1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Guckian, K.M. Krugh, T.R. Kool, E.T. 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 N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N P N 72 N O N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N C Y 84 N C Y 85 N C N 86 N C Y 87 N C N 88 N F Y 89 N C N 90 N F Y 91 N C N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 N C N 118 R C Y 119 N N Y 120 N C Y 121 N N Y 122 N C N 123 N C N 124 N O N 125 N N N 126 N C N 127 N N N 128 N N Y 129 N C N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N O N 145 N P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 R C N 156 N N N 157 N C N 158 N O N 159 N N N 160 N C N 161 N O N 162 N C N 163 N C N 164 N C N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N doub N 98 N sing Y 99 N sing Y 100 N doub N 101 N sing Y 102 N sing N 103 N sing Y 104 N sing N 105 N sing N 106 N sing N 107 N sing Y 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing Y 134 N sing Y 135 N sing Y 136 N doub N 137 N sing Y 138 N sing N 139 N sing Y 140 N doub N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N doub N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N doub N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing US Nat.Struct.Biol. NSBIEW 2024 1072-8368 5 954 959 10.1038/2930 9808039 Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair. 1998 10.2210/pdb1bw7/pdb pdb_00001bw7 THERE IS A CHIRALITY PROBLEM AROUND C1' OF RESIDUE G 12 IN CHAIN B 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 DIFLUOROTOLUENE IS A NONPOLAR ISOSTERE FOR THYMINE 3615.372 DNA (5'-D(*CP*GP*CP*AP*TP*(DFT)P*GP*TP*TP*AP*CP*C)-3') 1 syn polymer DIFLUOROTOLUENE IS A NONPOLAR ISOSTERE FOR THYMINE 3711.442 DNA (5'-D(*GP*GP*TP*AP*AP*CP*AP*AP*TP*GP*CP*G)-3') 1 syn polymer no yes (DC)(DG)(DC)(DA)(DT)(DFT)(DG)(DT)(DT)(DA)(DC)(DC) CGCATNGTTACC A polydeoxyribonucleotide no no (DG)(DG)(DT)(DA)(DA)(DC)(DA)(DA)(DT)(DG)(DC)(DG) GGTAACAATGCG 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 -4.151 1 19 A 1 B 12 -1.433 A_DC1:DG12_B 1 -12.711 0.267 0.458 -0.215 6.159 1 19 A 2 B 11 -1.302 A_DG2:DC11_B 2 -5.916 -0.371 0.456 -0.220 -0.618 1 19 A 3 B 10 -1.273 A_DC3:DG10_B 3 -11.025 0.490 0.370 -0.262 -0.669 1 20 A 4 B 9 -0.863 A_DA4:DT9_B 4 -11.060 0.205 0.293 -0.091 -7.915 1 20 A 5 B 8 -4.343 A_DT5:DA8_B 5 -17.723 -0.256 0.535 -0.172 2.292 1 19 A 7 B 6 -0.791 A_DG7:DC6_B 6 -6.879 -0.519 0.343 -0.255 8.337 1 20 A 8 B 5 -3.221 A_DT8:DA5_B 7 -10.581 -0.121 0.425 -0.141 7.340 1 20 A 9 B 4 -1.236 A_DT9:DA4_B 8 -14.018 -0.058 -0.176 -0.104 1.846 1 20 A 10 B 3 -2.691 A_DA10:DT3_B 9 -7.837 0.116 0.231 -0.125 4.496 1 19 A 11 B 2 -0.872 A_DC11:DG2_B 10 -12.951 0.172 0.054 -0.177 -12.668 1 19 A 12 B 1 -2.835 A_DC12:DG1_B 11 -12.823 0.515 0.828 -0.336 2.327 30.070 A A 1 2 16.118 B B 12 11 2.644 8.258 0.016 -0.817 AA_DC1DG2:DC11DG12_BB 1 0.836 -1.632 28.927 -2.886 0.102 3.309 44.660 A A 2 3 -1.796 B B 11 10 3.299 -1.364 0.030 -0.424 AA_DG2DC3:DG10DC11_BB 2 1.512 -1.990 44.616 -0.432 0.100 2.622 34.615 A A 3 4 10.930 B B 10 9 2.859 6.467 -0.252 -1.054 AA_DC3DA4:DT9DG10_BB 3 -0.278 0.470 34.022 -2.613 0.387 3.398 35.181 A A 4 5 -7.429 B B 9 8 3.283 -4.478 -0.392 -1.049 AA_DA4DT5:DA8DT9_BB 4 -1.108 1.837 34.887 -1.051 0.479 5.563 68.825 A A 5 7 5.011 B B 8 6 5.663 5.657 0.976 -1.729 AA_DT5DG7:DC6DA8_BB 5 3.754 -3.325 68.530 -1.889 -0.625 3.098 37.474 A A 7 8 -2.745 B B 6 5 3.053 -1.762 -0.591 -0.366 AA_DG7DT8:DA5DC6_BB 6 -2.435 3.794 37.358 -0.352 0.619 2.942 40.787 A A 8 9 1.884 B B 5 4 2.958 1.309 0.222 -0.533 AA_DT8DT9:DA4DA5_BB 7 5.861 -8.438 40.361 -0.896 0.267 2.376 34.331 A A 9 10 22.680 B B 4 3 3.021 13.052 0.141 -1.096 AA_DT9DA10:DT3DA4_BB 8 -2.994 5.203 31.684 -3.617 -0.642 3.022 38.480 A A 10 11 -4.339 B B 3 2 3.011 -2.857 -0.178 -0.308 AA_DA10DC11:DG2DT3_BB 9 0.678 -1.030 38.372 -0.140 0.347 3.374 41.451 A A 11 12 -1.282 B B 2 1 3.478 -0.904 0.697 -1.141 AA_DC11DC12:DG1DG2_BB 10 -5.898 8.360 41.038 -1.511 -1.647 chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software struct_conn repository Initial release Version format compliance Version format compliance Advisory Data collection Database references Derived calculations 1 0 1998-10-07 1 1 2008-04-27 1 2 2011-07-13 1 3 2011-12-28 1 4 2024-04-10 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag BNL Y RCSB 1998-09-30 REL MEAN STRUCTURE. NULL 50 1 NOESY DQF-COSY NOESYWATERGATE 100mM NACL 7.4 293 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RESTRAINED MOLECULAR DYNAMICS MSI refinement Insight II DISCOVER structure solution Insight II 500 Varian UNITY C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A A 4 n 4 DA 4 A T 5 n 5 DT 5 A T 6 n 6 DFT 6 A G 7 n 7 DG 7 A T 8 n 8 DT 8 A T 9 n 9 DT 9 A A 10 n 10 DA 10 A C 11 n 11 DC 11 A C 12 n 12 DC 12 A G 1 n 1 DG 1 B G 2 n 2 DG 2 B T 3 n 3 DT 3 B A 4 n 4 DA 4 B A 5 n 5 DA 5 B C 6 n 6 DC 6 B A 7 n 7 DA 7 B A 8 n 8 DA 8 B T 9 n 9 DT 9 B G 10 n 10 DG 10 B C 11 n 11 DC 11 B G 12 n 12 DG 12 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 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DG 2 0.053 SIDE CHAIN 1 A DA 4 0.082 SIDE CHAIN 1 A DG 7 0.088 SIDE CHAIN 1 A DC 12 0.080 SIDE CHAIN 1 B DG 2 0.065 SIDE CHAIN 1 B DT 3 0.068 SIDE CHAIN 1 B DG 10 0.069 SIDE CHAIN 1 B DC 11 0.072 SIDE CHAIN 1 3.38 0.50 111.50 114.88 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 2.41 0.40 121.90 124.31 A A A N3 C4 C5 DC DC DC 3 3 3 N 1 -4.49 0.50 117.00 112.51 A A A C4 C5 C6 DA DA DA 4 4 4 N 1 4.39 0.50 117.70 122.09 A A A C5 C6 N1 DA DA DA 4 4 4 N 1 -4.90 0.60 118.60 113.70 A A A N1 C6 N6 DA DA DA 4 4 4 N 1 -3.94 0.60 122.30 118.36 A A A N3 C2 O2 DT DT DT 5 5 5 N 1 3.68 0.60 119.00 122.68 A A A C4 C5 C7 DT DT DT 5 5 5 N 1 2.43 0.30 108.30 110.73 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 3.38 0.50 111.50 114.88 A A A C5 C6 N1 DG DG DG 7 7 7 N 1 -3.92 0.60 122.30 118.38 A A A N3 C2 O2 DT DT DT 8 8 8 N 1 -3.84 0.60 122.30 118.46 A A A N3 C2 O2 DT DT DT 9 9 9 N 1 -3.84 0.60 122.90 119.06 A A A C6 C5 C7 DT DT DT 9 9 9 N 1 -4.27 0.50 117.00 112.73 A A A C4 C5 C6 DA DA DA 10 10 10 N 1 4.40 0.50 117.70 122.10 A A A C5 C6 N1 DA DA DA 10 10 10 N 1 -4.66 0.60 118.60 113.94 A A A N1 C6 N6 DA DA DA 10 10 10 N 1 21.45 2.50 111.00 132.45 B B B O5' C5' C4' DG DG DG 1 1 1 N 1 3.11 0.50 111.50 114.61 B B B C5 C6 N1 DG DG DG 1 1 1 N 1 3.23 0.50 111.50 114.73 B B B C5 C6 N1 DG DG DG 2 2 2 N 1 -3.96 0.60 122.30 118.34 B B B N3 C2 O2 DT DT DT 3 3 3 N 1 -4.25 0.50 117.00 112.75 B B B C4 C5 C6 DA DA DA 4 4 4 N 1 4.47 0.50 117.70 122.17 B B B C5 C6 N1 DA DA DA 4 4 4 N 1 -4.68 0.60 118.60 113.92 B B B N1 C6 N6 DA DA DA 4 4 4 N 1 -4.14 0.50 117.00 112.86 B B B C4 C5 C6 DA DA DA 5 5 5 N 1 4.46 0.50 117.70 122.16 B B B C5 C6 N1 DA DA DA 5 5 5 N 1 -3.83 0.60 118.60 114.77 B B B N1 C6 N6 DA DA DA 5 5 5 N 1 -4.18 0.50 117.00 112.82 B B B C4 C5 C6 DA DA DA 7 7 7 N 1 3.97 0.50 117.70 121.67 B B B C5 C6 N1 DA DA DA 7 7 7 N 1 -4.66 0.60 118.60 113.94 B B B N1 C6 N6 DA DA DA 7 7 7 N 1 -4.10 0.50 117.00 112.90 B B B C4 C5 C6 DA DA DA 8 8 8 N 1 4.11 0.50 117.70 121.81 B B B C5 C6 N1 DA DA DA 8 8 8 N 1 -4.30 0.60 118.60 114.30 B B B N1 C6 N6 DA DA DA 8 8 8 N 1 4.33 0.60 119.00 123.33 B B B C4 C5 C7 DT DT DT 9 9 9 N 1 -4.83 0.60 122.90 118.07 B B B C6 C5 C7 DT DT DT 9 9 9 N 1 3.40 0.50 111.50 114.90 B B B C5 C6 N1 DG DG DG 10 10 10 N 1 3.23 0.50 111.50 114.73 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 A A C5 C7 DT DT 5 5 0.043 0.006 1.496 1.539 N 1 A A C5 C7 DT DT 8 8 0.047 0.006 1.496 1.543 N 1 A A C5 C7 DT DT 9 9 0.047 0.006 1.496 1.543 N 1 B B C5 C7 DT DT 3 3 0.042 0.006 1.496 1.538 N 1 B B C5 C7 DT DT 9 9 0.044 0.006 1.496 1.540 N SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A REPLICABLE DIFLUOROTOLUENE-ADENINE PAIR 1 N N 2 N N covale 1.612 both A DT 5 A O3' DT 5 1_555 A DFT 6 A P DFT 6 1_555 covale 1.622 both A DFT 6 A O3' DFT 6 1_555 A DG 7 A P DG 7 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 12 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 12 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 12 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 11 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 9 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 9 B O4 DT 9 1_555 hydrog DT-DA PAIR A DT 5 A O4 DT 5 1_555 B DA 7 B N6 DA 7 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 8 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 8 B N6 DA 8 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 6 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 6 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 6 B N4 DC 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 4 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 4 B N6 DA 4 1_555 hydrog WATSON-CRICK A DA 10 A N1 DA 10 1_555 B DT 3 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 3 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 1 B N2 DG 1 1_555 DNA DNA, DIFLUOROTOLUENE 1BW7 PDB 1 1BW7 1BW7 PDB 2 1BW7 1 12 1BW7 1 12 1BW7 A 1 1 12 1 12 1BW7 1 12 1BW7 B 2 1 12 1 P 1