0.040667 0.000000 0.000000 0.000000 0.024728 0.000000 0.000000 0.000000 0.015207 0.00000 0.00000 0.00000 Czarny, A. Boykin, D.W. Wood, A.A. Nunn, C.M. Neidle, S. Zhao, M. Wilson, W.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 24.590 40.440 65.760 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 H2 O 18.015 WATER non-polymer C23 H20 N6 O 396.445 5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer 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 O N 72 N P 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 N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H 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 H N 146 N H N 147 N C N 148 N C N 149 N C Y 150 N C Y 151 N C Y 152 N C Y 153 N C Y 154 N C Y 155 N C Y 156 N C Y 157 N C Y 158 N C Y 159 N C Y 160 N C Y 161 N C Y 162 N C Y 163 N C Y 164 N C Y 165 N C Y 166 N C Y 167 N C Y 168 N C Y 169 N C N 170 N N N 171 N N Y 172 N N Y 173 N N Y 174 N N Y 175 N N N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N MG 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 sing N 75 N sing N 76 N doub 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 sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub 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 N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing 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 Y 163 N sing Y 164 N doub Y 165 N doub N 166 N sing Y 167 N sing N 168 N sing Y 169 N doub Y 170 N sing Y 171 N sing Y 172 N sing N 173 N sing Y 174 N sing Y 175 N sing Y 176 N doub Y 177 N doub Y 178 N sing Y 179 N sing Y 180 N sing Y 181 N sing Y 182 N doub N 183 N sing Y 184 N sing N 185 N sing Y 186 N sing Y 187 N doub Y 188 N sing Y 189 N sing Y 190 N doub Y 191 N doub N 192 N sing Y 193 N sing N 194 N sing Y 195 N doub N 196 N sing Y 197 N sing N 198 N sing N 199 N sing Y 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 23 3678 3684 10.1093/nar/23.18.3678 7478996 Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2. 1995 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 117 4716 4717 Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA 1995 US Biochemistry BICHAW 0033 0006-2960 30 10294 Low Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G 1991 10.2210/pdb109d/pdb pdb_0000109d 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 AREA DETECTOR XENTRONICS x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE ENRAF-NONIUS 3663.392 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 396.445 5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 90 nat water no no (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 2.23 44.88 5.955 1 19 A 1 B 24 -0.490 A_DC1:DG24_B 1 -13.604 0.227 -0.224 -0.183 -0.896 1 19 A 2 B 23 -3.452 A_DG2:DC23_B 2 -8.828 -0.035 0.260 -0.233 -0.627 1 19 A 3 B 22 -1.400 A_DC3:DG22_B 3 -5.057 0.013 -0.005 -0.140 11.866 1 19 A 4 B 21 -2.655 A_DG4:DC21_B 4 -4.328 -0.152 -0.025 -0.038 6.887 1 20 A 5 B 20 0.156 A_DA5:DT20_B 5 -19.745 0.096 -0.197 -0.068 -6.398 1 20 A 6 B 19 2.897 A_DA6:DT19_B 6 -17.803 0.047 0.554 -0.226 0.750 1 20 A 7 B 18 18.116 A_DT7:DA18_B 7 -7.168 -0.656 0.761 -0.184 -7.253 1 20 A 8 B 17 -2.478 A_DT8:DA17_B 8 -18.250 -0.151 -0.063 -0.194 -10.992 1 19 A 9 B 16 -1.696 A_DC9:DG16_B 9 -8.317 -0.013 -0.006 -0.113 4.340 1 19 A 10 B 15 -0.710 A_DG10:DC15_B 10 -1.819 -0.011 0.087 -0.210 5.431 1 19 A 11 B 14 -2.624 A_DC11:DG14_B 11 -19.539 0.076 0.098 -0.146 4.047 1 19 A 12 B 13 -4.384 A_DG12:DC13_B 12 8.262 -0.154 -0.283 -0.212 3.541 38.145 A A 1 2 14.228 B B 24 23 3.562 9.194 -0.289 0.288 AA_DC1DG2:DC23DG24_BB 1 -4.363 6.753 36.811 -0.845 -0.168 3.360 39.416 A A 2 3 -9.569 B B 23 22 3.438 -6.420 0.633 0.487 AA_DG2DC3:DG22DC23_BB 2 3.367 -5.019 38.769 1.517 -0.521 3.211 30.555 A A 3 4 14.162 B B 22 21 3.158 7.390 -0.189 0.650 AA_DC3DG4:DC21DG22_BB 3 1.357 -2.600 29.638 -0.217 0.625 3.495 36.576 A A 4 5 2.863 B B 21 20 3.495 1.794 0.041 0.217 AA_DG4DA5:DT20DC21_BB 4 2.883 -4.599 36.423 0.081 0.359 3.233 39.587 A A 5 6 9.496 B B 20 19 3.505 6.367 0.315 -0.697 AA_DA5DA6:DT19DT20_BB 5 -7.700 11.483 38.355 -1.811 -1.410 3.006 28.417 A A 6 7 -22.765 B B 19 18 3.120 -10.896 0.833 -0.212 AA_DA6DT7:DA18DT19_BB 6 1.365 -2.853 26.250 2.009 -1.391 2.877 41.805 A A 7 8 14.494 B B 18 17 3.311 10.172 -0.831 -0.433 AA_DT7DT8:DA17DA18_BB 7 8.910 -12.695 39.651 -1.645 2.073 3.497 41.032 A A 8 9 0.495 B B 17 16 3.494 0.347 -0.016 0.373 AA_DT8DC9:DG16DA17_BB 8 -0.219 0.312 41.030 0.492 -0.003 3.280 29.819 A A 9 10 6.499 B B 16 15 3.202 3.333 0.182 1.181 AA_DC9DG10:DC15DG16_BB 9 -2.888 5.632 29.498 1.604 -0.952 3.019 41.392 A A 10 11 -19.159 B B 15 14 3.445 -13.319 -0.913 0.915 AA_DG10DC11:DG14DC15_BB 10 -1.243 1.788 39.261 2.744 1.156 3.601 39.989 A A 11 12 -6.238 B B 14 13 3.637 -4.249 0.879 0.906 AA_DC11DG12:DC13DG14_BB 11 4.677 -6.865 39.507 1.867 -0.687 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1995-05-08 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y NDB 1995-02-15 REL REL IBB 5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE MG MAGNESIUM ION HOH water IBB 25 2 IBB IBB 25 A MO6 26 3 MG MG 26 A HOH 29 4 HOH HOH 29 A HOH 30 4 HOH HOH 30 A HOH 31 4 HOH HOH 31 A HOH 33 4 HOH HOH 33 A HOH 34 4 HOH HOH 34 A HOH 37 4 HOH HOH 37 A HOH 38 4 HOH HOH 38 A HOH 40 4 HOH HOH 40 A HOH 41 4 HOH HOH 41 A HOH 42 4 HOH HOH 42 A HOH 43 4 HOH HOH 43 A HOH 44 4 HOH HOH 44 A HOH 45 4 HOH HOH 45 A HOH 47 4 HOH HOH 47 A HOH 49 4 HOH HOH 49 A HOH 50 4 HOH HOH 50 A HOH 52 4 HOH HOH 52 A HOH 54 4 HOH HOH 54 A HOH 55 4 HOH HOH 55 A HOH 58 4 HOH HOH 58 A HOH 60 4 HOH HOH 60 A HOH 62 4 HOH HOH 62 A HOH 63 4 HOH HOH 63 A HOH 65 4 HOH HOH 65 A HOH 66 4 HOH HOH 66 A HOH 67 4 HOH HOH 67 A HOH 69 4 HOH HOH 69 A HOH 70 4 HOH HOH 70 A HOH 72 4 HOH HOH 72 A HOH 75 4 HOH HOH 75 A HOH 76 4 HOH HOH 76 A HOH 78 4 HOH HOH 78 A HOH 79 4 HOH HOH 79 A HOH 80 4 HOH HOH 80 A HOH 83 4 HOH HOH 83 A HOH 86 4 HOH HOH 86 A HOH 87 4 HOH HOH 87 A HOH 88 4 HOH HOH 88 A HOH 89 4 HOH HOH 89 A HOH 90 4 HOH HOH 90 A HOH 91 4 HOH HOH 91 A HOH 92 4 HOH HOH 92 A HOH 93 4 HOH HOH 93 A HOH 94 4 HOH HOH 94 A HOH 95 4 HOH HOH 95 A HOH 100 4 HOH HOH 100 A HOH 101 4 HOH HOH 101 A HOH 102 4 HOH HOH 102 A HOH 103 4 HOH HOH 103 A HOH 104 4 HOH HOH 104 A HOH 105 4 HOH HOH 105 A HOH 106 4 HOH HOH 106 A HOH 107 4 HOH HOH 107 A HOH 108 4 HOH HOH 108 A HOH 109 4 HOH HOH 109 A MO6 26 4 HOH HOH 111 A MO6 26 4 HOH HOH 112 A MO6 26 4 HOH HOH 113 A MO6 26 4 HOH HOH 114 A MO6 26 4 HOH HOH 115 A MO6 26 4 HOH HOH 116 A HOH 27 4 HOH HOH 27 B HOH 28 4 HOH HOH 28 B HOH 32 4 HOH HOH 32 B HOH 35 4 HOH HOH 35 B HOH 36 4 HOH HOH 36 B HOH 39 4 HOH HOH 39 B HOH 46 4 HOH HOH 46 B HOH 48 4 HOH HOH 48 B HOH 51 4 HOH HOH 51 B HOH 53 4 HOH HOH 53 B HOH 56 4 HOH HOH 56 B HOH 57 4 HOH HOH 57 B HOH 59 4 HOH HOH 59 B HOH 61 4 HOH HOH 61 B HOH 64 4 HOH HOH 64 B HOH 68 4 HOH HOH 68 B HOH 71 4 HOH HOH 71 B HOH 73 4 HOH HOH 73 B HOH 74 4 HOH HOH 74 B HOH 77 4 HOH HOH 77 B HOH 81 4 HOH HOH 81 B HOH 82 4 HOH HOH 82 B HOH 84 4 HOH HOH 84 B HOH 85 4 HOH HOH 85 B HOH 96 4 HOH HOH 96 B HOH 97 4 HOH HOH 97 B HOH 98 4 HOH HOH 98 B HOH 99 4 HOH HOH 99 B HOH 110 4 HOH HOH 110 B C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B G 14 n 2 DG 14 B C 15 n 3 DC 15 B G 16 n 4 DG 16 B A 17 n 5 DA 17 B A 18 n 6 DA 18 B T 19 n 7 DT 19 B T 20 n 8 DT 20 B C 21 n 9 DC 21 B G 22 n 10 DG 22 B C 23 n 11 DC 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric A HOH 111 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 112 E O HOH 1_555 93.1 A HOH 111 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 113 E O HOH 1_555 95.5 A HOH 112 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 113 E O HOH 1_555 87.0 A HOH 111 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 114 E O HOH 1_555 174.7 A HOH 112 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 114 E O HOH 1_555 91.3 A HOH 113 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 114 E O HOH 1_555 87.5 A HOH 111 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 115 E O HOH 1_555 90.9 A HOH 112 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 115 E O HOH 1_555 171.6 A HOH 113 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 115 E O HOH 1_555 85.3 A HOH 114 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 115 E O HOH 1_555 85.0 A HOH 111 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 116 E O HOH 1_555 93.6 A HOH 112 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 116 E O HOH 1_555 91.1 A HOH 113 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 116 E O HOH 1_555 170.7 A HOH 114 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 116 E O HOH 1_555 83.5 A HOH 115 E O HOH 1_555 A MG 26 D MG MG 1_555 A HOH 116 E O HOH 1_555 96.0 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 -4.54 0.70 108.00 103.46 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 8.87 1.20 119.70 128.57 A A A C3' O3' P DG DG DC 2 2 3 Y 1 -11.22 1.60 120.90 109.68 A A A P O5' C5' DC DC DC 3 3 3 N 1 -6.00 0.80 105.90 99.90 A A A O4' C1' C2' DC DC DC 3 3 3 N 1 4.96 0.30 108.30 113.26 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 -3.48 0.40 104.50 101.02 A A A O4' C4' C3' DA DA DA 6 6 6 N 1 6.59 0.70 110.30 116.89 A A A C1' O4' C4' DA DA DA 6 6 6 N 1 -6.03 0.80 105.90 99.87 A A A O4' C1' C2' DA DA DA 6 6 6 N 1 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 -13.10 0.60 118.60 105.50 A A A C6 N1 C2 DA DA DA 6 6 6 N 1 7.42 0.50 129.30 136.72 A A A N1 C2 N3 DA DA DA 6 6 6 N 1 -4.87 0.70 126.80 121.93 A A A N3 C4 C5 DA DA DA 6 6 6 N 1 6.76 0.50 117.70 124.46 A A A C5 C6 N1 DA DA DA 6 6 6 N 1 3.51 0.50 103.90 107.41 A A A C5 N7 C8 DA DA DA 6 6 6 N 1 2.40 0.40 105.80 108.20 A A A N9 C4 C5 DA DA DA 6 6 6 N 1 -6.34 0.80 123.70 117.36 A A A C5 C6 N6 DA DA DA 6 6 6 N 1 9.65 1.20 119.70 129.35 A A A C3' O3' P DA DA DT 6 6 7 Y 1 -3.46 0.40 104.50 101.04 A A A O4' C4' C3' DT DT DT 7 7 7 N 1 5.23 0.30 108.30 113.53 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 -3.25 0.50 121.30 118.05 A A A C6 N1 C2 DT DT DT 7 7 7 N 1 -5.71 0.60 115.20 109.49 A A A N3 C4 C5 DT DT DT 7 7 7 N 1 6.03 0.60 118.00 124.03 A A A C4 C5 C6 DT DT DT 7 7 7 N 1 -6.57 0.60 122.30 115.73 A A A N3 C2 O2 DT DT DT 7 7 7 N 1 -6.15 0.60 122.90 116.75 A A A C6 C5 C7 DT DT DT 7 7 7 N 1 -2.66 0.40 104.50 101.84 A A A O4' C4' C3' DT DT DT 8 8 8 N 1 3.81 0.60 114.60 118.41 A A A N1 C2 N3 DT DT DT 8 8 8 N 1 4.77 0.60 118.00 122.77 A A A C4 C5 C6 DT DT DT 8 8 8 N 1 -4.16 0.60 122.30 118.14 A A A N3 C2 O2 DT DT DT 8 8 8 N 1 -6.93 0.70 108.00 101.07 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -2.94 0.40 104.50 101.56 A A A O4' C4' C3' DG DG DG 12 12 12 N 1 7.86 1.20 119.70 127.56 B B B C3' O3' P DC DC DG 13 13 14 Y 1 -3.16 0.40 104.50 101.34 B B B O4' C4' C3' DC DC DC 15 15 15 N 1 -5.05 0.80 105.90 100.85 B B B O4' C1' C2' DC DC DC 15 15 15 N 1 2.58 0.30 108.30 110.88 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 4.12 0.50 119.90 124.02 B B B C2 N3 C4 DC DC DC 15 15 15 N 1 -3.48 0.40 121.90 118.42 B B B N3 C4 C5 DC DC DC 15 15 15 N 1 11.47 1.20 119.70 131.17 B B B C3' O3' P DA DA DA 17 17 18 Y 1 8.24 0.70 110.30 118.54 B B B C1' O4' C4' DA DA DA 18 18 18 N 1 -10.70 0.80 105.90 95.20 B B B O4' C1' C2' DA DA DA 18 18 18 N 1 14.36 0.60 118.60 132.96 B B B C6 N1 C2 DA DA DA 18 18 18 N 1 -8.36 0.50 129.30 120.94 B B B N1 C2 N3 DA DA DA 18 18 18 N 1 6.27 0.50 110.60 116.87 B B B C2 N3 C4 DA DA DA 18 18 18 N 1 -5.39 0.70 126.80 121.41 B B B N3 C4 C5 DA DA DA 18 18 18 N 1 -5.28 0.50 117.00 111.72 B B B C4 C5 C6 DA DA DA 18 18 18 N 1 -5.47 0.40 105.80 100.33 B B B N9 C4 C5 DA DA DA 18 18 18 N 1 10.84 0.80 127.40 138.24 B B B N3 C4 N9 DA DA DA 18 18 18 N 1 -11.70 0.60 118.60 106.90 B B B N1 C6 N6 DA DA DA 18 18 18 N 1 13.33 0.80 123.70 137.03 B B B C5 C6 N6 DA DA DA 18 18 18 N 1 -12.64 1.60 120.90 108.26 B B B P O5' C5' DT DT DT 19 19 19 N 1 2.63 0.30 108.30 110.93 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 -4.55 0.60 115.20 110.65 B B B N3 C4 C5 DT DT DT 19 19 19 N 1 4.15 0.60 118.00 122.15 B B B C4 C5 C6 DT DT DT 19 19 19 N 1 -4.24 0.40 104.50 100.26 B B B O4' C4' C3' DT DT DT 20 20 20 N 1 -5.08 0.70 108.00 102.92 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 -9.71 1.60 120.90 111.19 B B B P O5' C5' DC DC DC 21 21 21 N 1 -5.37 0.70 108.00 102.63 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 3.61 0.60 118.90 122.51 B B B N1 C2 O2 DC DC DC 21 21 21 N 1 2.91 0.30 108.30 111.21 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 3.66 0.30 108.30 111.96 B B B O4' C1' N1 DC DC DC 23 23 23 N 1 -11.67 1.90 112.60 100.93 B B B N9 C1' C2' DG DG DG 24 24 24 N 1 8.01 0.30 108.30 116.31 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 3.55 0.50 113.10 116.65 B B B N7 C8 N9 DG DG DG 24 24 24 N 1 -3.10 0.40 106.40 103.30 B B B C8 N9 C4 DG DG DG 24 24 24 N 1 -5.08 0.70 119.90 114.82 B B B N3 C2 N2 DG DG DG 24 24 24 N 1 3.73 0.60 119.90 123.63 B B B N1 C6 O6 DG DG DG 24 24 24 N 1 A A C3' C2' DC DC 3 3 -0.052 0.008 1.516 1.464 N 1 A A C5 N7 DG DG 4 4 -0.041 0.006 1.388 1.347 N 1 A A C6 N1 DA DA 6 6 0.063 0.007 1.351 1.414 N 1 A A N9 C4 DA DA 6 6 0.042 0.006 1.374 1.416 N 1 A A C5 N7 DG DG 10 10 -0.037 0.006 1.388 1.351 N 1 B B N1 C2 DA DA 18 18 -0.114 0.009 1.339 1.225 N 1 B B C2 N3 DA DA 18 18 -0.157 0.009 1.331 1.174 N 1 B B N3 C4 DA DA 18 18 0.126 0.006 1.344 1.470 N 1 B B C6 N1 DA DA 18 18 -0.076 0.007 1.351 1.275 N 1 B B C5 N7 DA DA 18 18 -0.040 0.006 1.388 1.348 N 1 B B N9 C4 DA DA 18 18 0.099 0.006 1.374 1.473 N 1 B B C5 N7 DG DG 22 22 -0.043 0.006 1.388 1.345 N 1 B B C5 N7 DG DG 24 24 -0.043 0.006 1.388 1.345 N 0.1970000 0.1970000 2.000 8.000 4016 1 2.000 2.000 8.000 84 607 37 486 0 0.020 4.30 109D 1 87.000 refinement X-PLOR VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N metalc 2.179 A MG 26 D MG MG 1_555 A HOH 111 E O HOH 1_555 metalc 2.192 A MG 26 D MG MG 1_555 A HOH 112 E O HOH 1_555 metalc 2.200 A MG 26 D MG MG 1_555 A HOH 113 E O HOH 1_555 metalc 2.305 A MG 26 D MG MG 1_555 A HOH 114 E O HOH 1_555 metalc 2.206 A MG 26 D MG MG 1_555 A HOH 115 E O HOH 1_555 metalc 2.251 A MG 26 D MG MG 1_555 A HOH 116 E O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 21 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog DA-DA MISPAIR A DA 6 A N6 DA 6 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA 109D PDB 1 109D 1 12 109D 1 12 109D A 1 1 12 13 24 109D 13 24 109D B 1 1 12 BINDING SITE FOR RESIDUE IBB A 25 A IBB 25 Software 12 BINDING SITE FOR RESIDUE MG A 26 A MG 26 Software 6 A DA 5 A DA 5 12 1_555 A DA 6 A DA 6 12 1_555 A DT 7 A DT 7 12 1_555 A DT 8 A DT 8 12 1_555 A DC 9 A DC 9 12 1_555 A HOH 40 E HOH 12 1_555 A HOH 62 E HOH 12 1_555 A HOH 66 E HOH 12 1_555 B DA 18 B DA 6 12 1_555 B DT 19 B DT 7 12 1_555 B DT 20 B DT 8 12 1_555 B DC 21 B DC 9 12 1_555 A HOH 111 E HOH 6 1_555 A HOH 112 E HOH 6 1_555 A HOH 113 E HOH 6 1_555 A HOH 114 E HOH 6 1_555 A HOH 115 E HOH 6 1_555 A HOH 116 E HOH 6 1_555 19 P 21 21 21