0.033079 0.019098 0.000000 0.000000 0.038196 0.000000 0.000000 0.000000 0.008386 0.00000 0.00000 0.00000 Ferraroni, M. Bazzicalupi, C. Gratteri, P. Bilia, A.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90.00 90.00 120.00 30.231 30.231 119.247 Ca 2 40.078 CALCIUM ION non-polymer C21 H18 N O4 1 348.372 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium chelerythrine 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 N 1 N CA Y 2 N C Y 3 N C Y 4 N C Y 5 N C Y 6 N C Y 7 N C Y 8 N C Y 9 N C Y 10 N N Y 11 N C Y 12 N C Y 13 N C N 14 N C Y 15 N C Y 16 N C Y 17 N C Y 18 N C N 19 N O N 20 N C N 21 N O N 22 N C Y 23 N C Y 24 N C N 25 N O N 26 N C N 27 N O 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 O N 47 N P N 48 N O N 49 N O N 50 N O N 51 N C N 52 R C N 53 N O N 54 S C N 55 N O N 56 N C N 57 R C Y 58 N N Y 59 N C Y 60 N N Y 61 N C Y 62 N C N 63 N N Y 64 N N Y 65 N C Y 66 N N Y 67 N C N 68 N H N 69 N H N 70 N H 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 O N 83 N P N 84 N O N 85 N O N 86 N O N 87 N C N 88 R C N 89 N O N 90 S C N 91 N O N 92 N C N 93 R C N 94 N N N 95 N C N 96 N O N 97 N N N 98 N C N 99 N N N 100 N C N 101 N C 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 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 O N 117 N P N 118 N O N 119 N O N 120 N O N 121 N C N 122 R C N 123 N O N 124 S C N 125 N O N 126 N C N 127 R C Y 128 N N Y 129 N C Y 130 N N Y 131 N C N 132 N C N 133 N O N 134 N N N 135 N C N 136 N N N 137 N N Y 138 N C 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 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 O N 154 N P N 155 N O N 156 N O N 157 N O N 158 N C N 159 R C N 160 N O N 161 S C N 162 N O N 163 N C N 164 R C N 165 N N N 166 N C N 167 N O N 168 N N N 169 N C N 170 N O N 171 N C N 172 N C N 173 N C 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 186 N H N 187 N H N 188 N H N 189 N O N 190 N H N 191 N H Y 1 N doub Y 2 N sing Y 3 N sing Y 4 N sing Y 5 N doub Y 6 N sing Y 7 N sing Y 8 N doub Y 9 N sing Y 10 N sing Y 11 N sing Y 12 N doub Y 13 N doub N 14 N sing Y 15 N doub Y 16 N sing Y 17 N sing Y 18 N sing Y 19 N sing Y 20 N doub N 21 N sing Y 22 N doub N 23 N sing N 24 N sing N 25 N sing Y 26 N doub N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing 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 doub 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 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 Y 72 N sing Y 73 N sing Y 74 N doub N 75 N sing Y 76 N sing Y 77 N sing Y 78 N doub N 79 N sing Y 80 N doub N 81 N sing N 82 N sing Y 83 N sing Y 84 N doub N 85 N sing Y 86 N sing N 87 N sing N 88 N sing N 89 N doub 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 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 doub N 113 N sing N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N doub 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 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 Y 145 N sing Y 146 N sing Y 147 N doub N 148 N sing Y 149 N sing N 150 N sing Y 151 N doub N 152 N doub N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N doub N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N doub 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 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 doub N 187 N sing N 188 N sing N 189 N sing N 190 N doub N 191 N sing N 192 N sing N 193 N doub N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing To be Published 0353 The crystal structure of Chelerythrine bound to DNA d(CGTACG) 10.2210/pdb4d9y/pdb pdb_00004d9y 100 1 CCD 2011-03-13 PILATUS 2M double-crystal Si(111) SINGLE WAVELENGTH M x-ray 1 1.000 1.0 5.2R ELETTRA 1.000 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1809.217 DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') 4 syn polymer 348.372 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium 1 syn non-polymer 40.078 CALCIUM ION 1 syn non-polymer 18.015 water 11 nat water no no (DC)(DG)(DT)(DA)(DC)(DG) CGTACG A,B,C,D polydeoxyribonucleotide n n n n n n 1 2.19 43.89 VAPOR DIFFUSION 6.5 MPD, MgCl2, NaCl, KCL, spermine, pH 6.5, VAPOR DIFFUSION, temperature 296K 296 -19.257 1 19 B 208 A 105 -6.882 B_DG208:DC105_A 1 -5.579 -0.289 0.297 -0.286 4.724 1 20 B 209 A 104 -4.004 B_DT209:DA104_A 2 -13.910 0.750 -0.493 0.224 -6.397 1 20 B 210 A 103 7.029 B_DA210:DT103_A 3 -4.631 1.153 0.882 -0.139 1.049 1 19 B 211 A 102 -0.752 B_DC211:DG102_A 4 7.937 0.898 0.324 -0.194 -5.707 1 19 C 302 D 411 10.803 C_DG302:DC411_D 5 -3.501 -0.344 -0.163 0.041 -8.841 1 20 C 303 D 410 -11.888 C_DT303:DA410_D 6 -7.406 -0.098 1.254 -0.605 6.144 C 304 D 409 -0.577 C_DA304:DT409_D 7 -9.485 -0.047 0.330 0.428 11.921 1 19 C 305 D 408 -3.863 C_DC305:DG408_D 8 -13.514 0.375 0.433 -0.444 2.336 32.601 B B 208 209 7.479 A A 105 104 2.698 4.136 -0.757 -0.322 BB_DG208DT209:DA104DC105_AA 1 8.949 -16.183 31.113 -1.140 2.576 3.270 43.067 B B 209 210 5.272 A A 104 103 3.490 3.820 0.123 -0.623 BB_DT209DA210:DT103DA104_AA 2 -11.817 16.308 41.319 -1.247 -1.399 3.119 24.717 B B 210 211 -2.364 A A 103 102 3.173 -1.005 -0.037 -0.519 BB_DA210DC211:DG102DT103_AA 3 5.025 -11.823 24.188 -0.914 1.573 3.188 -69.852 B C 211 302 -5.078 A D 102 411 3.325 5.801 0.400 1.098 BC_DC211DG302:DC411DG102_DA 4 7.108 6.221 -69.323 -1.167 0.603 3.662 29.322 C C 302 303 2.841 D D 411 410 3.599 1.387 -1.040 -0.405 CC_DG302DT303:DA410DC411_DD 5 -13.277 27.191 26.166 -1.153 -1.315 2.944 39.925 C C 303 304 -10.568 D D 410 409 2.864 -7.111 0.367 -0.691 CC_DT303DA304:DT409DA410_DD 6 9.793 -14.554 38.118 -0.266 0.490 2.768 35.703 C C 304 305 14.273 D D 409 408 3.113 8.661 0.808 -0.811 CC_DA304DC305:DG408DT409_DD 7 -2.680 4.416 34.569 -2.468 -1.672 software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Refinement description Refinement description Data collection Database references Derived calculations Refinement description 1 0 2013-01-23 1 1 2013-03-13 1 2 2017-11-15 1 3 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 Coptisine RCSB Y RCSB 2012-01-12 REL REL CTI 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium CA CALCIUM ION HOH water synthetic DNA sample 3NP6 PDB ENTRY 3NP6 PDB experimental model CTI 606 2 CTI CTI 201 A CA 501 3 CA CA 501 B HOH 709 4 HOH HOH 301 A HOH 708 4 HOH HOH 601 B HOH 701 4 HOH HOH 602 B HOH 702 4 HOH HOH 603 B HOH 703 4 HOH HOH 401 C HOH 710 4 HOH HOH 402 C HOH 704 4 HOH HOH 501 D HOH 705 4 HOH HOH 502 D HOH 706 4 HOH HOH 503 D HOH 707 4 HOH HOH 504 D HOH 711 4 HOH HOH 505 D 3.500 3.500 26.170 26.170 DC 101 n 1 DC 101 A DG 102 n 2 DG 102 A DT 103 n 3 DT 103 A DA 104 n 4 DA 104 A DC 105 n 5 DC 105 A DG 106 n 6 DG 106 A DC 207 n 1 DC 207 B DG 208 n 2 DG 208 B DT 209 n 3 DT 209 B DA 210 n 4 DA 210 B DC 211 n 5 DC 211 B DG 212 n 6 DG 212 B DC 301 n 1 DC 301 C DG 302 n 2 DG 302 C DT 303 n 3 DT 303 C DA 304 n 4 DA 304 C DC 305 n 5 DC 305 C DG 306 n 6 DG 306 C DC 407 n 1 DC 407 D DG 408 n 2 DG 408 D DT 409 n 3 DT 409 D DA 410 n 4 DA 410 D DC 411 n 5 DC 411 D DG 412 n 6 DG 412 D 0.2196 author_and_software_defined_assembly PISA 2 dimeric author_and_software_defined_assembly PISA 2 dimeric 550 -6 2720 370 -2 2640 B DG 212 B OP1 DG 6 1_555 B CA 501 F CA CA 1_555 D DG 412 D OP1 DG 6 1_555 68.8 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 101 A O5' DC 1 1 Y 1 A C5' DC 101 A C5' DC 1 1 Y 1 A C4' DC 101 A C4' DC 1 1 Y 1 A O4' DC 101 A O4' DC 1 1 Y 1 A C3' DC 101 A C3' DC 1 1 Y 1 A C2' DC 101 A C2' DC 1 1 Y 1 A C1' DC 101 A C1' DC 1 1 Y 1 A N1 DC 101 A N1 DC 1 1 Y 1 A C2 DC 101 A C2 DC 1 1 Y 1 A O2 DC 101 A O2 DC 1 1 Y 1 A N3 DC 101 A N3 DC 1 1 Y 1 A C4 DC 101 A C4 DC 1 1 Y 1 A N4 DC 101 A N4 DC 1 1 Y 1 A C5 DC 101 A C5 DC 1 1 Y 1 A C6 DC 101 A C6 DC 1 1 Y 1 C O5' DC 301 C O5' DC 1 1 Y 1 C C5' DC 301 C C5' DC 1 1 Y 1 C C4' DC 301 C C4' DC 1 1 Y 1 C O4' DC 301 C O4' DC 1 1 Y 1 C C3' DC 301 C C3' DC 1 1 Y 1 C C2' DC 301 C C2' DC 1 1 Y 1 C C1' DC 301 C C1' DC 1 1 Y 1 C N1 DC 301 C N1 DC 1 1 Y 1 C C2 DC 301 C C2 DC 1 1 Y 1 C O2 DC 301 C O2 DC 1 1 Y 1 C N3 DC 301 C N3 DC 1 1 Y 1 C C4 DC 301 C C4 DC 1 1 Y 1 C N4 DC 301 C N4 DC 1 1 Y 1 C C5 DC 301 C C5 DC 1 1 Y 1 C C6 DC 301 C C6 DC 1 1 Y 1 1.92 0.30 108.30 110.22 A A A O4' C1' N1 DT DT DT 103 103 103 N 1 -7.69 1.00 110.10 102.41 A A A C1' O4' C4' DC DC DC 105 105 105 N 1 2.20 0.30 108.30 110.50 A A A O4' C1' N1 DC DC DC 105 105 105 N 1 -6.59 1.00 110.10 103.51 B B B C1' O4' C4' DC DC DC 211 211 211 N 1 1.99 0.30 108.30 110.29 B B B O4' C1' N9 DG DG DG 212 212 212 N 1 -6.09 1.00 110.10 104.01 C C C C1' O4' C4' DT DT DT 303 303 303 N 1 2.35 0.30 108.30 110.65 C C C O4' C1' N1 DT DT DT 303 303 303 N 1 -3.75 0.60 118.90 115.15 D D D N1 C2 O2 DC DC DC 411 411 411 N 1 -4.34 0.70 108.00 103.66 D D D O4' C1' N9 DG DG DG 412 412 412 N 54.1262 Crystal was merohedrally twinned with a fraction of 0.46 and twin law -h, -k, l 0.3140 0.2196 2.10 20.0 209 4087 93.9 1.000 1.000 Reflections were chosen in thin resolution shells 1 FREE R 0.0 MOLECULAR REPLACEMENT PDB ENTRY 3NP6 Engh & Huber 2.10 20.0 11 488 27 450 0 0.006 0.026 0.005 0.373 2.19 85.29 46.830 2.100 30.0 4D9Y 4087 -3.000 0.089 1 13.390 99.000 0.226 2.100 2.230 5.340 1 97.800 0.187 2.230 2.380 7.620 1 99.700 0.117 2.380 2.570 12.230 1 98.900 0.111 2.570 2.810 14.290 1 99.000 0.092 2.810 3.140 16.980 1 99.400 0.089 3.140 3.630 18.840 1 99.300 0.085 3.630 4.430 19.330 1 99.500 0.078 4.430 6.230 18.790 1 99.300 0.083 6.230 30.0 17.570 1 97.900 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 George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package 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 reduction XDS data scaling XDS The crystal structure of Chelerythrine 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 2.215 B DG 212 B OP1 DG 6 1_555 B CA 501 F CA CA 1_555 metalc 2.269 B CA 501 F CA CA 1_555 D DG 412 D OP1 DG 6 1_555 hydrog WATSON-CRICK A DG 102 A N1 DG 2 1_555 B DC 211 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 102 A N2 DG 2 1_555 B DC 211 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 102 A O6 DG 2 1_555 B DC 211 B N4 DC 5 1_555 hydrog TYPE_4_PAIR A DG 102 A N2 DG 2 1_555 D DG 412 D N3 DG 6 1_555 hydrog TYPE_4_PAIR A DG 102 A N3 DG 2 1_555 D DG 412 D N2 DG 6 1_555 hydrog WATSON-CRICK A DT 103 A N3 DT 3 1_555 B DA 210 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 103 A O4 DT 3 1_555 B DA 210 B N6 DA 4 1_555 hydrog WATSON-CRICK A DA 104 A N1 DA 4 1_555 B DT 209 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 104 A N6 DA 4 1_555 B DT 209 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 105 A N3 DC 5 1_555 B DG 208 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 105 A N4 DC 5 1_555 B DG 208 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 105 A O2 DC 5 1_555 B DG 208 B N2 DG 2 1_555 hydrog TYPE_4_PAIR B DG 212 B N2 DG 6 1_555 C DG 302 C N3 DG 2 1_555 hydrog TYPE_4_PAIR B DG 212 B N3 DG 6 1_555 C DG 302 C N2 DG 2 1_555 hydrog WATSON-CRICK C DG 302 C N1 DG 2 1_555 D DC 411 D N3 DC 5 1_555 hydrog WATSON-CRICK C DG 302 C N2 DG 2 1_555 D DC 411 D O2 DC 5 1_555 hydrog WATSON-CRICK C DG 302 C O6 DG 2 1_555 D DC 411 D N4 DC 5 1_555 hydrog WATSON-CRICK C DT 303 C N3 DT 3 1_555 D DA 410 D N1 DA 4 1_555 hydrog WATSON-CRICK C DT 303 C O4 DT 3 1_555 D DA 410 D N6 DA 4 1_555 hydrog DA-DT PAIR C DA 304 C N1 DA 4 1_555 D DT 409 D N3 DT 3 1_555 hydrog WATSON-CRICK C DC 305 C N3 DC 5 1_555 D DG 408 D N1 DG 2 1_555 hydrog WATSON-CRICK C DC 305 C N4 DC 5 1_555 D DG 408 D O6 DG 2 1_555 hydrog WATSON-CRICK C DC 305 C O2 DC 5 1_555 D DG 408 D N2 DG 2 1_555 DNA DRUG-DNA COMPLEX, DOUBLE HELIX, DNA 4D9Y PDB 1 4D9Y CGTACG 101 106 4D9Y 101 106 4D9Y A 1 1 6 207 212 4D9Y 207 212 4D9Y B 1 1 6 301 306 4D9Y 301 306 4D9Y C 1 1 6 407 412 4D9Y 407 412 4D9Y D 1 1 6 BINDING SITE FOR RESIDUE CTI A 201 A CTI 201 Software 11 BINDING SITE FOR RESIDUE CA B 501 B CA 501 Software 4 A DC 105 A DC 5 11 1_555 A DG 106 A DG 6 11 1_555 A HOH 301 G HOH 11 1_555 B DC 207 B DC 1 11 4_555 B DG 208 B DG 2 11 1_555 B HOH 602 H HOH 11 1_555 C DC 305 C DC 5 11 1_455 C DG 306 C DG 6 11 1_455 D DC 407 D DC 1 11 4_545 D DG 408 D DG 2 11 1_455 D HOH 502 J HOH 11 4_545 B DC 211 B DC 5 4 5_555 B DG 212 B DG 6 4 5_555 B DG 212 B DG 6 4 1_555 D DG 412 D DG 6 4 1_555 154 P 32 2 1