0.033023 0.019066 0.000000 0.000000 0.038132 0.000000 0.000000 0.000000 0.008451 0.000000 0.000000 0.000000 Ferraroni, M. Bazzicalupi, C. Gratteri, P. Bilia, A.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90.000 90.000 120.000 30.282 30.282 118.330 Ca 2 40.078 CALCIUM ION 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 C19 H14 N O4 1 320.319 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium Coptisine non-polymer N 1 N CA N 2 N O N 3 N P N 4 N O N 5 N O N 6 N O N 7 N C N 8 R C N 9 N O N 10 S C N 11 N O N 12 N C N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 N C N 49 R C N 50 N N N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N C N 57 N C 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 H N 72 N O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 N C N 83 R C Y 84 N N Y 85 N C Y 86 N N Y 87 N C N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N N Y 94 N C 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 H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C N 121 N N N 122 N C N 123 N O N 124 N N N 125 N C N 126 N O N 127 N C N 128 N C N 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 H N 145 N O N 146 N H N 147 N H N 148 N C N 149 N O N 150 N O 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 N N 161 N C N 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 N 169 N O N 170 N O N 171 N C 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 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 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 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 Y 155 N sing Y 156 N sing Y 157 N doub N 158 N sing Y 159 N sing Y 160 N sing Y 161 N doub Y 162 N doub Y 163 N doub Y 164 N sing Y 165 N sing N 166 N sing Y 167 N doub N 168 N sing Y 169 N sing N 170 N sing N 171 N sing Y 172 N doub Y 173 N doub Y 174 N doub Y 175 N sing Y 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 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 to be published 0353 The crystal structure of Coptisine bound to DNA d(CGTACG) 10.2210/pdb4d9x/pdb pdb_00004d9x 100 1 OXFORD ONYX CCD CCD 2010-08-09 OXFORD SINGLE WAVELENGTH M x-ray 1 1.542 1.0 1.542 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1809.217 DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') 4 syn polymer 40.078 CALCIUM ION 1 syn non-polymer 320.319 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium 1 syn non-polymer 18.015 water 15 nat water no no (DC)(DG)(DT)(DA)(DC)(DG) CGTACG A,B,C,D polydeoxyribonucleotide n n n n n n 1 2.16 43.16 VAPOR DIFFUSION 6.0 MPD, MgCl2, KCl, spermine, pH 6.0, VAPOR DIFFUSION, temperature 296K 296 -15.612 1 19 B 8 A 5 -2.049 B_DG8:DC5_A 1 -3.056 -0.768 0.614 -0.336 1.023 1 20 B 9 A 4 -5.999 B_DT9:DA4_A 2 -4.553 -0.731 -0.110 -0.146 -2.342 1 20 B 10 A 3 2.444 B_DA10:DT3_A 3 -5.190 -0.333 0.259 0.193 5.280 1 19 B 11 A 2 3.125 B_DC11:DG2_A 4 -1.288 0.610 0.344 -0.077 -7.651 1 19 C 2 D 11 -2.688 C_DG2:DC11_D 5 4.011 0.084 0.159 -0.386 -3.538 1 20 C 3 D 10 -4.216 C_DT3:DA10_D 6 -1.670 -0.942 -0.062 -0.226 -0.827 1 20 C 4 D 9 -6.888 C_DA4:DT9_D 7 -1.337 -0.490 0.021 -0.254 11.972 1 19 C 5 D 8 1.207 C_DC5:DG8_D 8 -0.651 0.719 -0.118 -0.461 2.536 32.306 B B 8 9 12.728 A A 5 4 2.976 6.999 -1.166 -0.723 BB_DG8DT9:DA4DC5_AA 1 5.197 -9.451 31.137 -2.365 2.886 3.274 41.995 B B 9 10 -3.470 A A 4 3 3.296 -2.481 0.047 -0.105 BB_DT9DA10:DT3DA4_AA 2 -4.488 6.276 41.695 0.114 -0.536 3.223 30.700 B B 10 11 7.511 A A 3 2 3.317 3.965 0.394 -0.419 BB_DA10DC11:DG2DT3_AA 3 -1.046 1.982 30.432 -1.573 -0.951 3.469 -69.729 B C 11 2 -4.224 A D 2 11 3.550 4.825 -0.169 1.299 BC_DC11DG2:DC11DG2_DA 4 2.231 1.953 -69.551 -1.322 -0.062 3.205 19.578 C C 2 3 6.025 D D 11 10 3.320 2.043 -0.293 -0.657 CC_DG2DT3:DA10DC11_DD 5 1.421 -4.190 19.420 -2.928 1.553 3.177 40.145 C C 3 4 2.142 D D 10 9 3.185 1.470 0.280 -0.410 CC_DT3DA4:DT9DA10_DD 6 1.601 -2.334 40.089 -0.760 -0.230 3.016 34.249 C C 4 5 10.300 D D 9 8 3.133 6.036 1.349 -0.300 CC_DA4DC5:DG8DT9_DD 7 -0.508 0.867 33.725 -1.409 -2.367 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Data collection Database references Derived calculations Refinement description 1 0 2013-01-23 1 1 2023-09-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id The same sequence complexed with Berberine The same sequence complexed with Sanguinarine The same sequence complexed with Chelerythrine RCSB Y RCSB 2012-01-12 REL REL CA CALCIUM ION KPT 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium HOH water 3NP6 PDB ENTRY 3NP6 PDB experimental model CA 1 2 CA CA 101 B KPT 1 3 KPT KPT 101 C HOH 1 4 HOH HOH 101 A HOH 6 4 HOH HOH 102 A HOH 8 4 HOH HOH 103 A HOH 9 4 HOH HOH 104 A HOH 11 4 HOH HOH 105 A HOH 14 4 HOH HOH 106 A HOH 7 4 HOH HOH 201 B HOH 10 4 HOH HOH 202 B HOH 3 4 HOH HOH 201 C HOH 12 4 HOH HOH 202 C HOH 2 4 HOH HOH 101 D HOH 4 4 HOH HOH 102 D HOH 5 4 HOH HOH 103 D HOH 13 4 HOH HOH 104 D HOH 15 4 HOH HOH 105 D 3.500 3.500 26.230 26.230 C 1 n 1 DC 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A C 7 n 1 DC 7 B G 8 n 2 DG 8 B T 9 n 3 DT 9 B A 10 n 4 DA 10 B C 11 n 5 DC 11 B G 12 n 6 DG 12 B C 1 n 1 DC 1 C G 2 n 2 DG 2 C T 3 n 3 DT 3 C A 4 n 4 DA 4 C C 5 n 5 DC 5 C G 6 n 6 DG 6 C C 7 n 1 DC 7 D G 8 n 2 DG 8 D T 9 n 3 DT 9 D A 10 n 4 DA 10 D C 11 n 5 DC 11 D G 12 n 6 DG 12 D 1 0.789 2 0.211 author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric 350 -3 2700 580 -8 2720 B DG 12 B OP1 DG 6 1_555 B CA 101 E CA CA 1_555 D DG 12 D OP1 DG 6 1_555 65.5 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 A O5' DC 1 A O5' DC 1 1 Y 1 A C5' DC 1 A C5' DC 1 1 Y 1 A C4' DC 1 A C4' DC 1 1 Y 1 A O4' DC 1 A O4' DC 1 1 Y 1 A C3' DC 1 A C3' DC 1 1 Y 1 A C2' DC 1 A C2' DC 1 1 Y 1 A C1' DC 1 A C1' DC 1 1 Y 1 A N1 DC 1 A N1 DC 1 1 Y 1 A C2 DC 1 A C2 DC 1 1 Y 1 A O2 DC 1 A O2 DC 1 1 Y 1 A N3 DC 1 A N3 DC 1 1 Y 1 A C4 DC 1 A C4 DC 1 1 Y 1 A N4 DC 1 A N4 DC 1 1 Y 1 A C5 DC 1 A C5 DC 1 1 Y 1 A C6 DC 1 A C6 DC 1 1 Y 1 C O5' DC 1 C O5' DC 1 1 Y 1 C C5' DC 1 C C5' DC 1 1 Y 1 C C4' DC 1 C C4' DC 1 1 Y 1 C O4' DC 1 C O4' DC 1 1 Y 1 C C3' DC 1 C C3' DC 1 1 Y 1 C C2' DC 1 C C2' DC 1 1 Y 1 C C1' DC 1 C C1' DC 1 1 Y 1 C N1 DC 1 C N1 DC 1 1 Y 1 C C2 DC 1 C C2 DC 1 1 Y 1 C O2 DC 1 C O2 DC 1 1 Y 1 C N3 DC 1 C N3 DC 1 1 Y 1 C C4 DC 1 C C4 DC 1 1 Y 1 C N4 DC 1 C N4 DC 1 1 Y 1 C C5 DC 1 C C5 DC 1 1 Y 1 C C6 DC 1 C C6 DC 1 1 Y 1 1.90 0.30 108.30 110.20 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 2.63 0.30 108.30 110.93 B B B O4' C1' N1 DC DC DC 11 11 11 N 1 4.08 0.30 108.30 112.38 C C C O4' C1' N1 DT DT DT 3 3 3 N 1 3.20 0.30 108.30 111.50 C C C O4' C1' N9 DA DA DA 4 4 4 N 1 -6.79 1.00 110.10 103.31 C C C C1' O4' C4' DC DC DC 5 5 5 N 1 3.21 0.30 108.30 111.51 C C C O4' C1' N1 DC DC DC 5 5 5 N 1 3.85 0.30 108.30 112.15 D D D O4' C1' N1 DC DC DC 7 7 7 N 1 2.45 0.30 108.30 110.75 D D D O4' C1' N9 DG DG DG 8 8 8 N 1 -3.26 0.50 129.30 126.04 D D D N1 C2 N3 DA DA DA 10 10 10 N 1 2.14 0.30 108.30 110.44 D D D O4' C1' N1 DC DC DC 11 11 11 N 1 7.26 1.20 119.70 126.96 D D D C3' O3' P DC DC DG 11 11 12 Y 45.380 24.6741 2.000 0.8990 0.8820 Used twin refinement twin fraction 0.204 0.3074 0.2614 0.2659 2.4400 30.0 254 2641 9.6000 99.5100 0.3123 0.2595 1.000 1.000 0.7534 0.1190 0.1476 0.0734 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.1480 0.0730 0.8000 0.8000 1.4000 PDB ENTRY 3NP6 MAXIMUM LIKELIHOOD MASK 2.4400 30.0 15 490 25 450 0 0.008 0.021 531 1.955 3.000 814 0.005 0.020 258 0.7340 0.4880 2.5060 15 175 190 20 94.0600 43.967 2.440 30.0 4D9X 2642 -3.000 0.108 1 17.480 99.500 0.611 2.440 2.590 4.010 5437 404 1 97.300 0.352 2.590 2.770 7.200 5829 398 1 100.000 0.256 2.770 2.990 9.780 5067 351 1 100.000 0.123 2.990 3.270 18.290 4732 328 1 100.000 0.092 3.270 3.640 25.430 4258 306 1 100.000 0.085 3.640 4.190 28.210 3748 281 1 100.000 0.077 4.190 5.110 28.350 3277 245 1 100.000 0.072 5.110 7.090 29.500 2459 193 1 100.000 0.067 7.090 30.0 28.820 1462 136 1 99.300 data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package phasing Alexei Vaguine alexei@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/molrep.html MOLREP program refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 data collection CrysalisPro data reduction XDS data scaling XDS The crystal structure of Coptisine bound to DNA d(CGTACG) 1 N N 1 N N 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N 4 N N 4 N N metalc 2.198 B DG 12 B OP1 DG 6 1_555 B CA 101 E CA CA 1_555 metalc 3.059 B CA 101 E CA CA 1_555 D DG 12 D OP1 DG 6 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 11 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 5 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 10 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 10 B N6 DA 4 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 9 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 9 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 8 B N2 DG 2 1_555 hydrog TYPE_4_PAIR B DG 12 B N2 DG 6 1_555 C DG 2 C N3 DG 2 1_555 hydrog TYPE_4_PAIR B DG 12 B N3 DG 6 1_555 C DG 2 C N2 DG 2 1_555 hydrog WATSON-CRICK C DG 2 C N1 DG 2 1_555 D DC 11 D N3 DC 5 1_555 hydrog WATSON-CRICK C DG 2 C N2 DG 2 1_555 D DC 11 D O2 DC 5 1_555 hydrog WATSON-CRICK C DG 2 C O6 DG 2 1_555 D DC 11 D N4 DC 5 1_555 hydrog WATSON-CRICK C DT 3 C N3 DT 3 1_555 D DA 10 D N1 DA 4 1_555 hydrog WATSON-CRICK C DT 3 C O4 DT 3 1_555 D DA 10 D N6 DA 4 1_555 hydrog WATSON-CRICK C DA 4 C N1 DA 4 1_555 D DT 9 D N3 DT 3 1_555 hydrog WATSON-CRICK C DA 4 C N6 DA 4 1_555 D DT 9 D O4 DT 3 1_555 hydrog WATSON-CRICK C DC 5 C N3 DC 5 1_555 D DG 8 D N1 DG 2 1_555 hydrog WATSON-CRICK C DC 5 C N4 DC 5 1_555 D DG 8 D O6 DG 2 1_555 hydrog WATSON-CRICK C DC 5 C O2 DC 5 1_555 D DG 8 D N2 DG 2 1_555 DNA DRUG-DNA COMPLEX, DOUBLE HELIX, DNA 4D9X PDB 1 4D9X CGTACG 1 6 4D9X 1 6 4D9X A 1 1 6 7 12 4D9X 7 12 4D9X B 1 1 6 1 6 4D9X 1 6 4D9X C 1 1 6 7 12 4D9X 7 12 4D9X D 1 1 6 BINDING SITE FOR RESIDUE CA B 101 B CA 101 Software 3 BINDING SITE FOR RESIDUE KPT C 101 C KPT 101 Software 9 B DG 12 B DG 6 3 1_555 D DG 12 D DG 6 3 5_555 D DG 12 D DG 6 3 1_555 A DC 5 A DC 5 9 1_455 A DG 6 A DG 6 9 1_455 B DC 7 B DC 1 9 4_545 B DG 8 B DG 2 9 1_455 C DC 5 C DC 5 9 1_555 C DG 6 C DG 6 9 1_555 D DC 7 D DC 1 9 4_555 D DG 8 D DG 2 9 4_555 D DG 8 D DG 2 9 1_555 154 P 32 2 1