0.057000 0.000000 0.000000 0.000000 0.032774 0.000000 0.000000 0.000000 0.022619 0.00000 0.00000 0.00000 Mandal, P.K. Venkadesh, S. Vinayak, N. Gautham, N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 17.544 30.512 44.210 Ba 2 137.327 BARIUM 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 N 1 N BA 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 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 To be published 0353 Barium-DNA interactions 10.2210/pdb3fqb/pdb pdb_00003fqb 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 mirrors IMAGE PLATE 2008-09-17 MARRESEARCH mirrors SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE BRUKER AXS MICROSTAR 1794.206 5'-D(*CP*AP*CP*GP*CP*G)-3' 1 syn polymer 1825.216 5'-D(*CP*GP*CP*GP*TP*G)-3' 1 syn polymer 137.327 BARIUM ION 1 syn non-polymer 18.015 water 39 nat water no no (DC)(DA)(DC)(DG)(DC)(DG) CACGCG A polydeoxyribonucleotide no no (DC)(DG)(DC)(DG)(DT)(DG) CGCGTG B polydeoxyribonucleotide n n n n n n n n n n n n 1 1.63 24.75 VAPOR DIFFUSION, HANGING DROP 6.99 50mM Sodium cacoldylate, 10mM Barium chloride, 0.5mM Spermine, 30% (v/v) Methyl pentane diol , pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 Sodium cacoldylate 1 Barium chloride 1 Spermine 1 MPD 1 Sodium cacoldylate 2 Barium chloride 2 MPD 2 2.429 1 19 A 1 B 12 -0.919 A_DC1:DG12_B 1 -2.584 -0.321 -0.073 -0.070 -6.443 1 20 A 2 B 11 2.687 A_DA2:DT11_B 2 -4.232 0.040 0.207 -0.171 2.468 1 19 A 3 B 10 2.892 A_DC3:DG10_B 3 1.489 -0.208 0.111 -0.240 -7.852 1 19 A 4 B 9 4.793 A_DG4:DC9_B 4 -1.095 0.256 0.059 -0.136 6.098 1 19 A 5 B 8 2.263 A_DC5:DG8_B 5 -1.651 -0.413 0.248 -0.241 -5.472 1 19 A 6 B 7 3.549 A_DG6:DC7_B 6 4.933 0.348 -0.026 -0.259 4.844 -12.072 A A 1 2 13.995 B B 12 11 3.710 -2.901 -0.083 5.449 AA_DC1DA2:DT11DG12_BB 1 -1.954 -9.428 -11.556 -20.931 -3.750 3.116 -50.914 A A 2 3 3.925 B B 11 10 3.181 -3.372 0.202 -0.888 AA_DA2DC3:DG10DT11_BB 2 0.922 1.073 -50.802 1.259 0.296 5.549 -8.043 A A 3 4 24.439 B B 10 9 3.728 -3.318 0.044 5.269 AA_DC3DG4:DC9DG10_BB 3 -0.869 -6.399 -7.276 -23.259 -3.429 3.010 -52.873 A A 4 5 4.148 B B 9 8 3.079 -3.691 -0.079 -0.935 AA_DG4DC5:DG8DC9_BB 4 -1.185 -1.332 -52.741 1.272 -0.160 5.121 -6.405 A A 5 6 28.368 B B 8 7 3.764 -2.889 0.066 5.264 AA_DC5DG6:DC7DG8_BB 5 3.210 31.522 -4.731 -26.499 23.493 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Data collection Database references Derived calculations 1 0 2009-02-10 1 1 2011-07-13 1 2 2024-03-20 _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 RCSB Y PDBJ 2009-01-07 REL REL BA BARIUM ION HOH water BA 1 3 BA BA 7 A HOH 2 4 HOH HOH 8 A HOH 9 4 HOH HOH 9 A HOH 10 4 HOH HOH 10 A HOH 7 4 HOH HOH 11 A HOH 12 4 HOH HOH 12 A HOH 13 4 HOH HOH 13 A HOH 14 4 HOH HOH 14 A HOH 15 4 HOH HOH 15 A HOH 17 4 HOH HOH 17 A HOH 18 4 HOH HOH 18 A HOH 19 4 HOH HOH 19 A HOH 20 4 HOH HOH 20 A HOH 25 4 HOH HOH 25 A HOH 28 4 HOH HOH 28 A HOH 29 4 HOH HOH 29 A HOH 30 4 HOH HOH 30 A HOH 31 4 HOH HOH 31 A HOH 34 4 HOH HOH 34 A HOH 35 4 HOH HOH 35 A HOH 37 4 HOH HOH 37 A HOH 39 4 HOH HOH 39 A HOH 1 4 HOH HOH 1 B HOH 3 4 HOH HOH 3 B HOH 4 4 HOH HOH 4 B HOH 5 4 HOH HOH 5 B HOH 6 4 HOH HOH 6 B HOH 8 4 HOH HOH 14 B HOH 11 4 HOH HOH 15 B HOH 16 4 HOH HOH 16 B HOH 21 4 HOH HOH 21 B HOH 22 4 HOH HOH 22 B HOH 23 4 HOH HOH 23 B HOH 24 4 HOH HOH 24 B HOH 26 4 HOH HOH 26 B HOH 27 4 HOH HOH 27 B HOH 32 4 HOH HOH 32 B HOH 33 4 HOH HOH 33 B HOH 36 4 HOH HOH 36 B HOH 38 4 HOH HOH 38 B C 1 n 1 DC 1 A A 2 n 2 DA 2 A C 3 n 3 DC 3 A G 4 n 4 DG 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 C 9 n 3 DC 9 B G 10 n 4 DG 10 B T 11 n 5 DT 11 B G 12 n 6 DG 12 B author_and_software_defined_assembly PISA 2 dimeric 860 -13 2310 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 4.05 0.30 108.30 112.35 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.59 0.50 106.80 110.39 A A A O4' C1' C2' DA DA DA 2 2 2 N 1 -3.32 0.50 129.30 125.98 A A A N1 C2 N3 DA DA DA 2 2 2 N 1 7.77 1.20 119.70 127.47 A A A C3' O3' P DA DA DC 2 2 3 A Y 1 -5.71 0.70 108.00 102.29 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 7.79 1.20 110.70 118.49 A A A O5' P OP2 DC DC DC 5 5 5 N 1 3.18 0.30 108.30 111.48 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 1.84 0.30 108.30 110.14 B B B O4' C1' N1 DC DC DC 7 7 7 N 1 3.50 0.50 106.80 110.30 B B B O4' C1' C2' DG DG DG 8 8 8 N 1 2.45 0.30 108.30 110.75 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 -6.09 0.70 108.00 101.91 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 2.51 0.40 110.80 113.31 B B B C4 C5 N7 DG DG DG 10 10 10 N 1 2.35 0.30 108.30 110.65 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 -5.89 0.70 108.00 102.11 B B B O4' C1' N9 DG DG DG 12 12 12 N 16.177 -0.05 0.00 0.00 0.05 0.00 0.00 0.942 0.950 0.22312 0.21689 0.21730 1.67 13.74 145 2427 2427 5.6 86.05 2.983 0.091 RANDOM 1 ISOTROPIC THROUGHOUT MOLECULAR REPLACEMENT 0.187 0.139 0.80 0.80 1.40 MAXIMUM LIKELIHOOD MASK 0.224 1.67 13.74 39 290 2 249 0 0.016 0.021 280 2.247 3.000 434 0.094 0.200 49 0.011 0.020 125 0.212 0.200 112 0.274 0.200 163 0.257 0.200 18 0.400 0.200 3 0.167 0.200 20 0.214 0.200 3 1.925 3.000 309 2.583 4.500 431 0.245 0.320 1.716 12 183 12 20 94.20 26.6 1.67 30 3FQB 3037 2791 0.0882 0.0635 1 6.1 4.54 91.9 0.2711 1.67 1.73 1.7 183 0.2330 4.37 89.6 data collection MAR345dtb phasing PHASER refinement REFMAC 5.2.0019 data reduction AUTOMAR data scaling SCALEPACK N Barium 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 DA 2 A N1 DA 2 1_555 B DT 11 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 11 B O4 DT 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 WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 7 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 7 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 7 B N4 DC 1 1_555 DNA Z-DNA Double Helix, DNA 3FQB PDB 1 3FQB 3FQB PDB 2 3FQB 1 6 3FQB 1 6 3FQB A 1 1 6 7 12 3FQB 7 12 3FQB B 2 1 6 BINDING SITE FOR RESIDUE BA A 7 A BA 7 Software 4 A DC 3 A DC 3 4 1_555 A DG 4 A DG 4 4 1_555 A DG 6 A DG 6 4 4_455 A HOH 30 D HOH 4 1_555 19 P 21 21 21