0.039246 0.000000 0.000000 0.000000 0.024237 0.000000 0.000000 0.000000 0.014952 0.00000 0.00000 0.00000 Coll, M. Aymami, J. Van Der Marel, G.A. Van Boom, J.H. Rich, A. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.480 41.260 66.880 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 C18 H26 N10 O3 430.464 NETROPSIN 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 N 92 N N Y 93 N C 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 H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H 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 H N 146 N H N 147 N C N 148 N N N 149 N N N 150 N N N 151 N C N 152 N C N 153 N O N 154 N N Y 155 N C Y 156 N C Y 157 N C Y 158 N N N 159 N C Y 160 N C N 161 N C N 162 N O N 163 N N Y 164 N C Y 165 N C Y 166 N C Y 167 N N N 168 N C Y 169 N C N 170 N C N 171 N O N 172 N N N 173 N C N 174 N C N 175 N C N 176 N N N 177 N N 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 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 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 doub N 153 N sing 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 doub N 164 N sing N 165 N sing N 166 N sing Y 167 N sing Y 168 N doub Y 169 N doub N 170 N sing Y 171 N sing N 172 N sing N 173 N sing Y 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N sing Y 183 N sing Y 184 N doub Y 185 N doub N 186 N sing Y 187 N sing N 188 N sing N 189 N sing Y 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N doub N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N sing US Biochemistry BICHAW 0033 0006-2960 28 310 320 10.1021/bi00427a042 2539859 Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. 1989 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 84 8385 8389 A Bifurcated Hydrogen-Bonded Conformation in the d(A.T) Base Pairs of the DNA Dodecamer d(CGCAAATTTGCG) and Its Complex with Distamycin 1987 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 82 1376 1380 The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin 1985 10.2210/pdb1dne/pdb pdb_00001dne 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 283.00 1 DIFFRACTOMETER NICOLET P3 x-ray 1 1.0 3663.392 DNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3') 2 syn polymer 430.464 NETROPSIN 1 syn non-polymer 18.015 water 60 nat water no no (DC)(DG)(DC)(DG)(DA)(DT)(DA)(DT)(DC)(DG)(DC)(DG) CGCGATATCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 2.40 48.73 VAPOR DIFFUSION 6.50 pH 6.50, VAPOR DIFFUSION, temperature 283.00K 283.00 ROOM TEMPERATURE WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE 1 WATER 2 MPD 2 5.314 1 19 A 1 B 24 -3.558 A_DC1:DG24_B 1 -5.149 0.102 0.197 -0.122 1.377 1 19 A 2 B 23 -6.101 A_DG2:DC23_B 2 -14.686 -0.122 -0.044 -0.471 -11.269 1 19 A 3 B 22 -2.685 A_DC3:DG22_B 3 -6.554 -0.273 0.706 -0.245 13.600 1 19 A 4 B 21 -2.103 A_DG4:DC21_B 4 -9.302 0.506 0.177 -0.409 1.227 1 20 A 5 B 20 2.705 A_DA5:DT20_B 5 -1.432 0.055 -0.125 -0.055 10.130 1 20 A 6 B 19 -0.786 A_DT6:DA19_B 6 -11.874 -0.383 -0.327 -0.353 -4.723 1 20 A 7 B 18 -2.367 A_DA7:DT18_B 7 -17.006 0.245 -0.139 -0.278 2.647 1 20 A 8 B 17 -5.199 A_DT8:DA17_B 8 -6.747 0.024 0.245 -0.163 -8.861 1 19 A 9 B 16 -3.823 A_DC9:DG16_B 9 -11.658 0.312 0.421 -0.350 7.974 1 19 A 10 B 15 -3.660 A_DG10:DC15_B 10 -11.125 0.537 0.268 -0.172 -11.679 1 19 A 11 B 14 -6.025 A_DC11:DG14_B 11 -15.428 0.439 1.135 -0.607 -5.120 1 19 A 12 B 13 3.086 A_DG12:DC13_B 12 -1.501 0.363 0.176 -0.122 3.566 42.518 A A 1 2 18.335 B B 24 23 3.468 13.099 -1.220 0.881 AA_DC1DG2:DC23DG24_BB 1 0.277 -0.388 40.538 -0.249 1.713 3.728 32.189 A A 2 3 -15.187 B B 23 22 3.777 -8.226 0.169 -1.025 AA_DG2DC3:DG22DC23_BB 2 -8.768 16.188 29.915 -0.099 -2.171 2.847 37.082 A A 3 4 9.745 B B 22 21 2.878 6.158 -0.827 0.709 AA_DC3DG4:DC21DG22_BB 3 4.206 -6.656 36.350 0.385 1.799 3.670 32.408 A A 4 5 3.285 B B 21 20 3.729 1.832 0.677 -0.657 AA_DG4DA5:DT20DC21_BB 4 -0.794 1.423 32.348 -1.541 -1.372 3.009 30.572 A A 5 6 -3.222 B B 20 19 3.056 -1.698 -0.450 0.491 AA_DA5DT6:DA19DT20_BB 5 1.027 -1.949 30.509 1.244 1.042 3.611 45.796 A A 6 7 -2.937 B B 19 18 3.600 -2.284 0.311 -0.081 AA_DT6DA7:DT18DA19_BB 6 2.674 -3.439 45.668 0.115 -0.143 2.955 26.267 A A 7 8 12.971 B B 18 17 3.180 5.831 -0.276 -0.720 AA_DA7DT8:DA17DT18_BB 7 -3.325 7.397 25.409 -3.082 -0.247 3.560 43.053 A A 8 9 -4.913 B B 17 16 3.566 -3.601 0.022 -0.059 AA_DT8DC9:DG16DA17_BB 8 0.296 -0.404 42.908 0.308 0.001 3.123 38.865 A A 9 10 1.813 B B 16 15 3.086 1.206 0.247 1.059 AA_DC9DG10:DC15DG16_BB 9 1.272 -1.913 38.827 1.452 -0.224 3.941 30.778 A A 10 11 -16.760 B B 15 14 3.965 -8.667 -0.988 -0.056 AA_DG10DC11:DG14DC15_BB 10 -8.399 16.241 28.366 2.032 -0.208 3.257 47.773 A A 11 12 -2.472 B B 14 13 3.267 -2.000 0.425 0.789 AA_DC11DG12:DC13DG14_BB 11 4.045 -5.001 47.572 1.133 -0.203 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 1989-01-09 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 BNL 1988-09-14 REL NT NETROPSIN HOH water NT 25 2 NT NT 25 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 33 3 HOH HOH 33 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 40 3 HOH HOH 40 A HOH 42 3 HOH HOH 42 A HOH 45 3 HOH HOH 45 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 A HOH 49 3 HOH HOH 49 A HOH 50 3 HOH HOH 50 A HOH 52 3 HOH HOH 52 A HOH 53 3 HOH HOH 53 A HOH 57 3 HOH HOH 57 A HOH 60 3 HOH HOH 60 A HOH 61 3 HOH HOH 61 A HOH 62 3 HOH HOH 62 A HOH 63 3 HOH HOH 63 A HOH 65 3 HOH HOH 65 A HOH 66 3 HOH HOH 66 A HOH 69 3 HOH HOH 69 A HOH 77 3 HOH HOH 77 A HOH 82 3 HOH HOH 82 A HOH 83 3 HOH HOH 83 A HOH 85 3 HOH HOH 85 A HOH 26 3 HOH HOH 26 B HOH 27 3 HOH HOH 27 B HOH 28 3 HOH HOH 28 B HOH 31 3 HOH HOH 31 B HOH 32 3 HOH HOH 32 B HOH 34 3 HOH HOH 34 B HOH 35 3 HOH HOH 35 B HOH 38 3 HOH HOH 38 B HOH 39 3 HOH HOH 39 B HOH 41 3 HOH HOH 41 B HOH 43 3 HOH HOH 43 B HOH 44 3 HOH HOH 44 B HOH 51 3 HOH HOH 51 B HOH 54 3 HOH HOH 54 B HOH 55 3 HOH HOH 55 B HOH 56 3 HOH HOH 56 B HOH 58 3 HOH HOH 58 B HOH 59 3 HOH HOH 59 B HOH 64 3 HOH HOH 64 B HOH 67 3 HOH HOH 67 B HOH 68 3 HOH HOH 68 B HOH 70 3 HOH HOH 70 B HOH 71 3 HOH HOH 71 B HOH 72 3 HOH HOH 72 B HOH 73 3 HOH HOH 73 B HOH 74 3 HOH HOH 74 B HOH 75 3 HOH HOH 75 B HOH 76 3 HOH HOH 76 B HOH 78 3 HOH HOH 78 B HOH 79 3 HOH HOH 79 B HOH 80 3 HOH HOH 80 B HOH 81 3 HOH HOH 81 B HOH 84 3 HOH HOH 84 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 T 6 n 6 DT 6 A A 7 n 7 DA 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 T 18 n 6 DT 18 B A 19 n 7 DA 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 A DG 2 0.050 SIDE CHAIN 1 A A O3' P DC DG 11 12 1.77 1 9.93 1.20 119.70 129.63 A A A C3' O3' P DC DC DG 1 1 2 Y 1 -14.70 1.50 119.60 104.90 A A A OP1 P OP2 DG DG DG 2 2 2 N 1 12.25 0.30 108.30 120.55 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 3.87 0.60 123.90 127.77 A A A N1 C2 N3 DG DG DG 2 2 2 N 1 8.17 0.60 119.90 128.07 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 -9.78 0.60 128.60 118.82 A A A C5 C6 O6 DG DG DG 2 2 2 N 1 8.13 1.20 119.70 127.83 A A A C3' O3' P DG DG DC 2 2 3 Y 1 12.14 1.90 104.00 116.14 A A A O3' P O5' DG DC DC 2 3 3 Y 1 -15.20 1.50 119.60 104.40 A A A OP1 P OP2 DC DC DC 3 3 3 N 1 -11.84 1.60 120.90 109.06 A A A P O5' C5' DC DC DC 3 3 3 N 1 -3.46 0.40 104.50 101.04 A A A O4' C4' C3' DC DC DC 3 3 3 N 1 -8.05 1.00 110.10 102.05 A A A C1' O4' C4' DC DC DC 3 3 3 N 1 -7.83 0.70 108.00 100.17 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 4.40 0.70 121.90 126.30 A A A N3 C2 O2 DC DC DC 3 3 3 N 1 -8.91 1.20 119.70 110.79 A A A C3' O3' P DC DC DG 3 3 4 Y 1 -16.06 1.50 119.60 103.54 A A A OP1 P OP2 DG DG DG 4 4 4 N 1 13.43 1.60 120.90 134.33 A A A P O5' C5' DG DG DG 4 4 4 N 1 -6.77 0.40 104.50 97.73 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 -7.29 1.00 110.10 102.81 A A A C1' O4' C4' DG DG DG 4 4 4 N 1 7.12 0.30 108.30 115.42 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -3.99 0.60 128.60 124.61 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 8.05 0.30 108.30 116.35 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 18.80 1.20 119.70 138.50 A A A C3' O3' P DA DA DT 5 5 6 Y 1 12.77 1.10 110.50 123.27 A A A O3' P OP1 DA DT DT 5 6 6 Y 1 -13.92 1.50 119.60 105.68 A A A OP1 P OP2 DT DT DT 6 6 6 N 1 -6.09 0.90 105.70 99.61 A A A O5' P OP1 DT DT DT 6 6 6 N 1 -11.05 1.60 120.90 109.85 A A A P O5' C5' DT DT DT 6 6 6 N 1 -4.31 0.40 104.50 100.19 A A A O4' C4' C3' DT DT DT 6 6 6 N 1 -5.85 0.70 102.20 96.35 A A A C4' C3' C2' DT DT DT 6 6 6 N 1 -5.67 0.80 123.10 117.43 A A A N1 C2 O2 DT DT DT 6 6 6 N 1 11.08 1.20 119.70 130.78 A A A C3' O3' P DT DT DA 6 6 7 Y 1 -13.03 1.50 119.60 106.57 A A A OP1 P OP2 DA DA DA 7 7 7 N 1 12.73 1.20 110.70 123.43 A A A O5' P OP2 DA DA DA 7 7 7 N 1 -7.62 0.80 109.40 101.78 A A A O5' C5' C4' DA DA DA 7 7 7 N 1 -4.45 0.70 102.20 97.75 A A A C4' C3' C2' DA DA DA 7 7 7 N 1 -9.47 0.80 102.40 92.93 A A A C3' C2' C1' DA DA DA 7 7 7 N 1 -6.81 0.80 105.90 99.09 A A A O4' C1' C2' DA DA DA 7 7 7 N 1 9.01 0.30 108.30 117.31 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 4.28 0.60 118.60 122.88 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 -13.12 1.90 104.00 90.88 A A A O3' P O5' DA DT DT 7 8 8 Y 1 -5.10 0.80 109.40 104.30 A A A O5' C5' C4' DT DT DT 8 8 8 N 1 -14.87 1.60 120.90 106.03 A A A P O5' C5' DT DT DT 8 8 8 N 1 4.76 0.30 108.30 113.06 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 4.48 0.60 114.60 119.08 A A A N1 C2 N3 DT DT DT 8 8 8 N 1 -5.87 0.60 127.20 121.33 A A A C2 N3 C4 DT DT DT 8 8 8 N 1 3.84 0.60 115.20 119.04 A A A N3 C4 C5 DT DT DT 8 8 8 N 1 14.32 1.20 119.70 134.02 A A A C3' O3' P DT DT DC 8 8 9 Y 1 8.47 1.20 110.70 119.17 A A A O5' P OP2 DC DC DC 9 9 9 N 1 -13.81 1.60 120.90 107.09 A A A P O5' C5' DC DC DC 9 9 9 N 1 -3.67 0.40 104.50 100.83 A A A O4' C4' C3' DC DC DC 9 9 9 N 1 -5.23 0.70 102.20 96.97 A A A C4' C3' C2' DC DC DC 9 9 9 N 1 -9.72 0.80 102.40 92.68 A A A C3' C2' C1' DC DC DC 9 9 9 N 1 4.47 0.30 108.30 112.77 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 4.84 0.70 121.90 126.74 A A A N3 C2 O2 DC DC DC 9 9 9 N 1 -6.69 1.10 118.80 112.11 A A A C2 N1 C1' DC DC DC 9 9 9 N 1 13.56 1.10 110.50 124.06 A A A O3' P OP1 DC DG DG 9 10 10 Y 1 -7.14 0.80 109.40 102.26 A A A O5' C5' C4' DG DG DG 10 10 10 N 1 -16.26 1.60 120.90 104.64 A A A P O5' C5' DG DG DG 10 10 10 N 1 14.29 0.30 108.30 122.59 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 -3.66 0.60 125.10 121.44 A A A C6 N1 C2 DG DG DG 10 10 10 N 1 5.07 0.50 111.50 116.57 A A A C5 C6 N1 DG DG DG 10 10 10 N 1 -5.54 0.80 109.40 103.86 A A A O5' C5' C4' DC DC DC 11 11 11 N 1 -13.43 1.60 120.90 107.47 A A A P O5' C5' DC DC DC 11 11 11 N 1 -2.79 0.40 104.50 101.71 A A A O4' C4' C3' DC DC DC 11 11 11 N 1 -10.21 1.00 110.10 99.89 A A A C1' O4' C4' DC DC DC 11 11 11 N 1 3.81 0.40 120.30 124.11 A A A C6 N1 C2 DC DC DC 11 11 11 N 1 -4.78 0.70 119.20 114.42 A A A N1 C2 N3 DC DC DC 11 11 11 N 1 4.32 0.50 119.90 124.22 A A A C2 N3 C4 DC DC DC 11 11 11 N 1 -4.13 0.60 118.90 114.77 A A A N1 C2 O2 DC DC DC 11 11 11 N 1 8.80 0.70 121.90 130.70 A A A N3 C2 O2 DC DC DC 11 11 11 N 1 4.31 0.70 118.00 122.31 A A A N3 C4 N4 DC DC DC 11 11 11 N 1 -17.31 1.20 119.70 102.39 A A A C3' O3' P DC DC DG 11 11 12 Y 1 15.70 1.20 110.70 126.40 A A A O5' P OP2 DG DG DG 12 12 12 N 1 2.35 0.30 108.30 110.65 A A A O4' C1' N9 DG DG DG 12 12 12 N 1 -4.82 0.60 125.10 120.28 A A A C6 N1 C2 DG DG DG 12 12 12 N 1 3.66 0.60 123.90 127.56 A A A N1 C2 N3 DG DG DG 12 12 12 N 1 3.60 0.50 111.50 115.10 A A A C5 C6 N1 DG DG DG 12 12 12 N 1 -4.90 0.70 119.90 115.00 A A A N3 C2 N2 DG DG DG 12 12 12 N 1 -8.18 0.80 109.40 101.22 B B B O5' C5' C4' DC DC DC 13 13 13 N 1 3.80 0.60 118.90 122.70 B B B N1 C2 O2 DC DC DC 13 13 13 N 1 -10.88 1.20 119.70 108.82 B B B C3' O3' P DC DC DG 13 13 14 Y 1 -4.32 0.60 125.10 120.78 B B B C6 N1 C2 DG DG DG 14 14 14 N 1 4.49 0.60 119.90 124.39 B B B N1 C6 O6 DG DG DG 14 14 14 N 1 -7.24 0.60 128.60 121.36 B B B C5 C6 O6 DG DG DG 14 14 14 N 1 -10.61 1.20 119.70 109.09 B B B C3' O3' P DG DG DC 14 14 15 Y 1 -10.07 1.50 119.60 109.53 B B B OP1 P OP2 DC DC DC 15 15 15 N 1 9.38 1.20 110.70 120.08 B B B O5' P OP2 DC DC DC 15 15 15 N 1 -7.11 1.00 110.10 102.99 B B B C1' O4' C4' DC DC DC 15 15 15 N 1 -7.29 0.80 105.90 98.61 B B B O4' C1' C2' DC DC DC 15 15 15 N 1 11.90 0.30 108.30 120.20 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 -19.11 1.50 119.60 100.49 B B B OP1 P OP2 DG DG DG 16 16 16 N 1 20.58 1.20 110.70 131.28 B B B O5' P OP2 DG DG DG 16 16 16 N 1 -6.42 0.80 109.40 102.98 B B B O5' C5' C4' DG DG DG 16 16 16 N 1 4.59 0.60 119.90 124.49 B B B N1 C6 O6 DG DG DG 16 16 16 N 1 -6.77 0.60 128.60 121.83 B B B C5 C6 O6 DG DG DG 16 16 16 N 1 -7.60 1.20 119.70 112.10 B B B C3' O3' P DG DG DA 16 16 17 Y 1 7.01 1.10 110.50 117.51 B B B O3' P OP1 DG DA DA 16 17 17 Y 1 -17.49 1.60 120.90 103.41 B B B P O5' C5' DA DA DA 17 17 17 N 1 3.84 0.30 108.30 112.14 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 3.74 0.60 118.60 122.34 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 -12.16 1.20 119.70 107.54 B B B C3' O3' P DA DA DT 17 17 18 Y 1 -11.61 1.90 104.00 92.39 B B B O3' P O5' DA DT DT 17 18 18 Y 1 11.16 1.20 110.70 121.86 B B B O5' P OP2 DT DT DT 18 18 18 N 1 -6.60 0.40 104.50 97.90 B B B O4' C4' C3' DT DT DT 18 18 18 N 1 -4.67 0.70 102.20 97.53 B B B C4' C3' C2' DT DT DT 18 18 18 N 1 2.06 0.30 108.30 110.36 B B B O4' C1' N1 DT DT DT 18 18 18 N 1 -3.02 0.50 121.30 118.28 B B B C6 N1 C2 DT DT DT 18 18 18 N 1 5.43 0.60 114.60 120.03 B B B N1 C2 N3 DT DT DT 18 18 18 N 1 -5.52 0.60 127.20 121.68 B B B C2 N3 C4 DT DT DT 18 18 18 N 1 -4.33 0.60 119.00 114.67 B B B C4 C5 C7 DT DT DT 18 18 18 N 1 9.05 1.10 110.50 119.55 B B B O3' P OP1 DT DA DA 18 19 19 Y 1 -13.31 1.50 119.60 106.29 B B B OP1 P OP2 DA DA DA 19 19 19 N 1 12.22 1.20 110.70 122.92 B B B O5' P OP2 DA DA DA 19 19 19 N 1 14.29 1.40 114.30 128.59 B B B N9 C1' C2' DA DA DA 19 19 19 N 1 -12.52 0.70 108.00 95.48 B B B O4' C1' N9 DA DA DA 19 19 19 N 1 3.81 0.60 118.60 122.41 B B B N1 C6 N6 DA DA DA 19 19 19 N 1 9.15 1.20 110.70 119.85 B B B O5' P OP1 DT DT DT 20 20 20 N 1 -5.88 0.40 104.50 98.62 B B B O4' C4' C3' DT DT DT 20 20 20 N 1 -5.91 0.80 102.40 96.49 B B B C3' C2' C1' DT DT DT 20 20 20 N 1 5.42 0.30 108.30 113.72 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 -3.70 0.60 127.20 123.50 B B B C2 N3 C4 DT DT DT 20 20 20 N 1 -12.51 1.90 104.00 91.49 B B B O3' P O5' DT DC DC 20 21 21 Y 1 9.93 1.20 110.70 120.63 B B B O5' P OP2 DC DC DC 21 21 21 N 1 -10.08 0.80 109.40 99.32 B B B O5' C5' C4' DC DC DC 21 21 21 N 1 -22.33 1.60 120.90 98.57 B B B P O5' C5' DC DC DC 21 21 21 N 1 7.66 0.30 108.30 115.96 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 4.55 0.70 118.00 122.55 B B B N3 C4 N4 DC DC DC 21 21 21 N 1 6.67 1.10 110.50 117.17 B B B O3' P OP2 DC DG DG 21 22 22 Y 1 -14.08 1.60 120.90 106.82 B B B P O5' C5' DG DG DG 22 22 22 N 1 -8.79 0.80 102.40 93.61 B B B C3' C2' C1' DG DG DG 22 22 22 N 1 5.98 0.30 108.30 114.28 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 -8.71 1.20 119.70 110.99 B B B C3' O3' P DG DG DC 22 22 23 Y 1 -7.68 0.40 104.50 96.82 B B B O4' C4' C3' DC DC DC 23 23 23 N 1 -11.98 1.00 110.10 98.12 B B B C1' O4' C4' DC DC DC 23 23 23 N 1 4.61 0.70 118.00 122.61 B B B N3 C4 N4 DC DC DC 23 23 23 N 1 -9.64 1.50 119.60 109.96 B B B OP1 P OP2 DG DG DG 24 24 24 N 1 -2.41 0.40 104.50 102.09 B B B O4' C4' C3' DG DG DG 24 24 24 N 1 -9.72 1.00 110.10 100.38 B B B C1' O4' C4' DG DG DG 24 24 24 N 1 -4.04 0.60 128.60 124.56 B B B C5 C6 O6 DG DG DG 24 24 24 N 1 A A N3 C4 DC DC 1 1 0.063 0.007 1.335 1.398 N 1 A A P OP2 DG DG 2 2 0.110 0.017 1.485 1.595 N 1 A A P O5' DG DG 2 2 -0.093 0.010 1.593 1.500 N 1 A A C2' C1' DG DG 2 2 0.072 0.010 1.519 1.591 N 1 A A P O5' DC DC 3 3 -0.070 0.010 1.593 1.523 N 1 A A C2' C1' DC DC 3 3 -0.060 0.010 1.518 1.458 N 1 A A O4' C1' DC DC 3 3 0.092 0.011 1.420 1.512 N 1 A A P OP2 DG DG 4 4 0.155 0.017 1.485 1.640 N 1 A A P O5' DG DG 4 4 -0.091 0.010 1.593 1.502 N 1 A A O3' P DA DT 5 6 -0.137 0.012 1.607 1.470 Y 1 A A P O5' DT DT 6 6 0.099 0.010 1.593 1.692 N 1 A A P O5' DT DT 8 8 0.128 0.010 1.593 1.721 N 1 A A P OP1 DC DC 9 9 0.121 0.017 1.485 1.606 N 1 A A P OP2 DG DG 10 10 0.112 0.017 1.485 1.597 N 1 A A P O5' DG DG 10 10 0.106 0.010 1.593 1.699 N 1 A A O3' P DC DG 11 12 0.160 0.012 1.607 1.767 Y 1 B B O3' P DC DG 13 14 0.092 0.012 1.607 1.699 Y 1 B B P OP1 DG DG 16 16 0.145 0.017 1.485 1.630 N 1 B B P O5' DG DG 16 16 -0.151 0.010 1.593 1.442 N 1 B B O4' C1' DG DG 16 16 0.095 0.011 1.420 1.515 N 1 B B O3' P DA DT 17 18 0.093 0.012 1.607 1.700 Y 1 B B C2' C1' DA DA 19 19 -0.089 0.010 1.518 1.429 N 1 B B O4' C1' DA DA 19 19 0.091 0.011 1.420 1.511 N 1 B B N9 C4 DA DA 19 19 -0.048 0.006 1.374 1.326 N 1 B B P O5' DC DC 21 21 0.091 0.010 1.593 1.684 N 1 B B O5' C5' DC DC 21 21 0.125 0.016 1.440 1.565 N 1 B B P OP1 DG DG 22 22 0.136 0.017 1.485 1.621 N 1 B B P OP2 DG DG 22 22 -0.109 0.017 1.485 1.376 N 1 B B P O5' DG DG 22 22 0.084 0.010 1.593 1.677 N 1 B B P OP1 DG DG 24 24 0.108 0.017 1.485 1.593 N 1 B B O4' C1' DG DG 24 24 0.090 0.011 1.420 1.510 N 1 A B O3' N2 DG DG 12 22 1.77 1_555 2_664 0.2010000 2.400 20.000 1848 1 2.000 TR isotropic TR isotropic 2.400 20.000 60 577 31 486 0 fix fix 2.400 1DNE 5696 1848 1.000 1 refinement NUCLSQ MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2 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 DT 6 A N3 DT 6 1_555 B DA 19 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 19 B N6 DA 7 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 18 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 18 B O4 DT 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 1DNE PDB 1 1DNE 1 12 1DNE 1 12 1DNE A 1 1 12 13 24 1DNE 13 24 1DNE B 1 1 12 BINDING SITE FOR RESIDUE NT A 25 A NT 25 Software 12 A DG 4 A DG 4 12 1_555 A DA 5 A DA 5 12 1_555 A DT 6 A DT 6 12 1_555 A DA 7 A DA 7 12 1_555 A DT 8 A DT 8 12 1_555 A DC 9 A DC 9 12 1_555 B DA 17 B DA 5 12 1_555 B DT 18 B DT 6 12 1_555 B DA 19 B DA 7 12 1_555 B DT 20 B DT 8 12 1_555 B DC 21 B DC 9 12 1_555 B DG 22 B DG 10 12 1_555 19 P 21 21 21