A 7 8 -53.710 B B 20 19 0.332 106.369 1.216 3.208 AA_P7DT8:DA19DNR20_BB 7 -135.366 -68.351 -103.028 -1.601 0.615 2.787 38.398 A A 8 9 -2.999 B B 19 18 2.832 -1.971 -0.344 0.625 AA_DT8DC9:DG18DA19_BB 8 1.110 -1.688 38.333 1.161 0.642 3.515 38.616 A A 9 10 3.519 B B 18 17 3.480 2.325 -0.578 0.317 AA_DC9DC10:DG17DG18_BB 9 -1.826 2.763 38.507 0.172 0.633 3.229 38.611 A A 10 11 4.939 B B 17 16 3.221 3.261 0.271 0.379 AA_DC10DG11:DC16DG17_BB 10 -1.535 2.325 38.449 0.176 -0.597 3.020 39.358 A A 11 12 -13.697 B B 16 15 3.226 -9.147 -0.166 0.566 AA_DG11DC12:DG15DC16_BB 11 -0.796 1.192 38.314 1.891 0.155 2.836 39.651 A A 12 13 -3.075 B B 15 14 2.853 -2.085 0.335 0.419 AA_DC12DG13:DC14DG15_BB 12 1.042 -1.537 39.585 0.829 -0.387 database_2 entity_poly 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 Polymer sequence 1 0 2002-04-17 1 1 2008-04-28 1 2 2011-07-13 2 0 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag 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 position. 1lai is the Solution structure of the B-DNA duplex CGCGGTGTCCGCG 1LAS IS THE Solution structure of the B-DNA duplex CGCGGTXTCCGCG (X=PdG) containing the 1,N2-propanodeoxyguanosine adduct with the deoxyribose at C20 opposite PdG in the C3' endo conformation. RCSB Y RCSB 2002-03-29 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 5.2 ambient 303 K 100 mM NaCl 5.2 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 P 7 n 7 P 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 DNR 20 n 7 DNR 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 A P 7 A P 7 DG B DNR 20 B DNR 7 DC 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 2.56 0.30 108.30 110.86 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 2.50 0.30 108.30 110.80 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.64 0.50 113.10 117.74 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 2.48 0.30 108.30 110.78 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 -2.61 0.40 106.40 103.79 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 3.33 0.30 108.30 111.63 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 DG DG DG 5 5 5 N 1 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 DG DG DG 5 5 5 N 1 2.93 0.30 108.30 111.23 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 2.76 0.30 108.30 111.06 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 3.00 0.30 108.30 111.30 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.03 0.30 108.30 111.33 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 2.35 0.30 108.30 110.65 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.68 0.50 113.10 117.78 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 2.94 0.30 108.30 111.24 A A A O4' C1' N1 DC DC DC 12 12 12 N 1 2.73 0.30 108.30 111.03 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 4.50 0.50 113.10 117.60 A A A N7 C8 N9 DG DG DG 13 13 13 N 1 -2.94 0.40 106.40 103.46 A A A C8 N9 C4 DG DG DG 13 13 13 N 1 2.96 0.30 108.30 111.26 B B B O4' C1' N1 DC DC DC 14 14 14 N 1 2.34 0.30 108.30 110.64 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 4.65 0.50 113.10 117.75 B B B N7 C8 N9 DG DG DG 15 15 15 N 1 -2.54 0.40 106.40 103.86 B B B C8 N9 C4 DG DG DG 15 15 15 N 1 3.10 0.30 108.30 111.40 B B B O4' C1' N1 DC DC DC 16 16 16 N 1 2.18 0.30 108.30 110.48 B B B O4' C1' N9 DG DG DG 17 17 17 N 1 4.65 0.50 113.10 117.75 B B B N7 C8 N9 DG DG DG 17 17 17 N 1 -2.63 0.40 106.40 103.77 B B B C8 N9 C4 DG DG DG 17 17 17 N 1 2.73 0.30 108.30 111.03 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.48 0.50 113.10 117.58 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -2.63 0.40 106.40 103.77 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 2.95 0.30 108.30 111.25 B B B O4' C1' N9 DA DA DA 19 19 19 N 1 3.67 0.50 113.80 117.47 B B B N7 C8 N9 DA DA DA 19 19 19 N 1 2.88 0.30 108.30 111.18 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 3.40 0.30 108.30 111.70 B B B O4' C1' N1 DC DC DC 22 22 22 N 1 3.03 0.30 108.30 111.33 B B B O4' C1' N1 DC DC DC 23 23 23 N 1 2.40 0.30 108.30 110.70 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 4.66 0.50 113.10 117.76 B B B N7 C8 N9 DG DG DG 24 24 24 N 1 -2.41 0.40 106.40 103.99 B B B C8 N9 C4 DG DG DG 24 24 24 N 1 3.17 0.30 108.30 111.47 B B B O4' C1' N1 DC DC DC 25 25 25 N 1 2.73 0.30 108.30 111.03 B B B O4' C1' N9 DG DG DG 26 26 26 N 1 4.53 0.50 113.10 117.63 B B B N7 C8 N9 DG DG DG 26 26 26 N 1 -2.82 0.40 106.40 103.58 B B B C8 N9 C4 DG DG DG 26 26 26 N minimized average Solution Structure of the B-DNA Duplex CGCGGTXTCCGCG (X=PdG) Containing the 1,N2-propanodeoxyguanosine Adduct with the Deoxyribose at C20 Opposite PdG in the C2' Endo Conformation. 1 N N 2 N N covale 1.615 both A DT 6 A O3' DT 6 1_555 A P 7 A P P 7 1_555 covale 1.613 both A P 7 A O3' P 7 1_555 A DT 8 A P DT 8 1_555 covale 1.617 both B DA 19 B O3' DA 6 1_555 B DNR 20 B P DNR 7 1_555 covale 1.614 both B DNR 20 B O3' DNR 7 1_555 B DA 21 B 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 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 P-DNR PAIR A P 7 A O6 P 7 1_555 B DNR 20 B N4 DNR 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 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, propanodeoxyguanosine 1LAQ PDB 1 1LAQ 1LAQ PDB 2 1LAQ 1 13 1LAQ 1 13 1LAQ A 1 1 13 14 26 1LAQ 14 26 1LAQ B 2 1 13