0.041497 0.000000 0.000000 0.000000 0.025112 0.000000 0.000000 0.000000 0.015239 0.00000 0.00000 0.00000 Nguyen, B. Lee, M.P.H. Hamelberg, D. Joubert, A. Bailly, C. Brun, R. Neidle, S. Wilson, W.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 24.098 39.821 65.620 C17 H22 N9 3 352.417 3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM CGP40215A; BIS[[3-(AMINOIMINOMETHYL)PHENYL]METHYLENE] CARBONIMIDIC DIHYDRAZIDE non-polymer 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 Mg 2 24.305 MAGNESIUM ION non-polymer Y 1 N C Y 2 N C Y 3 N C Y 4 N C Y 5 N C Y 6 N C N 7 N C N 8 N N N 9 N C N 10 N N N 11 N N N 12 N N N 13 N C N 14 N N N 15 N N N 16 N N N 17 N C Y 18 N C Y 19 N C Y 20 N C Y 21 N C Y 22 N C Y 23 N C N 24 N C N 25 N N N 26 N N 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 H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N O N 50 N P N 51 N O N 52 N O N 53 N O N 54 N C N 55 R C N 56 N O N 57 S C N 58 N O N 59 N C N 60 R C Y 61 N N Y 62 N C Y 63 N N Y 64 N C Y 65 N C N 66 N N Y 67 N N Y 68 N C Y 69 N N Y 70 N C N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N O N 86 N P N 87 N O N 88 N O N 89 N O N 90 N C N 91 R C N 92 N O N 93 S C N 94 N O N 95 N C N 96 R C N 97 N N N 98 N C N 99 N O N 100 N N N 101 N C N 102 N N N 103 N C N 104 N C N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N O N 120 N P N 121 N O N 122 N O N 123 N O N 124 N C N 125 R C N 126 N O N 127 S C N 128 N O N 129 N C N 130 R C Y 131 N N Y 132 N C Y 133 N N Y 134 N C N 135 N C N 136 N O N 137 N N N 138 N C N 139 N N N 140 N N Y 141 N C N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N O N 157 N P N 158 N O N 159 N O N 160 N O N 161 N C N 162 R C N 163 N O N 164 S C N 165 N O N 166 N C N 167 R C N 168 N N N 169 N C N 170 N O N 171 N N N 172 N C N 173 N O N 174 N C N 175 N C N 176 N C 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 O N 193 N H N 194 N H N 195 N MG Y 1 N doub Y 2 N sing N 3 N sing Y 4 N sing N 5 N sing Y 6 N doub N 7 N sing Y 8 N sing N 9 N sing Y 10 N doub N 11 N sing N 12 N sing N 13 E doub N 14 N sing N 15 N sing N 16 N doub 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 N 24 N sing N 25 E doub N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub N 31 N sing N 32 N sing Y 33 N doub Y 34 N sing Y 35 N sing N 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing Y 41 N doub N 42 N sing N 43 N sing N 44 N doub 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 doub 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 sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing Y 73 N sing Y 74 N sing Y 75 N doub N 76 N sing Y 77 N sing Y 78 N sing Y 79 N doub N 80 N sing Y 81 N doub N 82 N sing N 83 N sing Y 84 N sing Y 85 N doub N 86 N sing Y 87 N sing N 88 N sing N 89 N sing N 90 N doub N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing 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 doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N doub 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 sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing Y 146 N sing Y 147 N sing Y 148 N doub N 149 N sing Y 150 N sing N 151 N sing Y 152 N doub N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N doub 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 sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N doub N 192 N sing N 193 N sing N 194 N doub N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing US J.Am.Chem.Soc. JACSAT 0004 0002-7863 124 13680 13681 10.1021/ja027953c 12431090 Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove 2002 10.2210/pdb1m6f/pdb pdb_00001m6f 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 104 1 Yale Focussing Mirrors IMAGE PLATE 2002-06-27 RIGAKU RAXIS IV SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 3663.392 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 352.417 3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM 1 syn non-polymer 18.015 water 117 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 1 2.06 40.25 VAPOR DIFFUSION, HANGING DROP 6.5 MGCL2 2UL OF 75MM, DNA DOUBLE-STRANDED 3UL OF 2MM, MPD 2UL OF 25%, DRUG 2UL OF 4.5MM, SODIUM CACODYLATE 40MM. MPD IN RESERVOIR 700UL OF 50%., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K 285 MGCL2 1 DNA 1 MPD 1 DRUG 1 MPD 2 3.244 1 19 A 1001 B 2024 1.610 A_DC1001:DG2024_B 1 -21.070 0.289 0.021 -0.123 -2.095 1 19 A 1002 B 2023 -3.862 A_DG1002:DC2023_B 2 -3.969 -0.076 0.050 -0.124 -2.376 1 19 A 1003 B 2022 0.609 A_DC1003:DG2022_B 3 -4.947 0.179 0.245 -0.158 10.292 1 19 A 1004 B 2021 -2.845 A_DG1004:DC2021_B 4 -8.114 -0.365 -0.043 -0.177 3.942 1 20 A 1005 B 2020 4.985 A_DA1005:DT2020_B 5 -20.661 0.189 -0.443 -0.195 0.562 1 20 A 1006 B 2019 6.953 A_DA1006:DT2019_B 6 -13.458 0.183 -0.027 -0.189 0.724 1 20 A 1007 B 2018 10.298 A_DT1007:DA2018_B 7 -14.353 -0.136 0.007 -0.182 -2.084 1 20 A 1008 B 2017 5.279 A_DT1008:DA2017_B 8 -18.398 -0.109 -0.304 -0.233 -8.031 1 19 A 1009 B 2016 0.197 A_DC1009:DG2016_B 9 -8.661 0.053 -0.059 -0.177 7.225 1 19 A 1010 B 2015 -1.245 A_DG1010:DC2015_B 10 -8.021 -0.068 0.266 -0.242 7.457 1 19 A 1011 B 2014 -3.478 A_DC1011:DG2014_B 11 -25.121 0.195 0.371 -0.174 9.995 1 19 A 1012 B 2013 -2.811 A_DG1012:DC2013_B 12 25.409 -0.428 -0.316 -0.226 3.446 33.167 A A 1001 1002 11.486 B B 2024 2023 3.488 6.516 -0.380 0.116 AA_DC1001DG1002:DC2023DG2024_BB 1 -0.017 0.030 32.538 -0.969 0.662 3.250 42.693 A A 1002 1003 -2.433 B B 2023 2022 3.274 -1.771 0.900 0.596 AA_DG1002DC1003:DG2022DC2023_BB 2 0.095 -0.130 42.658 0.996 -1.227 3.127 27.007 A A 1003 1004 19.558 B B 2022 2021 3.220 8.925 -0.422 0.603 AA_DC1003DG1004:DC2021DG2022_BB 3 4.463 -9.780 25.127 -0.996 2.048 3.447 40.468 A A 1004 1005 7.575 B B 2021 2020 3.459 5.221 0.044 0.173 AA_DG1004DA1005:DT2020DC2021_BB 4 3.321 -4.819 40.012 -0.371 0.331 3.104 36.242 A A 1005 1006 9.199 B B 2020 2019 3.219 5.691 0.277 -0.230 AA_DA1005DA1006:DT2019DT2020_BB 5 -3.640 5.884 35.628 -1.149 -0.944 3.208 28.292 A A 1006 1007 -1.658 B B 2019 2018 3.197 -0.810 0.083 -0.467 AA_DA1006DT1007:DA2018DT2019_BB 6 -0.323 0.661 28.279 -0.771 -0.242 3.172 37.615 A A 1007 1008 1.603 B B 2018 2017 3.217 1.033 -0.428 -0.028 AA_DT1007DT1008:DA2017DA2018_BB 7 3.088 -4.795 37.479 -0.174 1.057 3.408 41.807 A A 1008 1009 -1.146 B B 2017 2016 3.413 -0.818 -0.022 0.221 AA_DT1008DC1009:DG2016DA2017_BB 8 0.409 -0.573 41.797 0.399 0.075 3.325 28.248 A A 1009 1010 18.998 B B 2016 2015 3.211 9.095 0.369 1.063 AA_DC1009DG1010:DC2015DG2016_BB 9 -3.003 6.272 26.606 -0.002 -1.476 3.060 47.046 A A 1010 1011 -17.290 B B 2015 2014 3.310 -13.595 -1.028 0.790 AA_DG1010DC1011:DG2014DC2015_BB 10 -5.556 7.066 44.819 2.108 0.830 3.338 35.126 A A 1011 1012 -21.083 B B 2014 2013 3.574 -12.408 1.450 0.583 AA_DC1011DG1012:DC2013DG2014_BB 11 5.717 -9.715 32.438 3.010 -1.460 software chem_comp chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Derived calculations Structure summary Refinement description 1 0 2002-11-15 1 1 2008-04-28 1 2 2011-07-13 1 3 2017-10-11 1 4 2024-02-14 1 5 2024-04-03 _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2002-07-16 REL REL MG MAGNESIUM ION CGQ 3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM HOH water 2DBE DNA PART OF NDB ENTRY GDL009 PDB experimental model MO6 4026 2 MG MG 4026 A CGQ 3025 3 CGQ CGQ 3025 B HOH 8002 4 HOH HOH 8002 A HOH 8004 4 HOH HOH 8004 A HOH 8009 4 HOH HOH 8009 A HOH 8010 4 HOH HOH 8010 A HOH 8011 4 HOH HOH 8011 A HOH 8013 4 HOH HOH 8013 A HOH 8014 4 HOH HOH 8014 A HOH 8016 4 HOH HOH 8016 A HOH 8018 4 HOH HOH 8018 A HOH 8019 4 HOH HOH 8019 A HOH 8020 4 HOH HOH 8020 A HOH 8021 4 HOH HOH 8021 A HOH 8022 4 HOH HOH 8022 A HOH 8025 4 HOH HOH 8025 A HOH 8028 4 HOH HOH 8028 A HOH 8031 4 HOH HOH 8031 A HOH 8032 4 HOH HOH 8032 A HOH 8034 4 HOH HOH 8034 A HOH 8035 4 HOH HOH 8035 A HOH 8036 4 HOH HOH 8036 A HOH 8037 4 HOH HOH 8037 A HOH 8038 4 HOH HOH 8038 A HOH 8039 4 HOH HOH 8039 A HOH 8040 4 HOH HOH 8040 A HOH 8041 4 HOH HOH 8041 A HOH 8044 4 HOH HOH 8044 A HOH 8051 4 HOH HOH 8051 A HOH 8054 4 HOH HOH 8054 A HOH 8056 4 HOH HOH 8056 A HOH 8057 4 HOH HOH 8057 A HOH 8058 4 HOH HOH 8058 A HOH 8059 4 HOH HOH 8059 A HOH 8060 4 HOH HOH 8060 A HOH 8065 4 HOH HOH 8065 A HOH 8067 4 HOH HOH 8067 A HOH 8068 4 HOH HOH 8068 A HOH 8071 4 HOH HOH 8071 A HOH 8075 4 HOH HOH 8075 A HOH 8078 4 HOH HOH 8078 A HOH 8084 4 HOH HOH 8084 A HOH 8085 4 HOH HOH 8085 A HOH 8086 4 HOH HOH 8086 A HOH 8087 4 HOH HOH 8087 A HOH 8088 4 HOH HOH 8088 A HOH 8090 4 HOH HOH 8090 A HOH 8091 4 HOH HOH 8091 A HOH 8094 4 HOH HOH 8094 A HOH 8095 4 HOH HOH 8095 A HOH 8096 4 HOH HOH 8096 A HOH 8097 4 HOH HOH 8097 A HOH 8100 4 HOH HOH 8100 A HOH 8101 4 HOH HOH 8101 A HOH 8102 4 HOH HOH 8102 A HOH 8105 4 HOH HOH 8105 A HOH 8109 4 HOH HOH 8109 A HOH 8110 4 HOH HOH 8110 A HOH 8111 4 HOH HOH 8111 A MO6 4026 4 HOH HOH 8113 A MO6 4026 4 HOH HOH 8114 A MO6 4026 4 HOH HOH 8115 A MO6 4026 4 HOH HOH 8116 A MO6 4026 4 HOH HOH 8117 A HOH 8001 4 HOH HOH 8001 B HOH 8003 4 HOH HOH 8003 B HOH 8005 4 HOH HOH 8005 B HOH 8006 4 HOH HOH 8006 B HOH 8007 4 HOH HOH 8007 B HOH 8008 4 HOH HOH 8008 B HOH 8012 4 HOH HOH 8012 B HOH 8015 4 HOH HOH 8015 B HOH 8017 4 HOH HOH 8017 B HOH 8023 4 HOH HOH 8023 B HOH 8024 4 HOH HOH 8024 B HOH 8026 4 HOH HOH 8026 B HOH 8027 4 HOH HOH 8027 B HOH 8029 4 HOH HOH 8029 B HOH 8030 4 HOH HOH 8030 B HOH 8033 4 HOH HOH 8033 B HOH 8042 4 HOH HOH 8042 B HOH 8043 4 HOH HOH 8043 B HOH 8045 4 HOH HOH 8045 B HOH 8046 4 HOH HOH 8046 B HOH 8047 4 HOH HOH 8047 B HOH 8048 4 HOH HOH 8048 B HOH 8049 4 HOH HOH 8049 B HOH 8050 4 HOH HOH 8050 B HOH 8052 4 HOH HOH 8052 B HOH 8053 4 HOH HOH 8053 B HOH 8055 4 HOH HOH 8055 B HOH 8061 4 HOH HOH 8061 B HOH 8062 4 HOH HOH 8062 B HOH 8063 4 HOH HOH 8063 B HOH 8064 4 HOH HOH 8064 B HOH 8066 4 HOH HOH 8066 B HOH 8069 4 HOH HOH 8069 B HOH 8070 4 HOH HOH 8070 B HOH 8072 4 HOH HOH 8072 B HOH 8073 4 HOH HOH 8073 B HOH 8074 4 HOH HOH 8074 B HOH 8076 4 HOH HOH 8076 B HOH 8077 4 HOH HOH 8077 B HOH 8079 4 HOH HOH 8079 B HOH 8080 4 HOH HOH 8080 B HOH 8081 4 HOH HOH 8081 B HOH 8082 4 HOH HOH 8082 B HOH 8083 4 HOH HOH 8083 B HOH 8089 4 HOH HOH 8089 B HOH 8092 4 HOH HOH 8092 B HOH 8093 4 HOH HOH 8093 B HOH 8098 4 HOH HOH 8098 B HOH 8099 4 HOH HOH 8099 B HOH 8103 4 HOH HOH 8103 B HOH 8104 4 HOH HOH 8104 B HOH 8106 4 HOH HOH 8106 B HOH 8107 4 HOH HOH 8107 B HOH 8108 4 HOH HOH 8108 B MO6 4026 4 HOH HOH 8112 B C 1001 n 1 DC 1001 A G 1002 n 2 DG 1002 A C 1003 n 3 DC 1003 A G 1004 n 4 DG 1004 A A 1005 n 5 DA 1005 A A 1006 n 6 DA 1006 A T 1007 n 7 DT 1007 A T 1008 n 8 DT 1008 A C 1009 n 9 DC 1009 A G 1010 n 10 DG 1010 A C 1011 n 11 DC 1011 A G 1012 n 12 DG 1012 A C 2013 n 1 DC 2013 B G 2014 n 2 DG 2014 B C 2015 n 3 DC 2015 B G 2016 n 4 DG 2016 B A 2017 n 5 DA 2017 B A 2018 n 6 DA 2018 B T 2019 n 7 DT 2019 B T 2020 n 8 DT 2020 B C 2021 n 9 DC 2021 B G 2022 n 10 DG 2022 B C 2023 n 11 DC 2023 B G 2024 n 12 DG 2024 B 0.202 0.205 0.199 0.202 0.271 0.277 289 5477 5636 author_defined_assembly 2 dimeric A HOH 8113 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8114 E O HOH 1_555 88.7 A HOH 8113 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8115 E O HOH 1_555 176.6 A HOH 8114 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8115 E O HOH 1_555 88.7 A HOH 8113 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8116 E O HOH 1_555 90.6 A HOH 8114 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8116 E O HOH 1_555 90.5 A HOH 8115 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8116 E O HOH 1_555 91.5 A HOH 8113 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8117 E O HOH 1_555 90.9 A HOH 8114 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8117 E O HOH 1_555 91.4 A HOH 8115 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8117 E O HOH 1_555 87.1 A HOH 8116 E O HOH 1_555 A MG 4026 C MG MG 1_555 A HOH 8117 E O HOH 1_555 177.6 A HOH 8113 E O HOH 1_555 A MG 4026 C MG MG 1_555 B HOH 8112 F O HOH 1_555 91.0 A HOH 8114 E O HOH 1_555 A MG 4026 C MG MG 1_555 B HOH 8112 F O HOH 1_555 179.6 A HOH 8115 E O HOH 1_555 A MG 4026 C MG MG 1_555 B HOH 8112 F O HOH 1_555 91.7 A HOH 8116 E O HOH 1_555 A MG 4026 C MG MG 1_555 B HOH 8112 F O HOH 1_555 89.6 A HOH 8117 E O HOH 1_555 A MG 4026 C MG MG 1_555 B HOH 8112 F O HOH 1_555 88.5 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 -6.86 0.70 108.00 101.14 A A A O4' C1' N1 DC DC DC 1001 1001 1001 N 1 7.26 1.20 119.70 126.96 A A A C3' O3' P DG DG DC 1002 1002 1003 Y 1 -5.39 0.70 108.00 102.61 A A A O4' C1' N1 DC DC DC 1003 1003 1003 N 1 -7.94 0.70 108.00 100.06 A A A O4' C1' N9 DA DA DA 1005 1005 1005 N 1 -8.48 0.70 108.00 99.52 A A A O4' C1' N9 DA DA DA 1006 1006 1006 N 1 9.66 1.40 114.30 123.96 A A A N1 C1' C2' DT DT DT 1007 1007 1007 N 1 -9.27 0.70 108.00 98.73 A A A O4' C1' N1 DT DT DT 1007 1007 1007 N 1 8.85 1.40 114.30 123.15 A A A N1 C1' C2' DT DT DT 1008 1008 1008 N 1 -8.04 0.70 108.00 99.96 A A A O4' C1' N1 DT DT DT 1008 1008 1008 N 1 -6.03 0.70 108.00 101.97 A A A O4' C1' N1 DC DC DC 1009 1009 1009 N 1 -8.99 0.70 108.00 99.01 A A A O4' C1' N1 DC DC DC 1011 1011 1011 N 1 -7.18 0.70 108.00 100.82 B B B O4' C1' N1 DC DC DC 2015 2015 2015 N 1 -4.64 0.70 108.00 103.36 B B B O4' C1' N9 DG DG DG 2016 2016 2016 N 1 -11.21 0.70 108.00 96.79 B B B O4' C1' N9 DA DA DA 2017 2017 2017 N 1 9.35 1.40 114.30 123.65 B B B N9 C1' C2' DA DA DA 2018 2018 2018 N 1 -12.08 0.70 108.00 95.92 B B B O4' C1' N9 DA DA DA 2018 2018 2018 N 1 -4.77 0.70 108.00 103.23 B B B O4' C1' N1 DT DT DT 2019 2019 2019 N 1 9.58 1.40 114.30 123.88 B B B N1 C1' C2' DT DT DT 2020 2020 2020 N 1 -9.64 0.70 108.00 98.36 B B B O4' C1' N1 DT DT DT 2020 2020 2020 N 1 4.01 0.60 119.90 123.91 B B B N3 C4 O4 DT DT DT 2020 2020 2020 N 1 8.54 1.40 114.30 122.84 B B B N1 C1' C2' DC DC DC 2021 2021 2021 N 1 -11.35 0.70 108.00 96.65 B B B O4' C1' N1 DC DC DC 2021 2021 2021 N 1 -4.81 0.80 102.40 97.59 B B B C3' C2' C1' DG DG DG 2022 2022 2022 N 1 -4.30 0.70 108.00 103.70 B B B O4' C1' N9 DG DG DG 2024 2024 2024 N 0.277 0.202 0.205 1.78 10.00 298 5636 5477 RANDOM 1 THROUGHOUT 4 2 MOLECULAR REPLACEMENT DNA PART OF NDB ENTRY GDL009 Engh & Huber 1.78 10.00 111 639 42 486 0 0.008 0.020 0.019 0.006 0.010 1.78 17.00 1M6F 6040 1 1 0.047 1 8.8 92.8 0.184 1.78 1.84 90.6 90.6 data scaling SCALEPACK model building X-PLOR refinement SHELXL-97 phasing X-PLOR Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N metalc 2.011 A MG 4026 C MG MG 1_555 A HOH 8113 E O HOH 1_555 metalc 2.031 A MG 4026 C MG MG 1_555 A HOH 8114 E O HOH 1_555 metalc 2.019 A MG 4026 C MG MG 1_555 A HOH 8115 E O HOH 1_555 metalc 2.023 A MG 4026 C MG MG 1_555 A HOH 8116 E O HOH 1_555 metalc 2.024 A MG 4026 C MG MG 1_555 A HOH 8117 E O HOH 1_555 metalc 2.019 A MG 4026 C MG MG 1_555 B HOH 8112 F O HOH 1_555 hydrog WATSON-CRICK A DC 1001 A N3 DC 1 1_555 B DG 2024 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1001 A N4 DC 1 1_555 B DG 2024 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1001 A O2 DC 1 1_555 B DG 2024 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 1002 A N1 DG 2 1_555 B DC 2023 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 1002 A N2 DG 2 1_555 B DC 2023 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 1002 A O6 DG 2 1_555 B DC 2023 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 1003 A N3 DC 3 1_555 B DG 2022 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 1003 A N4 DC 3 1_555 B DG 2022 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 1003 A O2 DC 3 1_555 B DG 2022 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 1004 A N1 DG 4 1_555 B DC 2021 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 1004 A N2 DG 4 1_555 B DC 2021 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 1004 A O6 DG 4 1_555 B DC 2021 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 1005 A N1 DA 5 1_555 B DT 2020 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 1005 A N6 DA 5 1_555 B DT 2020 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 1006 A N1 DA 6 1_555 B DT 2019 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 1006 A N6 DA 6 1_555 B DT 2019 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 1007 A N3 DT 7 1_555 B DA 2018 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 1007 A O4 DT 7 1_555 B DA 2018 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 1008 A N3 DT 8 1_555 B DA 2017 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 1008 A O4 DT 8 1_555 B DA 2017 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 1009 A N3 DC 9 1_555 B DG 2016 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 1009 A N4 DC 9 1_555 B DG 2016 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 1009 A O2 DC 9 1_555 B DG 2016 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 1010 A N1 DG 10 1_555 B DC 2015 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 1010 A N2 DG 10 1_555 B DC 2015 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 1010 A O6 DG 10 1_555 B DC 2015 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 1011 A N3 DC 11 1_555 B DG 2014 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 1011 A N4 DC 11 1_555 B DG 2014 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 1011 A O2 DC 11 1_555 B DG 2014 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 1012 A N1 DG 12 1_555 B DC 2013 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 1012 A N2 DG 12 1_555 B DC 2013 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 1012 A O6 DG 12 1_555 B DC 2013 B N4 DC 1 1_555 DNA Nucleic acids, minor groove binder, double helix, DNA-drug complex, DNA 1M6F PDB 1 1M6F 1001 1012 1M6F 1001 1012 1M6F A 1 1 12 2013 2024 1M6F 2013 2024 1M6F B 1 1 12 BINDING SITE FOR RESIDUE CGQ B 3025 B CGQ 3025 Software 14 BINDING SITE FOR RESIDUE MG A 4026 A MG 4026 Software 6 A DG 1004 A DG 4 14 1_455 A DA 1006 A DA 6 14 1_555 A DT 1007 A DT 7 14 1_555 A DT 1008 A DT 8 14 1_555 A DC 1009 A DC 9 14 1_555 B DA 2018 B DA 6 14 1_555 B DT 2019 B DT 7 14 1_555 B DT 2020 B DT 8 14 1_555 B DC 2021 B DC 9 14 1_555 B HOH 8017 F HOH 14 1_555 B HOH 8030 F HOH 14 1_555 B HOH 8033 F HOH 14 1_555 B HOH 8045 F HOH 14 1_555 B HOH 8099 F HOH 14 1_555 A HOH 8113 E HOH 6 1_555 A HOH 8114 E HOH 6 1_555 A HOH 8115 E HOH 6 1_555 A HOH 8116 E HOH 6 1_555 A HOH 8117 E HOH 6 1_555 B HOH 8112 F HOH 6 1_555 19 P 21 21 21