0.030066 0.000000 0.020456 0.000000 0.039920 0.000000 0.000000 0.000000 0.042739 0.00000 0.00000 0.00000 Deng, J. Pan, B. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 124.23 90.00 33.260 25.050 28.300 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 H13 N4 O7 P 332.207 y 2'-DEOXYINOSINE-5'-MONOPHOSPHATE DNA linking C22 H27 N9 O4 481.508 DISTAMYCIN A DISTAMYCIN; STALLIMYCIN non-polymer C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER 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 Y 92 N C 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 C N 107 N O N 108 N N Y 109 N C Y 110 N C Y 111 N C Y 112 N N Y 113 N C N 114 N C N 115 N C N 116 N O N 117 N N Y 118 N C Y 119 N C Y 120 N C Y 121 N N Y 122 N C N 123 N C N 124 N C N 125 N O N 126 N N Y 127 N C Y 128 N C Y 129 N C Y 130 N N Y 131 N C N 132 N C N 133 N C N 134 N O N 135 N N N 136 N C N 137 N C N 138 N C N 139 N N N 140 N N N 141 N H 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 H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N O N 169 N P N 170 N O N 171 N O N 172 N O N 173 N C N 174 R C N 175 N O N 176 S C N 177 N O N 178 N C N 179 R C N 180 N N N 181 N C N 182 N O N 183 N N N 184 N C N 185 N O N 186 N C N 187 N C N 188 N C 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 H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N O N 205 N H N 206 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 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 doub N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing N 114 N sing N 115 N sing Y 116 N sing Y 117 N doub Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing Y 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 doub N 129 N sing N 130 N sing N 131 N sing Y 132 N sing Y 133 N doub Y 134 N doub N 135 N sing Y 136 N sing N 137 N sing Y 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 doub N 145 N sing N 146 N sing N 147 N sing Y 148 N sing Y 149 N doub Y 150 N doub N 151 N sing Y 152 N sing N 153 N sing Y 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 doub 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 doub 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 doub 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 sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N doub N 205 N sing N 206 N sing N 207 N doub N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 59 2342 2344 10.1107/S0907444903020730 14646114 Structure of d(ITITACAC) complexed with distamycin at 1.6 A resolution. 2003 10.2210/pdb1jux/pdb pdb_00001jux 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298 1 IMAGE PLATE 1997-06-20 RIGAKU RAXIS IIC graphite SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 Octamer DNA 2396.589 5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3' 1 syn polymer 481.508 DISTAMYCIN A 1 syn non-polymer 18.015 water 36 nat water no no (DI)(DT)(DI)(DT)(DA)(DC)(DA)(DC) ITITACAC A polydeoxyribonucleotide n n n n n n n n 1 1.96 37.09 2.540 1 20 A 2 A 7 4.810 A_DT2:DA7_A 1 -5.610 0.065 -0.039 -0.144 1.901 1 20 A 4 A 5 -3.163 A_DT4:DA5_A 2 -14.770 0.047 0.048 -0.127 -1.902 1 20 A 5 A 4 -3.163 A_DA5:DT4_A 3 -14.770 -0.047 0.048 -0.127 -2.540 1 20 A 7 A 2 4.810 A_DA7:DT2_A 4 -5.610 -0.065 -0.039 -0.144 6.963 69.697 A A 2 4 11.133 A A 7 5 6.730 12.663 -1.846 1.458 AA_DT2DT4:DA5DA7_AA 1 -4.109 3.612 68.572 0.314 1.303 2.685 49.735 A A 4 5 -12.310 A A 5 4 3.362 -10.287 0.000 3.154 AA_DT4DA5:DT4DA5_AA 2 0.000 0.000 48.726 4.455 0.000 6.963 69.697 A A 5 7 11.133 A A 4 2 6.730 12.663 1.846 1.458 AA_DA5DA7:DT2DT4_AA 3 4.109 -3.612 68.572 0.314 -1.303 software chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Derived calculations 1 0 2004-01-27 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id DNA octamer d(IUATATAC) and Distamycin RCSB Y RCSB 2001-08-28 REL REL DMY DISTAMYCIN A HOH water DMA 45 2 DMY DMY 45 A HOH 9 3 HOH HOH 9 A HOH 10 3 HOH HOH 10 A HOH 11 3 HOH HOH 11 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 16 3 HOH HOH 16 A HOH 17 3 HOH HOH 17 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 A INO 1 n 1 DI 1 A THY 2 n 2 DT 2 A INO 3 n 3 DI 3 A THY 4 n 4 DT 4 A ADE 5 n 5 DA 5 A CYT 6 n 6 DC 6 A ADE 7 n 7 DA 7 A CYT 8 n 8 DC 8 A 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A DI 3 0.064 SIDE CHAIN 1 A DA 5 0.068 SIDE CHAIN 0.179 0.149 1.6 10 234 2609 2468 94.6 random 1 2 MOLECULAR REPLACEMENT 1.6 10 36 230 35 159 0 1.60 10.00 1JUX 2609 2468 2.000 1 phasing AMoRE refinement CNS 1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC) and d(ITITACAC):Binding of Two Distamycin Drugs Side-by-Side 1 N N 2 N N 3 N N One strand in the assymetric unit. The duplex is generated by the 2 fold axis. hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 A DA 7 A N1 DA 7 2_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 A DA 7 A N6 DA 7 2_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 5 A N1 DA 5 2_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 5 A N6 DA 5 2_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 A DT 4 A N3 DT 4 2_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 A DT 4 A O4 DT 4 2_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 A DT 2 A N3 DT 2 2_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 A DT 2 A O4 DT 2 2_555 DNA DNA, Octamer, Distamycin, Side-by-Side 1JUX PDB 1 1JUX 1 8 1JUX 1 8 1JUX A 1 1 8 BINDING SITE FOR RESIDUE DMY A 45 A DMY 45 Software 13 A DT 2 A DT 2 13 1_555 A DI 3 A DI 3 13 1_555 A DT 4 A DT 4 13 2_555 A DA 5 A DA 5 13 2_555 A DC 6 A DC 6 13 2_555 A DA 7 A DA 7 13 2_555 A DC 8 A DC 8 13 3_454 A DC 8 A DC 8 13 2_555 A HOH 10 C HOH 13 1_555 A HOH 18 C HOH 13 1_555 A HOH 36 C HOH 13 3_454 A HOH 37 C HOH 13 2_555 A HOH 42 C HOH 13 1_555 5 C 1 2 1