1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kool, E.T. Krugh, T.R. Guckian, K.M. 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 C12 H15 F2 O6 P 324.214 1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-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 C13 H17 N2 O6 P 328.258 1-[2-DEOXYRIBOFURANOSYL]-4-METHYL-BENZOIMIDAZOLE-5'-MONOPHOSPHATE DNA linking US J.Am.Chem.Soc. JACSAT 0004 0002-7863 122 6841 6847 -1 Solution Structure of a Nonpolar, Non-Hydrogen-Bonded Base Pair Surrogate in DNA 2000 10.2210/pdb1eek/pdb pdb_00001eek 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3615.372 5'-D(*CP*GP*CP*AP*TP*(DFT)P*GP*TP*TP*AP*CP*C)-3' 1 syn polymer 3708.478 5'-D(*GP*GP*TP*AP*AP*CP*(MBZ)P*AP*TP*GP*CP*G)-3' 1 syn polymer no yes (DC)(DG)(DC)(DA)(DT)(DFT)(DG)(DT)(DT)(DA)(DC)(DC) CGCATNGTTACC 1 polydeoxyribonucleotide no yes (DG)(DG)(DT)(DA)(DA)(DC)(MBZ)(DA)(DT)(DG)(DC)(DG) GGTAACNATGCG 2 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 20.698 1 19 1 1 2 12 -0.926 1_DC1:DG12_2 1 -25.110 0.352 -0.165 -0.115 -0.026 1 19 1 2 2 11 -1.656 1_DG2:DC11_2 2 -11.244 -0.591 0.193 -0.265 -5.540 1 19 1 3 2 10 -1.156 1_DC3:DG10_2 3 -12.167 0.479 0.176 -0.198 -5.841 1 20 1 4 2 9 -1.706 1_DA4:DT9_2 4 -5.014 0.235 0.320 -0.082 1.424 1 20 1 5 2 8 -1.895 1_DT5:DA8_2 5 -10.434 -0.397 0.562 -0.146 -5.607 1 19 1 7 2 6 -2.043 1_DG7:DC6_2 6 -4.594 -0.465 -0.329 -0.236 -6.276 1 20 1 8 2 5 -2.336 1_DT8:DA5_2 7 -10.573 -0.244 0.264 -0.089 -2.821 1 20 1 9 2 4 -1.289 1_DT9:DA4_2 8 -15.481 -0.016 -0.011 -0.110 8.408 1 20 1 10 2 3 -2.727 1_DA10:DT3_2 9 -10.135 0.054 0.322 -0.096 12.919 1 19 1 11 2 2 -1.655 1_DC11:DG2_2 10 -14.851 0.299 -0.190 -0.160 -5.458 1 19 1 12 2 1 -1.986 1_DC12:DG1_2 11 -12.276 0.555 0.375 -0.244 2.677 36.487 1 1 1 2 24.915 2 2 12 11 3.345 15.099 -0.149 -0.915 11_DC1DG2:DC11DG12_22 1 -5.456 9.002 32.874 -3.495 -0.496 3.132 43.394 1 1 2 3 4.986 2 2 11 10 3.191 3.682 0.174 -0.630 11_DG2DC3:DG10DC11_22 2 0.830 -1.124 43.238 -1.198 -0.158 2.424 32.609 1 1 3 4 17.284 2 2 10 9 2.925 9.566 -0.319 -1.363 11_DC3DA4:DT9DG10_22 3 -1.369 2.474 31.181 -3.821 0.368 3.033 33.496 1 1 4 5 -2.563 2 2 9 8 2.983 -1.475 -0.401 -0.720 11_DA4DT5:DA8DT9_22 4 -2.614 4.542 33.365 -1.025 0.300 6.845 68.613 1 1 5 7 -0.227 2 2 8 6 6.802 -0.255 0.931 0.515 11_DT5DG7:DC6DA8_22 5 4.842 -4.298 68.462 0.477 -0.450 3.074 31.711 1 1 7 8 8.631 2 2 6 5 3.283 4.678 -0.488 -1.462 11_DG7DT8:DA5DC6_22 6 -5.410 9.981 30.915 -3.523 -0.087 2.845 39.252 1 1 8 9 7.235 2 2 5 4 2.938 4.840 0.280 -0.719 11_DT8DT9:DA4DA5_22 7 4.354 -6.509 38.730 -1.584 0.046 2.027 29.089 1 1 9 10 25.332 2 2 4 3 2.724 12.316 -0.022 -1.056 11_DT9DA10:DT3DA4_22 8 -2.834 5.828 26.254 -4.168 -0.431 2.940 38.999 1 1 10 11 1.330 2 2 3 2 2.974 0.887 -0.375 -0.651 11_DA10DC11:DG2DT3_22 9 1.737 -2.603 38.952 -1.072 0.751 3.318 33.380 1 1 11 12 4.262 2 2 2 1 3.543 2.442 0.863 -1.550 11_DC11DC12:DG1DG2_22 10 -3.473 6.062 33.117 -3.125 -2.109 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2000-02-16 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag solution structure of an F - A pair RCSB Y RCSB 2000-02-01 REL 1 2D NOESY 100 mM 7.4 ambient 15 K restrained molecular dynamics 3 mM DNA, phosphate buffer, 100% D2O 100% D2O 500 Varian UNITY C 1 n 1 DC 1 1 G 2 n 2 DG 2 1 C 3 n 3 DC 3 1 A 4 n 4 DA 4 1 T 5 n 5 DT 5 1 DFT 6 n 6 DFT 6 1 G 7 n 7 DG 7 1 T 8 n 8 DT 8 1 T 9 n 9 DT 9 1 A 10 n 10 DA 10 1 C 11 n 11 DC 11 1 C 12 n 12 DC 12 1 G 1 n 1 DG 1 2 G 2 n 2 DG 2 2 T 3 n 3 DT 3 2 A 4 n 4 DA 4 2 A 5 n 5 DA 5 2 C 6 n 6 DC 6 2 MBZ 7 n 7 MBZ 7 2 A 8 n 8 DA 8 2 T 9 n 9 DT 9 2 G 10 n 10 DG 10 2 C 11 n 11 DC 11 2 G 12 n 12 DG 12 2 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 1 DA 4 0.118 SIDE CHAIN 1 1 DT 5 0.100 SIDE CHAIN 1 2.35 0.30 108.30 110.65 1 1 1 O4' C1' N1 DC DC DC 1 1 1 N 1 1.86 0.30 108.30 110.16 1 1 1 O4' C1' N1 DT DT DT 8 8 8 N 1 2.32 0.30 108.30 110.62 1 1 1 O4' C1' N9 DA DA DA 10 10 10 N 1 5.51 0.30 108.30 113.81 1 1 1 O4' C1' N1 DC DC DC 12 12 12 N 1 19.65 2.50 111.00 130.65 2 2 2 O5' C5' C4' DG DG DG 1 1 1 N 1 2.73 0.30 108.30 111.03 2 2 2 O4' C1' N9 DG DG DG 1 1 1 N 1 3.79 0.30 108.30 112.09 2 2 2 O4' C1' N9 DA DA DA 4 4 4 N 1 3.21 0.30 108.30 111.51 2 2 2 O4' C1' N1 DC DC DC 6 6 6 N SOLUTION STRUCTURE OF A NONPOLAR, NON HYDROGEN BONDED BASE PAIR SURROGATE IN DNA. 1 N N 2 N N covale 1.613 both 1 DT 5 A O3' DT 5 1_555 1 DFT 6 A P DFT 6 1_555 covale 1.624 both 1 DFT 6 A O3' DFT 6 1_555 1 DG 7 A P DG 7 1_555 covale 1.597 both 2 DC 6 B O3' DC 6 1_555 2 MBZ 7 B P MBZ 7 1_555 covale 1.613 one 2 MBZ 7 B O3' MBZ 7 1_555 2 DA 8 B P DA 8 1_555 hydrog WATSON-CRICK 1 DC 1 A N3 DC 1 1_555 2 DG 12 B N1 DG 12 1_555 hydrog WATSON-CRICK 1 DC 1 A N4 DC 1 1_555 2 DG 12 B O6 DG 12 1_555 hydrog WATSON-CRICK 1 DC 1 A O2 DC 1 1_555 2 DG 12 B N2 DG 12 1_555 hydrog WATSON-CRICK 1 DG 2 A N1 DG 2 1_555 2 DC 11 B N3 DC 11 1_555 hydrog WATSON-CRICK 1 DG 2 A N2 DG 2 1_555 2 DC 11 B O2 DC 11 1_555 hydrog WATSON-CRICK 1 DG 2 A O6 DG 2 1_555 2 DC 11 B N4 DC 11 1_555 hydrog WATSON-CRICK 1 DC 3 A N3 DC 3 1_555 2 DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK 1 DC 3 A N4 DC 3 1_555 2 DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK 1 DC 3 A O2 DC 3 1_555 2 DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK 1 DA 4 A N1 DA 4 1_555 2 DT 9 B N3 DT 9 1_555 hydrog WATSON-CRICK 1 DA 4 A N6 DA 4 1_555 2 DT 9 B O4 DT 9 1_555 hydrog WATSON-CRICK 1 DT 5 A N3 DT 5 1_555 2 DA 8 B N1 DA 8 1_555 hydrog WATSON-CRICK 1 DT 5 A O4 DT 5 1_555 2 DA 8 B N6 DA 8 1_555 hydrog WATSON-CRICK 1 DG 7 A N1 DG 7 1_555 2 DC 6 B N3 DC 6 1_555 hydrog WATSON-CRICK 1 DG 7 A N2 DG 7 1_555 2 DC 6 B O2 DC 6 1_555 hydrog WATSON-CRICK 1 DG 7 A O6 DG 7 1_555 2 DC 6 B N4 DC 6 1_555 hydrog WATSON-CRICK 1 DT 8 A N3 DT 8 1_555 2 DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK 1 DT 8 A O4 DT 8 1_555 2 DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK 1 DT 9 A N3 DT 9 1_555 2 DA 4 B N1 DA 4 1_555 hydrog WATSON-CRICK 1 DT 9 A O4 DT 9 1_555 2 DA 4 B N6 DA 4 1_555 hydrog WATSON-CRICK 1 DA 10 A N1 DA 10 1_555 2 DT 3 B N3 DT 3 1_555 hydrog WATSON-CRICK 1 DA 10 A N6 DA 10 1_555 2 DT 3 B O4 DT 3 1_555 hydrog WATSON-CRICK 1 DC 11 A N3 DC 11 1_555 2 DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK 1 DC 11 A N4 DC 11 1_555 2 DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK 1 DC 11 A O2 DC 11 1_555 2 DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK 1 DC 12 A N3 DC 12 1_555 2 DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK 1 DC 12 A N4 DC 12 1_555 2 DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK 1 DC 12 A O2 DC 12 1_555 2 DG 1 B N2 DG 1 1_555 DNA DNA, Nonpolar, isosteric, DNA base analogs 1EEK PDB 1 1EEK 1EEK PDB 2 1EEK 1 12 1EEK 1 12 1EEK 1 1 1 12 1 12 1EEK 1 12 1EEK 2 2 1 12 1 P 1