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/pdb1kb1/pdb pdb_00001kb1 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 3374.210 5'-D(*GP*CP*AP*TP*GP*CP*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)(DC)(DG)(DT)(DA)(DC)(DG) GCATGCGTACG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -10.090 1 19 A 1 B 11 -2.544 A_DC1:DG11_B 1 -2.093 0.609 0.183 -0.229 -5.982 1 19 A 2 B 10 -1.984 A_DG2:DC10_B 2 -1.481 -0.624 0.137 -0.252 -1.270 1 20 A 3 B 9 -2.453 A_DT3:DA9_B 3 -5.652 -0.211 0.171 -0.129 -0.064 1 20 A 4 B 8 -2.560 A_DA4:DT8_B 4 -9.040 0.247 0.111 -0.106 2.239 1 19 A 5 B 7 -0.731 A_DC5:DG7_B 5 -4.749 0.825 0.063 -0.269 -2.655 1 A 6 B 6 6.068 A_S6G6:DC6_B 6 -3.214 -1.147 0.262 -0.108 -5.032 1 19 A 7 B 5 -0.994 A_DC7:DG5_B 7 1.818 0.732 0.355 -0.266 -1.558 1 20 A 8 B 4 -2.863 A_DA8:DT4_B 8 -8.438 0.212 0.060 -0.086 7.371 1 20 A 9 B 3 -3.013 A_DT9:DA3_B 9 -8.607 -0.351 0.070 -0.096 5.948 1 19 A 10 B 2 -1.175 A_DG10:DC2_B 10 1.228 -0.645 0.274 -0.269 -5.266 1 19 A 11 B 1 -0.769 A_DC11:DG1_B 11 3.870 0.684 0.316 -0.239 2.630 31.837 A A 1 2 7.928 B B 11 10 2.766 4.332 0.567 -1.109 AA_DC1DG2:DC10DG11_BB 1 2.501 -4.578 31.451 -2.678 -0.654 3.038 39.349 A A 2 3 -1.259 B B 10 9 3.018 -0.847 -0.102 -1.085 AA_DG2DT3:DA9DC10_BB 2 0.566 -0.840 39.336 -1.518 0.214 2.318 35.998 A A 3 4 18.803 B B 9 8 2.831 11.430 0.193 -1.229 AA_DT3DA4:DT8DA9_BB 3 1.004 -1.651 34.177 -3.304 -0.197 2.992 40.590 A A 4 5 1.352 B B 8 7 3.005 0.938 -0.270 -0.788 AA_DA4DC5:DG7DT8_BB 4 -0.799 1.152 40.572 -1.232 0.308 2.606 32.339 A A 5 6 11.642 B B 7 6 2.867 6.443 0.623 -1.028 AA_DC5S6G6:DC6DG7_BB 5 -0.373 0.673 31.705 -2.809 -1.173 3.260 49.925 A A 6 7 -4.414 B B 6 5 3.232 -3.722 -0.491 -0.355 AA_S6G6DC7:DG5DC6_BB 6 -1.257 1.491 49.780 -0.152 0.491 2.374 36.265 A A 7 8 14.554 B B 5 4 2.721 8.956 -0.295 -0.943 AA_DC7DA8:DT4DG5_BB 7 3.644 -5.922 34.994 -2.510 0.880 2.780 32.430 A A 8 9 4.451 B B 4 3 2.849 2.483 -0.086 -0.839 AA_DA8DT9:DA3DT4_BB 8 -0.477 0.856 32.334 -1.879 0.081 2.795 34.899 A A 9 10 4.401 B B 3 2 2.929 2.634 0.352 -1.174 AA_DT9DG10:DC2DA3_BB 9 -3.051 5.097 34.673 -2.307 -0.992 3.768 50.904 A A 10 11 -14.693 B B 2 1 3.699 -12.514 0.015 -0.737 AA_DG10DC11:DG1DC2_BB 10 -1.284 1.507 49.425 0.157 -0.121 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 THYMINE RCSB Y RCSB 2001-11-05 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. 25 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .59A OR LESS. THE AVERAGE OF THESE 25 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 2D NOESY COSY DQF-COSY COSY45 TOCSY HETCO 2D NOESY 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA 6.78 ambient 298 K 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA 6.78 ambient 276 K RESTRAINED MOLECULAR DYNAMICS SIMULATIONS 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA 100% D2O 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA 10 % D2O, 90 % H2O BIOSYM TECHNOLOGIES, INC. processing Felix 95 AND 98 BRUNGER iterative matrix relaxation X-PLOR 3.857 BRUNGER refinement X-PLOR 3.857 600 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 C 6 n 6 DC 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 1.85 0.30 108.30 110.15 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 3.06 0.50 113.10 116.16 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 2.75 0.30 108.30 111.05 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 1.97 0.30 108.30 110.27 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 2.16 0.30 108.30 110.46 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 2.74 0.30 108.30 111.04 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 3.14 0.50 113.10 116.24 B B B N7 C8 N9 DG DG DG 1 1 1 N 1 2.41 0.30 108.30 110.71 B B B O4' C1' N1 DT DT DT 4 4 4 N 1 3.03 0.50 113.10 116.13 B B B N7 C8 N9 DG DG DG 5 5 5 N 1 3.13 0.50 113.10 116.23 B B B N7 C8 N9 DG DG DG 7 7 7 N 1 3.05 0.50 113.10 116.15 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 0.081 0.010 1.341 1.422 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 0.094 0.009 1.335 1.429 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 0.094 0.008 1.335 1.429 N 1 A A C5 C7 DT DT 9 9 0.037 0.006 1.496 1.533 N 1 A A C2 N2 DG DG 10 10 0.079 0.010 1.341 1.420 N 1 A A C4 N4 DC DC 11 11 0.094 0.009 1.335 1.429 N 1 B B C2 N2 DG DG 1 1 0.079 0.010 1.341 1.420 N 1 B B C4 N4 DC DC 2 2 0.094 0.009 1.335 1.429 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 0.037 0.006 1.496 1.533 N 1 B B C2 N2 DG DG 5 5 0.080 0.010 1.341 1.421 N 1 B B C4 N4 DC DC 6 6 0.094 0.009 1.335 1.429 N 1 B B C2 N2 DG DG 7 7 0.083 0.010 1.341 1.424 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 0.093 0.008 1.335 1.428 N 1 B B C4 N4 DC DC 10 10 0.096 0.009 1.335 1.431 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 CYTOSINE 1 N N 2 N N covale 1.619 both A DC 5 A O3' DC 5 1_555 A S6G 6 A P S6G 6 1_555 covale 1.618 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-DC PAIR A S6G 6 A N1 S6G 6 1_555 B DC 6 B O2 DC 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 1KB1 PDB 1 1KB1 1KB1 PDB 2 1KB1 1 11 1KB1 1 11 1KB1 A 1 1 11 1 11 1KB1 1 11 1KB1 B 2 1 11 1 P 1