1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Giri, I. Johnston, D.S. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C17 H14 O7 330.289 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 non-polymer 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 41 5462 5472 10.1021/bi012116t 11969407 MISPAIRING OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT WITH DEOXYADENOSINE RESULTS IN EXTRUSION OF THE MISMATCHED DA TOWARD THE MAJOR GROOVE 2002 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 3003.993 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3' 1 syn polymer 3108.065 5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3' 1 syn polymer 330.289 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 1 syn non-polymer no no (DA)(DC)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DT) ACATCGATCT A polydeoxyribonucleotide no no (DA)(DG)(DA)(DT)(DA)(DG)(DA)(DT)(DG)(DT) AGATAGATGT B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n 23.636 1 20 A 1 B 20 -3.284 A_DA1:DT20_B 1 -15.373 0.302 0.966 -0.135 7.918 1 19 A 2 B 19 -0.412 A_DC2:DG19_B 2 -12.410 0.239 0.126 -0.148 -10.484 1 20 A 3 B 18 -0.790 A_DA3:DT18_B 3 -3.413 0.343 -0.096 -0.063 -3.645 1 20 A 4 B 17 0.480 A_DT4:DA17_B 4 1.184 0.110 -0.069 -0.104 7.279 1 19 A 5 B 16 -1.440 A_DC5:DG16_B 5 1.640 0.069 -0.236 -0.160 1.776 1 20 A 7 B 14 3.513 A_DA7:DT14_B 6 -3.931 0.239 0.333 0.027 2.900 1 20 A 8 B 13 -0.876 A_DT8:DA13_B 7 -5.532 0.021 -0.121 -0.113 -1.107 1 19 A 9 B 12 -3.174 A_DC9:DG12_B 8 -3.330 0.276 -0.127 -0.208 -10.712 1 20 A 10 B 11 8.016 A_DT10:DA11_B 9 -11.834 0.047 -0.151 -0.078 3.835 35.361 A A 1 2 -3.586 B B 20 19 3.809 -2.174 0.156 -0.565 AA_DA1DC2:DG19DT20_BB 1 3.108 -5.126 35.164 -0.554 0.280 3.438 40.566 A A 2 3 10.115 B B 19 18 3.608 6.981 -0.417 -0.724 AA_DC2DA3:DT18DG19_BB 2 0.101 -0.146 39.986 -1.889 0.614 3.303 31.353 A A 3 4 -4.911 B B 18 17 3.276 -2.651 0.176 -0.511 AA_DA3DT4:DA17DT18_BB 3 -0.707 1.311 31.236 -0.442 -0.460 3.066 35.834 A A 4 5 0.942 B B 17 16 3.079 0.580 0.206 -0.287 AA_DT4DC5:DG16DA17_BB 4 -1.136 1.846 35.812 -0.544 -0.487 3.346 28.653 A A 7 8 -9.967 B B 14 13 3.334 -4.900 -0.542 -0.809 AA_DA7DT8:DA13DT14_BB 5 3.097 -6.300 28.073 -0.492 1.818 3.392 39.033 A A 8 9 0.760 B B 13 12 3.404 0.507 -0.067 -0.800 AA_DT8DC9:DG12DA13_BB 6 -2.193 3.284 38.970 -1.260 -0.175 3.384 29.047 A A 9 10 10.621 B B 12 11 3.465 5.281 1.115 -0.830 AA_DC9DT10:DA11DG12_BB 7 4.182 -8.412 28.271 -2.888 -1.246 atom_site chem_comp entity entity_poly entity_poly_seq ndb_struct_conf_na ndb_struct_na_base_pair_step pdbx_entity_nonpoly pdbx_entity_src_syn pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_mod_residue pdbx_struct_oper_list pdbx_validate_rmsd_angle struct_asym struct_conn struct_ref repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations Non-polymer description Polymer sequence Source and taxonomy Structure summary 1 0 2002-10-16 1 1 2008-04-28 1 2 2011-07-13 2 0 2019-01-30 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.group_PDB _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly_seq.mon_id _ndb_struct_na_base_pair_step.roll _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _struct_ref.pdbx_align_begin NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE RCSB Y RCSB 2002-08-28 REL REL AFN 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 32630 synthetic construct sample 1 10 32630 synthetic construct sample 1 10 40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging Final A and Final B, and after energy Minimization. This energy minimized structure was solvated, and explicit counterions were added. In all, 17 Na+ ions were added to neutralize the system using the Leap module in AMBER 6.0. The SHAKE algorithm constrained bonds involving protons to a tolerance of 0.0005 . A 1 fs time step was used. The rMD calculations were run for 1.4 ns, and coordinates were captured every 200 ps. The emergent structure from AMBER is Being reported Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure. 20 1 2D NOESY 2D TOCSY DQF-COSY P-COSY T1 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O 7.4 ATM 278 K For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O, buffer, containing 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.4 7.4 ATM 273 K There were 329 experimental distance restraints derived from nonexchangeable 1H NOEs by MARDIGRAS. These consisted of 181 intranucleotide restraints, 110 internucleotide restraints, and 38 adduct-DNA restraints distance geometry : MardiGras; simulated annealing molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing and Molecular Dynamics matrix relaxation : CORMA; 1 80 OD of d(ACATCAFBGATCT)d(AGATAGATGT) solution in NMR Buffer For observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O. For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O. Most experiments were performed at 5 C. Spectra of exchangeable protons were obtained at 0 C. Accelyris, Inc., San Diego, CA processing FELIX 97, 2000 Bruker collection XWINNMR 4.0 Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487 data analysis MARDIGRAS 3.2 A.T.Brunger refinement X-PLOR 3.1 Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) J. Phys. Chem. 40, 10269-10280 structure solution AMBER 6.0 Keepers, J. W., and James, T. L. (1984) J. Magn. Reson. 57, 404-426. data analysis CORMA 4.0 Accelyris, Inc., San Diego, CA structure solution INSIGHTII 2000 Frisch, M. J., Trucks, G. W., et al. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA. processing GAUSSIAN 98 1998 500 Bruker DRX 800 Bruker DRX 600 Bruker DRX X 6 3 AFN AFN 11 A A 1 n 1 DA 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A X 6 n 6 DG 6 A A 7 n 7 DA 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A A 11 n 1 DA 11 B G 12 n 2 DG 12 B A 13 n 3 DA 13 B T 14 n 4 DT 14 B A 15 n 5 DA 15 B G 16 n 6 DG 16 B A 17 n 7 DA 17 B T 18 n 8 DT 18 B G 19 n 9 DG 19 B T 20 n 10 DT 20 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 identity operation 0.0000000000 0.0000000000 0.0000000000 1 B DA 15 0.102 SIDE CHAIN 1 -4.24 0.60 118.60 114.36 A A A N1 C6 N6 DA DA DA 1 1 1 N 1 1.85 0.30 108.30 110.15 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.01 0.50 117.70 120.71 A A A C5 C6 N1 DA DA DA 3 3 3 N 1 -4.44 0.60 118.60 114.16 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 -4.56 0.60 122.90 118.34 A A A C6 C5 C7 DT DT DT 4 4 4 N 1 3.32 0.30 108.30 111.62 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -4.20 0.60 118.60 114.40 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 -4.88 0.60 122.90 118.02 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 3.88 0.60 118.90 122.78 A A A N1 C2 O2 DC DC DC 9 9 9 N 1 -4.49 0.70 121.90 117.41 A A A N3 C2 O2 DC DC DC 9 9 9 N 1 3.69 0.30 108.30 111.99 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 -3.99 0.60 122.90 118.91 A A A C6 C5 C7 DT DT DT 10 10 10 N 1 -4.37 0.60 118.60 114.23 B B B N1 C6 N6 DA DA DA 11 11 11 N 1 2.48 0.30 108.30 110.78 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 3.86 0.30 108.30 112.16 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 -4.61 0.60 122.90 118.29 B B B C6 C5 C7 DT DT DT 14 14 14 N 1 3.39 0.30 108.30 111.69 B B B O4' C1' N9 DA DA DA 15 15 15 N 1 3.15 0.50 117.70 120.85 B B B C5 C6 N1 DA DA DA 15 15 15 N 1 -4.17 0.60 118.60 114.43 B B B N1 C6 N6 DA DA DA 15 15 15 N 1 2.60 0.30 108.30 110.90 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 -3.74 0.60 122.90 119.16 B B B C6 C5 C7 DT DT DT 20 20 20 N 5'-D(*AP*CP*AP*TP*CP*(X)P*AP*TP*CP*T)-3' SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE 1 N N 2 N N 3 N N covale 1.507 sing A DG 6 A N7 DG 6 1_555 A AFN 11 C C8A AFN 1_555 hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 20 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 20 B O4 DT 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 19 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 19 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 19 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 18 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 18 B O4 DT 8 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 17 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 17 B N6 DA 7 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 16 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 16 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 16 B N2 DG 6 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 14 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 14 B O4 DT 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 13 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 13 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 12 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 12 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 12 B N2 DG 2 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 11 B N1 DA 1 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 11 B N6 DA 1 1_555 DNA AFLATOXIN B1- Guanine Adduct Opposite an Adenine, mimicking GA Transition, DNA 1MK6 PDB 1 1 1MK6 1MK6 PDB 2 1 1MK6 1 10 1MK6 1 10 1MK6 A 1 1 10 11 20 1MK6 11 20 1MK6 B 2 1 10