0.055701 0.000000 0.000000 0.000000 0.032445 0.000000 0.000000 0.000000 0.022424 0.00000 0.00000 0.00000 Bharanidharan, D. Thiyagarajan, S. Gautham, N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 17.953 30.821 44.596 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 H18 N6 Ru 3 203.253 RUTHENIUM (III) HEXAAMINE ION HEXAAMINORUTHENIUM 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 N N 148 N RU N 149 N N N 150 N N N 151 N N N 152 N N N 153 N N 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 H N 169 N H N 170 N H N 171 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 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 DK Acta Crystallogr.,Sect.F 1744-3091 63 1008 1013 10.1107/S1744309107047781 18084080 Hexammineruthenium(III) ion interactions with Z-DNA 2007 10.2210/pdb2hto/pdb pdb_00002hto 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 293 1 IMAGE PLATE 2004-06-16 MARRESEARCH NIL SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU300 1794.206 DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DA)-3') 1 syn polymer 1825.216 DNA (5'-D(*DTP*DGP*DCP*DGP*DCP*DG)-3') 1 syn polymer 203.253 RUTHENIUM (III) HEXAAMINE ION 1 syn non-polymer 18.015 water 48 nat water no no (DC)(DG)(DC)(DG)(DC)(DA) CGCGCA A polydeoxyribonucleotide no no (DT)(DG)(DC)(DG)(DC)(DG) TGCGCG B polydeoxyribonucleotide n n n n n n n n n n n n 1 1.704421 51.73 VAPOR DIFFUSION, HANGING DROP 6.9 MPD, sodium cacodylate, ruthenium hexammine chloride, spermine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 MPD 1 sodium cacodylate 1 ruthenium hexammine chloride 1 spermine 1 H2O 1 MPD 2 sodium cacodylate 2 ruthenium hexammine chloride 2 H2O 2 1.948 1 19 A 1 B 12 -3.343 A_DC1:DG12_B 1 4.080 -1.774 0.093 -0.239 -2.646 1 19 A 2 B 11 -0.130 A_DG2:DC11_B 2 -2.327 0.234 0.262 -0.095 4.218 1 19 A 3 B 10 1.458 A_DC3:DG10_B 3 1.308 -0.212 0.185 -0.079 0.652 1 19 A 4 B 9 2.748 A_DG4:DC9_B 4 -1.113 0.274 0.077 -0.184 1.419 1 19 A 5 B 8 0.656 A_DC5:DG8_B 5 0.694 -0.156 0.253 -0.117 -4.277 A 6 B 7 5.896 A_DA6:DT7_B 6 6.985 2.014 0.178 -0.394 2.384 -5.161 A A 1 2 -5.722 B B 12 11 3.644 0.484 -0.204 5.204 AA_DC1DG2:DC11DG12_BB 1 -2.919 -34.522 -4.229 -61.235 -23.062 3.230 -51.359 A A 2 3 3.157 B B 11 10 3.287 -2.735 0.156 -1.070 AA_DG2DC3:DG10DC11_BB 2 0.050 0.057 -51.291 1.421 0.183 5.794 -8.927 A A 3 4 30.549 B B 10 9 3.634 -4.528 0.066 5.290 AA_DC3DG4:DC9DG10_BB 3 0.723 4.876 -7.661 -17.480 3.056 3.421 -50.493 A A 4 5 3.443 B B 9 8 3.484 -2.935 0.043 -1.051 AA_DG4DC5:DG8DC9_BB 4 -1.810 -2.123 -50.383 1.452 -0.085 -0.893 -4.257 A A 5 6 -34.949 B B 8 7 3.700 2.182 0.325 5.198 AA_DC5DA6:DT7DG8_BB 5 2.851 45.660 -2.288 -82.575 20.838 chem_comp_atom chem_comp_bond database_2 struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2006-08-08 1 1 2008-05-01 1 2 2011-07-13 1 3 2024-03-13 1 4 2024-04-03 _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 The same NA in other space group RCSB Y PDBJ 2006-07-26 REL REL NRU RUTHENIUM (III) HEXAAMINE ION HOH water 1XA2 NDB ENTRY ZD0013 PDB experimental model NRU 13 3 NRU NRU 13 A HOH 15 4 HOH HOH 15 A HOH 18 4 HOH HOH 18 A HOH 19 4 HOH HOH 19 A HOH 21 4 HOH HOH 21 A HOH 24 4 HOH HOH 24 A HOH 25 4 HOH HOH 25 A HOH 26 4 HOH HOH 26 A HOH 28 4 HOH HOH 28 A HOH 29 4 HOH HOH 29 A HOH 33 4 HOH HOH 33 A HOH 36 4 HOH HOH 36 A HOH 37 4 HOH HOH 37 A HOH 38 4 HOH HOH 38 A HOH 43 4 HOH HOH 43 A HOH 48 4 HOH HOH 48 A HOH 54 4 HOH HOH 54 A HOH 59 4 HOH HOH 59 A HOH 61 4 HOH HOH 61 A HOH 14 4 HOH HOH 14 B HOH 16 4 HOH HOH 16 B HOH 17 4 HOH HOH 17 B HOH 20 4 HOH HOH 20 B HOH 22 4 HOH HOH 22 B HOH 23 4 HOH HOH 23 B HOH 27 4 HOH HOH 27 B HOH 30 4 HOH HOH 30 B HOH 31 4 HOH HOH 31 B HOH 32 4 HOH HOH 32 B HOH 34 4 HOH HOH 34 B HOH 35 4 HOH HOH 35 B HOH 39 4 HOH HOH 39 B HOH 40 4 HOH HOH 40 B HOH 41 4 HOH HOH 41 B HOH 42 4 HOH HOH 42 B HOH 44 4 HOH HOH 44 B HOH 45 4 HOH HOH 45 B HOH 46 4 HOH HOH 46 B HOH 47 4 HOH HOH 47 B HOH 49 4 HOH HOH 49 B HOH 50 4 HOH HOH 50 B HOH 51 4 HOH HOH 51 B HOH 52 4 HOH HOH 52 B HOH 53 4 HOH HOH 53 B HOH 55 4 HOH HOH 55 B HOH 56 4 HOH HOH 56 B HOH 57 4 HOH HOH 57 B HOH 58 4 HOH HOH 58 B HOH 60 4 HOH HOH 60 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 C 5 n 5 DC 5 A A 6 n 6 DA 6 A T 7 n 1 DT 7 B G 8 n 2 DG 8 B C 9 n 3 DC 9 B G 10 n 4 DG 10 B C 11 n 5 DC 11 B G 12 n 6 DG 12 B author_and_software_defined_assembly PISA 2 dimeric 830 -5 2410 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 -3.00 0.40 120.30 117.30 A A A C6 N1 C2 DC DC DC 1 1 1 N 1 -4.92 0.70 119.20 114.28 A A A N1 C2 N3 DC DC DC 1 1 1 N 1 5.10 0.50 119.90 125.00 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -6.21 0.50 117.40 111.19 A A A C4 C5 C6 DC DC DC 1 1 1 N 1 7.70 0.50 121.00 128.70 A A A C5 C6 N1 DC DC DC 1 1 1 N 1 8.07 0.70 121.90 129.97 A A A N3 C2 O2 DC DC DC 1 1 1 N 1 -2.50 0.40 106.40 103.90 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 -3.78 0.50 111.50 107.72 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 4.30 0.60 119.90 124.20 A A A N1 C6 O6 DG DG DG 4 4 4 N 1 -8.33 0.90 105.70 97.37 A A A O5' P OP1 DC DC DC 5 5 5 B B N 1 8.54 1.20 110.70 119.24 A A A O5' P OP2 DC DC DC 5 5 5 B B N 1 3.44 0.50 121.00 124.44 A A A C5 C6 N1 DC DC DC 5 5 5 N 1 4.44 0.60 118.60 123.04 A A A C6 N1 C2 DA DA DA 6 6 6 N 1 -8.57 0.50 129.30 120.73 A A A N1 C2 N3 DA DA DA 6 6 6 N 1 6.93 0.50 110.60 117.53 A A A C2 N3 C4 DA DA DA 6 6 6 N 1 4.61 0.50 103.90 108.51 A A A C5 N7 C8 DA DA DA 6 6 6 N 1 -3.54 0.50 113.80 110.26 A A A N7 C8 N9 DA DA DA 6 6 6 N 1 -3.84 0.60 123.70 119.86 B B B C5 C6 N1 DT DT DT 7 7 7 N 1 -5.67 0.80 123.10 117.43 B B B N1 C2 O2 DT DT DT 7 7 7 N 1 -4.23 0.40 104.50 100.27 B B B O4' C4' C3' DG DG DG 8 8 8 N 1 5.74 0.90 103.10 108.84 B B B C4' C3' C2' DG DG DG 8 8 8 N 1 -4.32 0.70 108.00 103.68 B B B O4' C1' N9 DG DG DG 8 8 8 N 1 -3.12 0.50 104.30 101.18 B B B C5 N7 C8 DG DG DG 8 8 8 N 1 5.72 0.50 113.10 118.82 B B B N7 C8 N9 DG DG DG 8 8 8 N 1 -2.68 0.40 106.40 103.72 B B B C8 N9 C4 DG DG DG 8 8 8 N 1 -4.24 0.70 120.20 115.96 B B B C5 C4 N4 DC DC DC 9 9 9 N 1 -4.97 0.40 120.30 115.33 B B B C6 N1 C2 DC DC DC 11 11 11 N 1 4.92 0.50 119.90 124.82 B B B C2 N3 C4 DC DC DC 11 11 11 N 1 -3.48 0.40 121.90 118.42 B B B N3 C4 C5 DC DC DC 11 11 11 N 1 5.15 0.50 121.00 126.15 B B B C5 C6 N1 DC DC DC 11 11 11 N 1 5.25 0.70 118.00 123.25 B B B N3 C4 N4 DC DC DC 11 11 11 N 1 3.21 0.50 111.90 115.11 B B B C2 N3 C4 DG DG DG 12 12 12 N 1 4.80 0.50 111.50 116.30 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 -3.76 0.40 110.80 107.04 B B B C4 C5 N7 DG DG DG 12 12 12 N 1 4.61 0.50 104.30 108.91 B B B C5 N7 C8 DG DG DG 12 12 12 N 1 6.47 0.60 130.40 136.87 B B B C6 C5 N7 DG DG DG 12 12 12 N 1 -6.01 0.60 119.90 113.89 B B B N1 C6 O6 DG DG DG 12 12 12 N 1 A A C5' C4' DC DC 1 1 0.055 0.007 1.512 1.567 N 1 A A N9 C4 DG DG 2 2 0.066 0.008 1.375 1.441 N 1 A A C6 N1 DG DG 4 4 0.045 0.007 1.391 1.436 N 1 A A O3' C3' DA DA 6 6 0.095 0.013 1.435 1.530 N 1 A A N3 C4 DA DA 6 6 0.054 0.006 1.344 1.398 N 1 A A N9 C4 DA DA 6 6 0.077 0.006 1.374 1.451 N 1 B B C2' C1' DG DG 8 8 -0.061 0.010 1.518 1.457 N 1 B B C5 N7 DG DG 10 10 0.056 0.006 1.388 1.444 N 16.782 0.12 0.00 0.00 0.00 0.00 -0.11 0.957 0.958 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.2174 0.18923 0.19134 1.54 25.35 254 3530 3276 7.2 90.08 2.085 0.072 RANDOM 1 Isotropic THROUGHOUT MOLECULAR REPLACEMENT 0.120 0.109 0.80 0.80 1.40 NDB ENTRY ZD0013 MAXIMUM LIKELIHOOD MASK 1.54 25.35 48 307 7 252 0 0.028 0.021 290 3.251 3.000 457 0.148 0.200 50 0.021 0.020 125 0.211 0.200 96 0.306 0.200 157 0.216 0.200 15 0.106 0.200 13 0.316 0.200 12 2.308 3.000 419 2.942 4.500 450 0.392 0.292 1.586 16 193 20 76.00 1.54 30.0 2HTO 3590 3590 0.0 0.0 0.0526 1 4.7 5.04 90.8 0.3578 1.54 1.60 1.8 4.84 94.2 refinement REFMAC 5.2.0019 data reduction AUTOMAR phasing AMoRE Ruthenium hexammine ion interactions with Z-DNA 1 N N 2 N N 3 N N 4 N N 4 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 12 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 12 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 12 B N2 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 DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 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 DA-DT PAIR A DA 6 A N6 DA 6 1_555 B DT 7 B O4 DT 1 1_555 DNA Z-DNA, DOUBLE HELIX, DNA 2HTO PDB 1 2HTO 2HTO PDB 2 2HTO 1 6 2HTO 1 6 2HTO A 1 1 6 7 12 2HTO 7 12 2HTO B 2 1 6 BINDING SITE FOR RESIDUE NRU A 13 A NRU 13 Software 13 A DC 1 A DC 1 13 2_554 A DC 3 A DC 3 13 4_455 A DG 4 A DG 4 13 4_455 A DC 5 A DC 5 13 1_555 A DA 6 A DA 6 13 1_555 A HOH 21 D HOH 13 1_555 A HOH 25 D HOH 13 4_455 A HOH 59 D HOH 13 2_554 B DT 7 B DT 1 13 1_555 B DG 8 B DG 2 13 4_455 B DG 12 B DG 6 13 2_554 B HOH 34 E HOH 13 2_554 B HOH 58 E HOH 13 4_455 19 P 21 21 21