1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 Bohon, J. De Los Santos, C.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C10 H14 N5 O6 P S 363.287 n 6-THIO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking UK Nucleic Acids Res. NARHAD 0389 0305-1048 31 1331 1338 10.1093/nar/gkg203 12582253 Structural effect of the anticancer agent 6-thioguanine on duplex DNA. 2003 10.2210/pdb1kbm/pdb pdb_00001kbm 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1 SINGLE WAVELENGTH M 1 1.0 3350.252 5'-D(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3' 1 syn polymer 3389.221 5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3' 1 syn polymer no yes (DC)(DG)(DT)(DA)(DC)(S6G)(DC)(DA)(DT)(DG)(DC) CGTACGCATGC A polydeoxyribonucleotide no no (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DC)(DG) GCATGTGTACG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -5.921 1 19 A 1 B 11 -2.849 A_DC1:DG11_B 1 -4.747 0.635 0.116 -0.251 -11.374 1 19 A 2 B 10 -1.562 A_DG2:DC10_B 2 -3.913 -0.619 0.038 -0.239 -11.111 1 20 A 3 B 9 -3.156 A_DT3:DA9_B 3 -4.109 -0.213 0.268 -0.111 -4.195 1 20 A 4 B 8 -5.898 A_DA4:DT8_B 4 -3.933 0.375 0.161 -0.070 9.644 1 19 A 5 B 7 2.092 A_DC5:DG7_B 5 -2.883 1.003 -0.061 -0.256 -10.506 A 6 B 6 15.812 A_S6G6:DT6_B 6 -6.131 -3.379 -0.119 -0.188 1.023 1 19 A 7 B 5 -0.688 A_DC7:DG5_B 7 -6.444 0.761 0.169 -0.274 -8.314 1 20 A 8 B 4 -0.396 A_DA8:DT4_B 8 -5.531 0.015 0.106 -0.127 4.016 1 20 A 9 B 3 -5.615 A_DT9:DA3_B 9 -6.989 -0.401 0.081 -0.051 11.207 1 19 A 10 B 2 -1.560 A_DG10:DC2_B 10 2.653 -0.688 0.448 -0.270 2.406 1 19 A 11 B 1 -0.616 A_DC11:DG1_B 11 2.705 0.691 0.199 -0.263 2.870 33.659 A A 1 2 7.986 B B 11 10 2.987 4.602 0.648 -1.073 AA_DC1DG2:DC10DG11_BB 1 3.699 -6.419 33.151 -2.530 -0.575 3.228 41.561 A A 2 3 -5.354 B B 10 9 3.162 -3.794 -0.096 -0.934 AA_DG2DT3:DA9DC10_BB 2 1.136 -1.604 41.381 -0.923 0.253 2.579 37.885 A A 3 4 8.483 B B 9 8 2.751 5.485 0.139 -1.056 AA_DT3DA4:DT8DA9_BB 3 2.729 -4.221 37.404 -2.203 0.073 2.850 36.223 A A 4 5 -0.333 B B 8 7 2.819 -0.207 0.638 -0.718 AA_DA4DC5:DG7DT8_BB 4 1.815 -2.920 36.179 -1.129 -0.804 2.580 33.192 A A 5 6 22.628 B B 7 6 2.961 12.615 0.951 -0.555 AA_DC5S6G6:DT6DG7_BB 5 1.376 -2.468 30.734 -2.838 -1.462 3.079 52.772 A A 6 7 2.022 B B 6 5 2.944 1.793 -1.279 0.493 AA_S6G6DC7:DG5DT6_BB 6 -6.124 6.904 52.412 0.448 1.073 2.916 41.199 A A 7 8 9.437 B B 5 4 3.021 6.612 0.100 -0.458 AA_DC7DA8:DT4DG5_BB 7 1.824 -2.604 40.649 -1.304 0.037 2.753 31.017 A A 8 9 3.501 B B 4 3 2.799 1.871 -0.526 -0.737 AA_DA8DT9:DA3DT4_BB 8 -0.149 0.278 30.962 -1.684 0.960 2.431 34.994 A A 9 10 8.510 B B 3 2 2.679 5.087 0.482 -0.996 AA_DT9DG10:DC2DA3_BB 9 -4.463 7.467 34.354 -2.261 -1.332 3.673 50.352 A A 10 11 -12.903 B B 2 1 3.609 -10.901 0.206 -0.686 AA_DG10DC11:DG1DC2_BB 10 -0.088 0.104 49.233 0.072 -0.249 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 2001-11-28 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 SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE CYTOSINE RCSB Y RCSB 2001-11-06 REL REL THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED BY THE FULL-RELAXATION MATRIX BACK-CALCULATION METHOD. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH-TEMPERATURE STEP MAKE UP THE 15 STRUCTURES. 29 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .52A OR LESS. THE AVERAGE OF THESE 29 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE. 1 NOESY COSY DQFCOSY COSY45 TOCSY HETCO NOESY 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA 6.78 AMBIENT 298 K 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA 6.78 AMBIENT 276 K RESTRAINED MOLECULAR DYNAMICS SIMULATIONS 2mM DNA, 25mM PHOSPHATE Buffer, 50mM NaCl, 0.5mM EDTA 100% D2O 2mM DNA, 25mM PHOSPHATE Buffer, 50mM NaCl, 0.5mM EDTA 10 % D2O, 90 % H20 BRUNGER refinement X-PLOR 3.851 BIOSYM TECHNOLOGIES, INC. processing Felix 95 AND 98 600 Varian INOVA 500 Varian INOVA C 1 n 1 DC 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A S6G 6 n 6 S6G 6 A C 7 n 7 DC 7 A A 8 n 8 DA 8 A T 9 n 9 DT 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 1 n 1 DG 1 B C 2 n 2 DC 2 B A 3 n 3 DA 3 B T 4 n 4 DT 4 B G 5 n 5 DG 5 B T 6 n 6 DT 6 B G 7 n 7 DG 7 B T 8 n 8 DT 8 B A 9 n 9 DA 9 B C 10 n 10 DC 10 B G 11 n 11 DG 11 B author_defined_assembly 2 dimeric A S6G 6 A S6G 6 DG 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 3.02 0.50 113.10 116.12 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 3.53 0.30 108.30 111.83 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 3.03 0.50 113.10 116.13 A A A N7 C8 N9 DG DG DG 10 10 10 N 1 2.54 0.30 108.30 110.84 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 3.13 0.50 113.10 116.23 B B B N7 C8 N9 DG DG DG 1 1 1 N 1 2.88 0.30 108.30 111.18 B B B O4' C1' N1 DT DT DT 4 4 4 N 1 3.06 0.50 113.10 116.16 B B B N7 C8 N9 DG DG DG 5 5 5 N 1 3.38 0.50 113.10 116.48 B B B N7 C8 N9 DG DG DG 7 7 7 N 1 -2.41 0.40 106.40 103.99 B B B C8 N9 C4 DG DG DG 7 7 7 N 1 3.01 0.50 113.10 116.11 B B B N7 C8 N9 DG DG DG 11 11 11 N 1 A A C4 N4 DC DC 1 1 0.095 0.009 1.335 1.430 N 1 A A C2 N2 DG DG 2 2 0.080 0.010 1.341 1.421 N 1 A A C5 C7 DT DT 3 3 0.037 0.006 1.496 1.533 N 1 A A C6 N6 DA DA 4 4 0.094 0.008 1.335 1.429 N 1 A A C4 N4 DC DC 5 5 0.095 0.009 1.335 1.430 N 1 A A C4 N4 DC DC 7 7 0.095 0.009 1.335 1.430 N 1 A A C6 N6 DA DA 8 8 0.096 0.008 1.335 1.431 N 1 A A C5 C7 DT DT 9 9 0.038 0.006 1.496 1.534 N 1 A A C2 N2 DG DG 10 10 0.080 0.010 1.341 1.421 N 1 A A C4 N4 DC DC 11 11 0.093 0.009 1.335 1.428 N 1 B B C2 N2 DG DG 1 1 0.081 0.010 1.341 1.422 N 1 B B C4 N4 DC DC 2 2 0.095 0.009 1.335 1.430 N 1 B B C6 N6 DA DA 3 3 0.093 0.008 1.335 1.428 N 1 B B C5 C7 DT DT 4 4 0.036 0.006 1.496 1.532 N 1 B B C2 N2 DG DG 5 5 0.084 0.010 1.341 1.425 N 1 B B C5 C7 DT DT 6 6 0.039 0.006 1.496 1.535 N 1 B B C2 N2 DG DG 7 7 0.081 0.010 1.341 1.422 N 1 B B C5 C7 DT DT 8 8 0.037 0.006 1.496 1.533 N 1 B B C6 N6 DA DA 9 9 0.094 0.008 1.335 1.429 N 1 B B C4 N4 DC DC 10 10 0.094 0.009 1.335 1.429 N 1 B B C2 N2 DG DG 11 11 0.086 0.010 1.341 1.427 N SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE THYMINE 1 N N 2 N N covale 1.617 both A DC 5 A O3' DC 5 1_555 A S6G 6 A P S6G 6 1_555 covale 1.619 both A S6G 6 A O3' S6G 6 1_555 A DC 7 A P DC 7 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 11 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 11 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 11 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 9 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 9 B N6 DA 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 7 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 7 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 7 B N2 DG 7 1_555 hydrog S6G-DT MISPAIR A S6G 6 A N1 S6G 6 1_555 B DT 6 B O2 DT 6 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 5 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 5 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 5 B N2 DG 5 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 4 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 4 B O4 DT 4 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 2 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 2 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 2 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 1 B N2 DG 1 1_555 DNA THIOGUANINE, 6-THIOGUANINE, TG, 6TG, S6G, THIOPURINE, DOUBLE HELIX, B-FORM DNA, DNA 1KBM PDB 1 1KBM 1KBM PDB 2 1KBM 1 11 1KBM 1 11 1KBM A 1 1 11 1 11 1KBM 1 11 1KBM B 2 1 11 1 P 1