0.039448 0.000000 0.000000 0.000000 0.024564 0.000000 0.000000 0.000000 0.015031 0.00000 0.00000 0.00000 Larsen, T. Goodsell, D.S. Cascio, D. Grzeskowiak, K. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.350 40.710 66.530 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C16 H15 N5 277.324 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE non-polymer 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 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 Y 37 N N Y 38 N C Y 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C Y 44 N C Y 45 N C N 46 N C N 47 N N N 48 N N Y 49 N C Y 50 N C Y 51 N C Y 52 N C Y 53 N C Y 54 N C N 55 N C N 56 N N N 57 N N 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 H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 N C N 84 R C N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N C N 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 H N 107 N O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 N C N 118 R C Y 119 N N Y 120 N C Y 121 N N Y 122 N C N 123 N C N 124 N O N 125 N N N 126 N C N 127 N N N 128 N N Y 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 O N 145 N P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 R C N 156 N N N 157 N C N 158 N O N 159 N N N 160 N C N 161 N O N 162 N C N 163 N C N 164 N C N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H 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 O N 181 N H N 182 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 Y 39 N sing Y 40 N sing N 41 N sing Y 42 N doub Y 43 N sing Y 44 N sing N 45 N sing Y 46 N doub Y 47 N sing N 48 N sing Y 49 N sing N 50 N sing Y 51 N doub N 52 N sing Y 53 N sing N 54 N sing Y 55 N doub N 56 N doub N 57 N sing N 58 N sing N 59 N sing N 60 N sing Y 61 N doub Y 62 N sing Y 63 N sing N 64 N sing Y 65 N doub N 66 N sing Y 67 N sing N 68 N sing Y 69 N doub N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing 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 doub N 115 N sing 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 Y 135 N sing Y 136 N sing Y 137 N doub N 138 N sing Y 139 N sing N 140 N sing Y 141 N doub N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub 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 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 sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N doub N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing US J.Biomol.Struct.Dyn. JBSDD6 0646 0739-1102 7 477 491 2627296 The structure of DAPI bound to DNA. 1989 10.2210/pdb1d30/pdb pdb_00001d30 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ROOM TEMPERATURE 1 AREA DETECTOR SDMS x-ray 1 1.0 3663.392 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 277.324 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE 1 syn non-polymer 18.015 water 25 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 2.34 47.50 VAPOR DIFFUSION 7.00 pH 7.00, VAPOR DIFFUSION, temperature 277.00K 277.00 WATER 1 MPD 1 SPERMINE 1 MG ACETATE 1 WATER 2 MPD 2 6.150 1 19 A 1 B 24 0.316 A_DC1:DG24_B 1 -12.814 0.046 -0.153 -0.096 2.126 1 19 A 2 B 23 -2.226 A_DG2:DC23_B 2 -20.075 -0.346 0.307 -0.168 -3.141 1 19 A 3 B 22 -5.884 A_DC3:DG22_B 3 -14.431 -0.054 -0.175 -0.213 8.717 1 19 A 4 B 21 -8.995 A_DG4:DC21_B 4 -12.580 -0.055 0.035 -0.391 -0.510 1 20 A 5 B 20 1.733 A_DA5:DT20_B 5 -15.040 -0.102 -0.257 -0.004 8.983 1 20 A 6 B 19 -4.366 A_DA6:DT19_B 6 -22.142 -0.086 0.661 -0.027 -3.842 1 20 A 7 B 18 6.146 A_DT7:DA18_B 7 -23.837 -0.041 0.175 -0.152 -6.864 1 20 A 8 B 17 -2.771 A_DT8:DA17_B 8 -23.138 0.124 0.097 -0.505 -10.111 1 19 A 9 B 16 2.144 A_DC9:DG16_B 9 -12.539 0.148 -0.022 -0.353 8.738 1 19 A 10 B 15 -1.228 A_DG10:DC15_B 10 -6.153 -0.100 0.038 -0.199 1.173 1 19 A 11 B 14 -4.409 A_DC11:DG14_B 11 -16.315 0.098 0.173 -0.460 -3.065 1 19 A 12 B 13 -4.381 A_DG12:DC13_B 12 5.579 -0.059 -0.594 -0.433 3.536 37.897 A A 1 2 10.790 B B 24 23 3.546 6.951 -0.192 0.289 AA_DC1DG2:DC23DG24_BB 1 -4.983 7.734 36.954 -0.531 -0.405 3.412 41.062 A A 2 3 -5.087 B B 23 22 3.465 -3.553 0.194 0.421 AA_DG2DC3:DG22DC23_BB 2 5.857 -8.386 40.511 1.009 0.397 3.371 30.736 A A 3 4 7.384 B B 22 21 3.313 3.902 -0.189 0.629 AA_DC3DG4:DC21DG22_BB 3 -1.635 3.093 30.451 0.401 0.029 3.417 34.341 A A 4 5 12.773 B B 21 20 3.510 7.483 0.383 -0.118 AA_DG4DA5:DT20DC21_BB 4 1.331 -2.272 33.514 -1.456 -0.425 2.982 36.135 A A 5 6 -2.170 B B 20 19 3.002 -1.336 -0.170 -0.357 AA_DA5DA6:DT19DT20_BB 5 -7.794 12.661 35.288 -0.401 -0.745 3.595 36.758 A A 6 7 2.372 B B 19 18 3.604 1.490 0.450 -0.840 AA_DA6DT7:DA18DT19_BB 6 5.797 -9.231 36.284 -1.556 0.161 3.348 35.322 A A 7 8 5.297 B B 18 17 3.357 3.209 -0.658 -0.199 AA_DT7DT8:DA17DA18_BB 7 -1.332 2.199 35.156 -0.816 0.883 3.397 41.891 A A 8 9 -7.890 B B 17 16 3.452 -5.626 -0.027 0.211 AA_DT8DC9:DG16DA17_BB 8 -0.549 0.770 41.525 0.913 -0.023 3.179 24.609 A A 9 10 4.291 B B 16 15 3.117 1.827 0.305 0.943 AA_DC9DG10:DC15DG16_BB 9 0.110 -0.259 24.542 1.671 -0.682 3.569 42.531 A A 10 11 -8.446 B B 15 14 3.648 -6.105 -0.864 0.618 AA_DG10DC11:DG14DC15_BB 10 -2.283 3.159 42.052 1.538 0.935 3.668 39.312 A A 11 12 -4.678 B B 14 13 3.715 -3.128 0.580 1.045 AA_DC11DG12:DC13DG14_BB 11 7.217 -10.794 38.548 1.977 0.115 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1992-04-15 1 1 2008-05-22 1 2 2011-07-13 1 3 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 BNL Y NDB 1991-01-04 REL REL DAP 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE HOH water DAP 25 2 DAP DAP 25 A HOH 26 3 HOH HOH 26 A HOH 28 3 HOH HOH 28 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 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 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 A HOH 27 3 HOH HOH 27 B HOH 29 3 HOH HOH 29 B HOH 34 3 HOH HOH 34 B HOH 40 3 HOH HOH 40 B HOH 41 3 HOH HOH 41 B HOH 44 3 HOH HOH 44 B HOH 45 3 HOH HOH 45 B HOH 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 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 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 -12.32 0.40 104.50 92.18 A A A O4' C4' C3' DC DC DC 1 1 1 N 1 10.79 1.20 115.70 126.49 A A A C5' C4' C3' DC DC DC 1 1 1 N 1 4.95 0.70 110.30 115.25 A A A C1' O4' C4' DC DC DC 1 1 1 N 1 7.93 0.30 108.30 116.23 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 7.87 0.60 118.90 126.77 A A A N1 C2 O2 DC DC DC 1 1 1 N 1 -8.84 0.70 121.90 113.06 A A A N3 C2 O2 DC DC DC 1 1 1 N 1 -15.41 2.20 105.20 89.79 A A A O3' P OP1 DC DG DG 1 2 2 Y 1 -6.82 0.80 109.40 102.58 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 2.39 0.30 108.30 110.69 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -10.17 0.90 116.20 106.03 A A A N1 C2 N2 DG DG DG 2 2 2 N 1 7.79 0.70 119.90 127.69 A A A N3 C2 N2 DG DG DG 2 2 2 N 1 -4.42 0.60 119.90 115.48 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 22.66 1.20 110.70 133.36 A A A O5' P OP1 DC DC DC 3 3 3 N 1 -10.29 0.90 105.70 95.41 A A A O5' P OP2 DC DC DC 3 3 3 N 1 7.60 1.20 115.70 123.30 A A A C5' C4' C3' DC DC DC 3 3 3 N 1 4.67 0.70 110.30 114.97 A A A C1' O4' C4' DC DC DC 3 3 3 N 1 -5.18 0.80 105.90 100.72 A A A O4' C1' C2' DC DC DC 3 3 3 N 1 5.27 0.30 108.30 113.57 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 3.03 0.50 121.00 124.03 A A A C5 C6 N1 DC DC DC 3 3 3 N 1 6.10 0.60 118.90 125.00 A A A N1 C2 O2 DC DC DC 3 3 3 N 1 -14.23 1.90 104.00 89.77 A A A O3' P O5' DC DG DG 3 4 4 Y 1 -13.90 2.20 105.20 91.30 A A A O3' P OP1 DC DG DG 3 4 4 Y 1 14.47 1.50 119.60 134.07 A A A OP1 P OP2 DG DG DG 4 4 4 N 1 8.26 1.20 110.70 118.96 A A A O5' P OP2 DG DG DG 4 4 4 N 1 6.69 1.10 109.80 116.49 A A A C5' C4' O4' DG DG DG 4 4 4 N 1 -5.51 0.80 105.90 100.39 A A A O4' C1' C2' DG DG DG 4 4 4 N 1 4.41 0.30 108.30 112.71 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -3.47 0.50 111.90 108.43 A A A C2 N3 C4 DG DG DG 4 4 4 N 1 3.09 0.50 128.60 131.69 A A A N3 C4 C5 DG DG DG 4 4 4 N 1 3.46 0.40 110.80 114.26 A A A C4 C5 N7 DG DG DG 4 4 4 N 1 -4.97 0.50 104.30 99.33 A A A C5 N7 C8 DG DG DG 4 4 4 N 1 3.50 0.50 113.10 116.60 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 6.88 0.60 119.90 126.78 A A A N1 C6 O6 DG DG DG 4 4 4 N 1 -5.43 0.60 128.60 123.17 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 -20.10 2.20 105.20 85.10 A A A O3' P OP1 DG DA DA 4 5 5 Y 1 -5.25 0.80 109.40 104.15 A A A O5' C5' C4' DA DA DA 5 5 5 N 1 -5.15 0.80 105.90 100.75 A A A O4' C1' C2' DA DA DA 5 5 5 N 1 9.40 0.30 108.30 117.70 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 -4.42 0.50 129.30 124.88 A A A N1 C2 N3 DA DA DA 5 5 5 N 1 4.35 0.50 110.60 114.95 A A A C2 N3 C4 DA DA DA 5 5 5 N 1 -6.10 0.60 118.60 112.50 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 5.31 0.80 123.70 129.01 A A A C5 C6 N6 DA DA DA 5 5 5 N 1 32.67 1.20 119.70 152.37 A A A C3' O3' P DA DA DA 5 5 6 Y 1 15.41 1.50 119.60 135.01 A A A OP1 P OP2 DA DA DA 6 6 6 N 1 -15.93 0.90 105.70 89.77 A A A O5' P OP1 DA DA DA 6 6 6 N 1 7.66 0.30 108.30 115.96 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 2.60 0.40 105.80 108.40 A A A N9 C4 C5 DA DA DA 6 6 6 N 1 -14.02 1.90 104.00 89.98 A A A O3' P O5' DA DT DT 6 7 7 Y 1 -18.18 2.20 105.20 87.02 A A A O3' P OP1 DA DT DT 6 7 7 Y 1 32.67 1.50 119.60 152.27 A A A OP1 P OP2 DT DT DT 7 7 7 N 1 -5.68 0.90 105.70 100.02 A A A O5' P OP1 DT DT DT 7 7 7 N 1 -8.91 0.80 105.90 96.99 A A A O4' C1' C2' DT DT DT 7 7 7 N 1 3.52 0.30 108.30 111.82 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 3.65 0.60 114.60 118.25 A A A N1 C2 N3 DT DT DT 7 7 7 N 1 -6.14 0.60 127.20 121.06 A A A C2 N3 C4 DT DT DT 7 7 7 N 1 3.94 0.60 115.20 119.14 A A A N3 C4 C5 DT DT DT 7 7 7 N 1 -6.74 0.60 122.30 115.56 A A A N3 C2 O2 DT DT DT 7 7 7 N 1 -4.29 0.70 124.90 120.61 A A A C5 C4 O4 DT DT DT 7 7 7 N 1 12.18 1.20 119.70 131.88 A A A C3' O3' P DT DT DT 7 7 8 Y 1 19.76 1.50 119.60 139.36 A A A OP1 P OP2 DT DT DT 8 8 8 N 1 -7.05 0.80 109.40 102.35 A A A O5' C5' C4' DT DT DT 8 8 8 N 1 -8.55 0.80 105.90 97.35 A A A O4' C1' C2' DT DT DT 8 8 8 N 1 4.82 0.30 108.30 113.12 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -5.01 0.50 121.30 116.29 A A A C6 N1 C2 DT DT DT 8 8 8 N 1 4.53 0.60 114.60 119.13 A A A N1 C2 N3 DT DT DT 8 8 8 N 1 -3.85 0.60 127.20 123.35 A A A C2 N3 C4 DT DT DT 8 8 8 N 1 -5.38 0.80 123.10 117.72 A A A N1 C2 O2 DT DT DT 8 8 8 N 1 8.60 0.60 119.00 127.60 A A A C4 C5 C7 DT DT DT 8 8 8 N 1 -8.12 0.60 122.90 114.78 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 27.48 1.20 119.70 147.18 A A A C3' O3' P DT DT DC 8 8 9 Y 1 18.67 1.50 119.60 138.27 A A A OP1 P OP2 DC DC DC 9 9 9 N 1 -7.57 0.80 109.40 101.83 A A A O5' C5' C4' DC DC DC 9 9 9 N 1 4.82 0.70 110.30 115.12 A A A C1' O4' C4' DC DC DC 9 9 9 N 1 7.91 1.20 102.50 110.41 A A A C3' C2' C1' DC DC DC 9 9 9 N 1 -13.02 0.80 105.90 92.88 A A A O4' C1' C2' DC DC DC 9 9 9 N 1 -10.93 0.70 108.00 97.07 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 -3.29 0.40 121.90 118.61 A A A N3 C4 C5 DC DC DC 9 9 9 N 1 -3.84 0.40 104.50 100.66 A A A O4' C4' C3' DG DG DG 10 10 10 N 1 -5.28 0.70 102.20 96.92 A A A C4' C3' C2' DG DG DG 10 10 10 N 1 -5.12 0.80 102.40 97.28 A A A C3' C2' C1' DG DG DG 10 10 10 N 1 11.68 0.30 108.30 119.98 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 3.74 0.50 111.50 115.24 A A A C5 C6 N1 DG DG DG 10 10 10 N 1 -11.93 0.90 105.70 93.77 A A A O5' P OP1 DC DC DC 11 11 11 N 1 -10.55 1.60 120.90 110.35 A A A P O5' C5' DC DC DC 11 11 11 N 1 -6.41 0.80 105.90 99.49 A A A O4' C1' C2' DC DC DC 11 11 11 N 1 -7.48 0.70 108.00 100.52 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -3.92 0.40 121.90 117.98 A A A N3 C4 C5 DC DC DC 11 11 11 N 1 8.34 0.70 118.00 126.34 A A A N3 C4 N4 DC DC DC 11 11 11 N 1 -4.54 0.70 120.20 115.66 A A A C5 C4 N4 DC DC DC 11 11 11 N 1 13.91 1.50 119.60 133.51 A A A OP1 P OP2 DG DG DG 12 12 12 N 1 -8.74 0.80 109.40 100.66 A A A O5' C5' C4' DG DG DG 12 12 12 N 1 11.02 1.60 120.90 131.92 A A A P O5' C5' DG DG DG 12 12 12 N 1 3.60 0.50 106.80 110.40 A A A O4' C1' C2' DG DG DG 12 12 12 N 1 -4.99 0.60 125.10 120.11 A A A C6 N1 C2 DG DG DG 12 12 12 N 1 4.48 0.50 111.50 115.98 A A A C5 C6 N1 DG DG DG 12 12 12 N 1 -4.70 0.60 119.90 115.20 A A A N1 C6 O6 DG DG DG 12 12 12 N 1 -7.80 0.80 109.40 101.60 B B B O5' C5' C4' DC DC DC 13 13 13 N 1 -6.81 0.80 105.90 99.09 B B B O4' C1' C2' DC DC DC 13 13 13 N 1 -8.52 0.70 108.00 99.48 B B B O4' C1' N1 DC DC DC 13 13 13 N 1 3.10 0.50 119.90 123.00 B B B C2 N3 C4 DC DC DC 13 13 13 N 1 5.55 0.70 121.90 127.45 B B B N3 C2 O2 DC DC DC 13 13 13 N 1 6.93 0.70 118.00 124.93 B B B N3 C4 N4 DC DC DC 13 13 13 N 1 -6.20 0.70 120.20 114.00 B B B C5 C4 N4 DC DC DC 13 13 13 N 1 20.12 1.20 119.70 139.82 B B B C3' O3' P DC DC DG 13 13 14 Y 1 24.74 1.50 119.60 144.34 B B B OP1 P OP2 DG DG DG 14 14 14 N 1 -15.00 0.90 105.70 90.70 B B B O5' P OP1 DG DG DG 14 14 14 N 1 -11.39 1.60 120.90 109.51 B B B P O5' C5' DG DG DG 14 14 14 N 1 5.23 0.60 106.00 111.23 B B B O4' C4' C3' DG DG DG 14 14 14 N 1 5.12 0.50 106.80 111.92 B B B O4' C1' C2' DG DG DG 14 14 14 N 1 8.47 1.10 110.50 118.97 B B B O3' P OP2 DG DC DC 14 15 15 Y 1 17.98 1.50 119.60 137.58 B B B OP1 P OP2 DC DC DC 15 15 15 N 1 -7.87 0.90 105.70 97.83 B B B O5' P OP1 DC DC DC 15 15 15 N 1 -8.81 0.80 105.90 97.09 B B B O4' C1' C2' DC DC DC 15 15 15 N 1 -5.79 0.70 108.00 102.21 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 3.25 0.50 121.00 124.25 B B B C5 C6 N1 DC DC DC 15 15 15 N 1 7.94 1.10 110.50 118.44 B B B O3' P OP2 DC DG DG 15 16 16 Y 1 4.91 0.30 108.30 113.21 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 3.94 0.50 111.50 115.44 B B B C5 C6 N1 DG DG DG 16 16 16 N 1 -4.43 0.60 119.90 115.47 B B B N1 C6 O6 DG DG DG 16 16 16 N 1 31.53 1.20 119.70 151.23 B B B C3' O3' P DG DG DA 16 16 17 Y 1 -9.48 1.50 119.60 110.12 B B B OP1 P OP2 DA DA DA 17 17 17 N 1 10.28 1.20 110.70 120.98 B B B O5' P OP2 DA DA DA 17 17 17 N 1 6.71 1.10 109.80 116.51 B B B C5' C4' O4' DA DA DA 17 17 17 N 1 -5.37 0.80 105.90 100.53 B B B O4' C1' C2' DA DA DA 17 17 17 N 1 15.44 0.30 108.30 123.74 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 8.13 0.60 118.60 126.73 B B B C6 N1 C2 DA DA DA 17 17 17 N 1 -9.30 0.50 129.30 120.00 B B B N1 C2 N3 DA DA DA 17 17 17 N 1 4.40 0.50 110.60 115.00 B B B C2 N3 C4 DA DA DA 17 17 17 N 1 -3.40 0.50 117.70 114.30 B B B C5 C6 N1 DA DA DA 17 17 17 N 1 -4.51 0.50 103.90 99.39 B B B C5 N7 C8 DA DA DA 17 17 17 N 1 4.13 0.50 113.80 117.93 B B B N7 C8 N9 DA DA DA 17 17 17 N 1 7.52 0.60 118.60 126.12 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 10.05 1.20 119.70 129.75 B B B C3' O3' P DA DA DA 17 17 18 Y 1 13.98 1.20 110.70 124.68 B B B O5' P OP2 DA DA DA 18 18 18 N 1 -5.34 0.40 104.50 99.16 B B B O4' C4' C3' DA DA DA 18 18 18 N 1 6.54 0.70 110.30 116.84 B B B C1' O4' C4' DA DA DA 18 18 18 N 1 -6.43 0.80 105.90 99.47 B B B O4' C1' C2' DA DA DA 18 18 18 N 1 15.20 0.30 108.30 123.50 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 5.48 0.60 118.60 124.08 B B B C6 N1 C2 DA DA DA 18 18 18 N 1 -8.11 0.50 129.30 121.19 B B B N1 C2 N3 DA DA DA 18 18 18 N 1 4.78 0.50 110.60 115.38 B B B C2 N3 C4 DA DA DA 18 18 18 N 1 11.21 1.50 119.60 130.81 B B B OP1 P OP2 DT DT DT 19 19 19 N 1 -3.32 0.40 104.50 101.18 B B B O4' C4' C3' DT DT DT 19 19 19 N 1 -6.50 1.00 110.10 103.60 B B B C1' O4' C4' DT DT DT 19 19 19 N 1 3.67 0.60 114.60 118.27 B B B N1 C2 N3 DT DT DT 19 19 19 N 1 -7.04 0.60 127.20 120.16 B B B C2 N3 C4 DT DT DT 19 19 19 N 1 6.02 0.60 115.20 121.22 B B B N3 C4 C5 DT DT DT 19 19 19 N 1 -4.44 0.60 119.90 115.46 B B B N3 C4 O4 DT DT DT 19 19 19 N 1 5.96 0.60 119.00 124.96 B B B C4 C5 C7 DT DT DT 19 19 19 N 1 -4.88 0.60 122.90 118.02 B B B C6 C5 C7 DT DT DT 19 19 19 N 1 -5.54 0.90 105.70 100.16 B B B O5' P OP2 DT DT DT 20 20 20 N 1 3.87 0.60 106.00 109.87 B B B O4' C4' C3' DT DT DT 20 20 20 N 1 -12.46 1.90 109.30 96.84 B B B C5' C4' O4' DT DT DT 20 20 20 N 1 -7.37 0.70 108.00 100.63 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 4.31 0.60 115.20 119.51 B B B N3 C4 C5 DT DT DT 20 20 20 N 1 -6.19 0.70 124.90 118.71 B B B C5 C4 O4 DT DT DT 20 20 20 N 1 21.87 1.20 119.70 141.57 B B B C3' O3' P DT DT DC 20 20 21 Y 1 7.93 1.10 110.50 118.43 B B B O3' P OP2 DT DC DC 20 21 21 Y 1 -11.22 0.90 105.70 94.48 B B B O5' P OP2 DC DC DC 21 21 21 N 1 -6.24 0.70 102.20 95.96 B B B C4' C3' C2' DC DC DC 21 21 21 N 1 -11.27 0.80 105.90 94.63 B B B O4' C1' C2' DC DC DC 21 21 21 N 1 3.06 0.50 119.90 122.96 B B B C2 N3 C4 DC DC DC 21 21 21 N 1 -3.71 0.40 121.90 118.19 B B B N3 C4 C5 DC DC DC 21 21 21 N 1 5.92 0.60 118.90 124.82 B B B N1 C2 O2 DC DC DC 21 21 21 N 1 -4.34 0.70 121.90 117.56 B B B N3 C2 O2 DC DC DC 21 21 21 N 1 11.38 1.10 109.80 121.18 B B B C5' C4' O4' DG DG DG 22 22 22 N 1 -5.32 0.80 102.40 97.08 B B B C3' C2' C1' DG DG DG 22 22 22 N 1 8.91 0.30 108.30 117.21 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 -10.16 0.90 116.20 106.04 B B B N1 C2 N2 DG DG DG 22 22 22 N 1 9.07 0.70 119.90 128.97 B B B N3 C2 N2 DG DG DG 22 22 22 N 1 12.54 1.50 119.60 132.14 B B B OP1 P OP2 DC DC DC 23 23 23 N 1 -5.72 0.90 105.70 99.98 B B B O5' P OP1 DC DC DC 23 23 23 N 1 11.59 1.40 114.30 125.89 B B B N1 C1' C2' DC DC DC 23 23 23 N 1 2.54 0.30 108.30 110.84 B B B O4' C1' N1 DC DC DC 23 23 23 N 1 -2.53 0.40 120.30 117.77 B B B C6 N1 C2 DC DC DC 23 23 23 N 1 5.14 0.50 121.00 126.14 B B B C5 C6 N1 DC DC DC 23 23 23 N 1 -5.43 0.70 118.00 112.57 B B B N3 C4 N4 DC DC DC 23 23 23 N 1 5.22 0.70 120.20 125.42 B B B C5 C4 N4 DC DC DC 23 23 23 N 1 8.93 1.20 120.80 129.73 B B B C6 N1 C1' DC DC DC 23 23 23 N 1 -6.94 1.10 118.80 111.86 B B B C2 N1 C1' DC DC DC 23 23 23 N 1 -14.34 1.50 119.60 105.26 B B B OP1 P OP2 DG DG DG 24 24 24 N 1 12.35 1.20 110.70 123.05 B B B O5' P OP2 DG DG DG 24 24 24 N 1 -4.28 0.40 104.50 100.22 B B B O4' C4' C3' DG DG DG 24 24 24 N 1 -5.53 0.70 102.20 96.67 B B B C4' C3' C2' DG DG DG 24 24 24 N 1 -5.02 0.80 102.40 97.38 B B B C3' C2' C1' DG DG DG 24 24 24 N 1 9.10 1.40 114.30 123.40 B B B N9 C1' C2' DG DG DG 24 24 24 N 1 -7.70 0.70 108.00 100.30 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 -4.18 0.60 125.10 120.92 B B B C6 N1 C2 DG DG DG 24 24 24 N 1 2.54 0.40 105.40 107.94 B B B N9 C4 C5 DG DG DG 24 24 24 N 1 A A P O5' DG DG 4 4 0.081 0.010 1.593 1.674 N 1 A A O3' P DG DA 4 5 0.109 0.012 1.607 1.716 Y 1 A A C4 C5 DA DA 6 6 -0.048 0.007 1.383 1.335 N 1 A A C5 N7 DA DA 6 6 0.037 0.006 1.388 1.425 N 1 A A O3' P DA DT 6 7 0.075 0.012 1.607 1.682 Y 1 A A O3' C3' DT DT 7 7 -0.036 0.006 1.419 1.383 N 1 A A C4 O4 DT DT 7 7 0.061 0.009 1.228 1.289 N 1 A A P OP1 DT DT 8 8 -0.149 0.017 1.485 1.336 N 1 A A P O5' DT DT 8 8 0.091 0.010 1.593 1.684 N 1 A A O4' C4' DT DT 8 8 -0.068 0.010 1.446 1.378 N 1 A A O3' C3' DT DT 8 8 -0.049 0.006 1.419 1.370 N 1 A A N3 C4 DT DT 8 8 -0.058 0.008 1.382 1.324 N 1 B B P O5' DG DG 14 14 0.084 0.010 1.593 1.677 N 1 B B C6 N1 DG DG 14 14 -0.052 0.007 1.391 1.339 N 1 B B C8 N9 DG DG 14 14 -0.046 0.007 1.374 1.328 N 1 B B N1 C2 DC DC 15 15 -0.067 0.010 1.397 1.330 N 1 B B O4' C4' DG DG 16 16 -0.062 0.010 1.446 1.384 N 1 B B C2' C1' DT DT 19 19 -0.063 0.010 1.518 1.455 N 1 B B C4 O4 DT DT 19 19 0.055 0.009 1.228 1.283 N 1 B B C6 N1 DT DT 20 20 -0.055 0.007 1.378 1.323 N 1 B B C4 O4 DT DT 20 20 0.058 0.009 1.228 1.286 N 1 B B P O5' DG DG 22 22 0.074 0.010 1.593 1.667 N 1 B B C5 N7 DG DG 22 22 0.046 0.006 1.388 1.434 N 0.2220000 2.400 10.000 2541 1 2.000 TR isotropic TR isotropic 2.400 10.000 25 532 21 486 0 fix fix 2.400 1D30 9292 2541 1 refinement NUCLSQ THE STRUCTURE OF DAPI BOUND TO DNA 1 N N 1 N N 2 N N 3 N N 3 N N 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 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 1D30 PDB 1 1D30 1 12 1D30 1 12 1D30 A 1 1 12 13 24 1D30 13 24 1D30 B 1 1 12 BINDING SITE FOR RESIDUE DAP A 25 A DAP 25 Software 10 A DA 6 A DA 6 10 1_555 A DT 7 A DT 7 10 1_555 A DT 8 A DT 8 10 1_555 A DC 9 A DC 9 10 1_555 A HOH 26 D HOH 10 1_555 B DA 17 B DA 5 10 1_555 B DA 18 B DA 6 10 1_555 B DT 19 B DT 7 10 1_555 B DT 20 B DT 8 10 1_555 B DC 21 B DC 9 10 1_555 19 P 21 21 21