0.055081 0.000000 0.000000 0.000000 0.033296 0.000000 0.000000 0.000000 0.023816 0.000000 0.000000 0.000000 Schuerman, G. Van Hecke, K. Van Meervelt, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 18.155 30.034 41.988 C9 H12 I N2 O8 P 434.078 n 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE DNA linking 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 H2 O 18.015 WATER non-polymer Co H18 N6 3 161.116 COBALT HEXAMMINE(III) non-polymer N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N O N 8 N O N 9 N I N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O N 22 N H 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 O N 35 N P N 36 N O N 37 N O N 38 N O N 39 N C N 40 R C N 41 N O N 42 S C N 43 N O N 44 N C N 45 R C Y 46 N N Y 47 N C Y 48 N N Y 49 N C Y 50 N C N 51 N N Y 52 N N Y 53 N C Y 54 N N Y 55 N C N 56 N H 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 O N 71 N P N 72 N O N 73 N O N 74 N O N 75 N C N 76 R C N 77 N O N 78 S C N 79 N O N 80 N C N 81 R C N 82 N N N 83 N C N 84 N O N 85 N N N 86 N C N 87 N N N 88 N C N 89 N C N 90 N H N 91 N H N 92 N H 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 O N 105 N P N 106 N O N 107 N O N 108 N O N 109 N C N 110 R C N 111 N O N 112 S C N 113 N O N 114 N C N 115 R C Y 116 N N Y 117 N C Y 118 N N Y 119 N C N 120 N C N 121 N O N 122 N N N 123 N C N 124 N N N 125 N N Y 126 N C N 127 N H N 128 N H 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 O N 142 N H N 143 N H N 144 N CO N 145 N N N 146 N N N 147 N N N 148 N N N 149 N N N 150 N N N 151 N H N 152 N H N 153 N H 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 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N sing N 9 N doub N 10 N doub 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 N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub 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 doub 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 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 Y 58 N sing Y 59 N sing Y 60 N doub N 61 N sing Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N doub N 67 N sing N 68 N sing Y 69 N sing Y 70 N doub N 71 N sing Y 72 N sing N 73 N sing N 74 N sing N 75 N doub N 76 N sing 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 N 97 N sing N 98 N doub N 99 N sing N 100 N doub N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing 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 Y 131 N sing Y 132 N sing Y 133 N doub N 134 N sing Y 135 N sing N 136 N sing Y 137 N doub N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N doub N 144 N sing N 145 N sing 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 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 59 1525 1528 10.1107/S0907444903012381 12876373 Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G]. 2003 10.2210/pdb1omk/pdb pdb_00001omk 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 120.0 1 IMAGE PLATE 1998-05-05 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.000 1.0 X11 EMBL/DESY, HAMBURG 1.000 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 1921.087 5'-D(*CP*AP*CP*GP*(5IU)P*G)-3' 2 syn polymer 161.116 COBALT HEXAMMINE(III) 2 syn non-polymer 18.015 water 43 nat water no yes (DC)(DA)(DC)(DG)(5IU)(DG) CACGUG A,B polydeoxyribonucleotide n n n n n n 1 1.49 17.43 VAPOR DIFFUSION, HANGING DROP 5.5 potassium cacodylate, MPD, magnesium chloride, potassium chloride, cobalt hexamine , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K 290.0 potassium cacodylate 1 MPD 1 magnesium chloride 1 potassium chloride 1 cobalt hexamine 1 MPD 2 potassium cacodylate 2 magnesium chloride 2 potassium chloride 2 7.594 1 19 A 1 B 12 0.421 A_DC1:DG12_B 1 8.691 -0.241 0.334 -0.135 -8.547 1 20 A 2 B 11 -1.784 A_DA2:5IU11_B 2 2.578 0.342 0.147 -0.289 1.492 1 19 A 3 B 10 1.479 A_DC3:DG10_B 3 2.474 -0.290 0.214 -0.191 -4.181 1 19 A 4 B 9 0.383 A_DG4:DC9_B 4 1.754 0.305 0.068 -0.167 -3.893 1 20 A 5 B 8 -0.413 A_5IU5:DA8_B 5 1.599 -0.094 -0.209 -0.134 2.572 1 19 A 6 B 7 0.707 A_DG6:DC7_B 6 -2.664 0.283 0.086 -0.162 2.301 -14.951 A A 1 2 -16.486 B B 12 11 4.055 4.218 -0.290 5.670 AA_DC1DA2:5IU11DG12_BB 1 2.058 8.044 -14.200 -25.305 0.600 3.211 -49.259 A A 2 3 1.097 B B 11 10 3.213 -0.914 0.344 -0.686 AA_DA2DC3:DG105IU11_BB 2 -2.123 -2.547 -49.208 0.891 0.257 4.012 -9.851 A A 3 4 4.527 B B 10 9 3.615 -0.776 -0.037 5.215 AA_DC3DG4:DC9DG10_BB 3 0.431 2.514 -9.811 -28.620 0.755 3.241 -42.976 A A 4 5 3.545 B B 9 8 3.395 -2.591 0.282 -1.796 AA_DG45IU5:DA8DC9_BB 4 4.515 6.177 -42.674 2.712 0.840 3.494 -12.366 A A 5 6 5.291 B B 8 7 3.176 -1.123 -0.106 5.326 AA_5IU5DG6:DC7DA8_BB 5 -3.406 -16.042 -11.836 -23.293 -4.833 software chem_comp_atom chem_comp_bond database_2 diffrn_source struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Derived calculations Refinement description 1 0 2003-11-04 1 1 2008-04-29 1 2 2011-07-13 1 3 2017-10-11 1 4 2024-02-14 1 5 2024-04-03 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _diffrn_source.pdbx_synchrotron_site _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2003-02-25 REL REL NCO COBALT HEXAMMINE(III) HOH water THE OLIGONUCLEOTIDE WAS SYNTHESIZED BY THE REGA-INSTITUTE KULEUVEN sample 242D NDB ENTRY ZDFB51 PDB experimental model NCO 30 2 NCO NCO 30 A NCO 31 2 NCO NCO 31 A HOH 101 3 HOH HOH 101 A HOH 102 3 HOH HOH 102 A HOH 103 3 HOH HOH 103 A HOH 105 3 HOH HOH 105 A HOH 106 3 HOH HOH 106 A HOH 109 3 HOH HOH 109 A HOH 111 3 HOH HOH 111 A HOH 112 3 HOH HOH 112 A HOH 114 3 HOH HOH 114 A HOH 115 3 HOH HOH 115 A HOH 120 3 HOH HOH 120 A HOH 121 3 HOH HOH 121 A HOH 123 3 HOH HOH 123 A HOH 124 3 HOH HOH 124 A HOH 125 3 HOH HOH 125 A HOH 129 3 HOH HOH 129 A HOH 130 3 HOH HOH 130 A HOH 132 3 HOH HOH 132 A HOH 133 3 HOH HOH 133 A HOH 134 3 HOH HOH 134 A HOH 137 3 HOH HOH 137 A HOH 140 3 HOH HOH 140 A HOH 143 3 HOH HOH 143 A HOH 104 3 HOH HOH 104 B HOH 107 3 HOH HOH 107 B HOH 108 3 HOH HOH 108 B HOH 110 3 HOH HOH 110 B HOH 113 3 HOH HOH 113 B HOH 116 3 HOH HOH 116 B HOH 117 3 HOH HOH 117 B HOH 118 3 HOH HOH 118 B HOH 119 3 HOH HOH 119 B HOH 122 3 HOH HOH 122 B HOH 126 3 HOH HOH 126 B HOH 127 3 HOH HOH 127 B HOH 128 3 HOH HOH 128 B HOH 131 3 HOH HOH 131 B HOH 135 3 HOH HOH 135 B HOH 136 3 HOH HOH 136 B HOH 138 3 HOH HOH 138 B HOH 139 3 HOH HOH 139 B HOH 141 3 HOH HOH 141 B HOH 142 3 HOH HOH 142 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 +U 5 n 5 5IU 5 A G 6 n 6 DG 6 A C 7 n 1 DC 7 B A 8 n 2 DA 8 B C 9 n 3 DC 9 B G 10 n 4 DG 10 B +U 11 n 5 5IU 11 B G 12 n 6 DG 12 B 0.159 0.167 5036 author_defined_assembly 2 dimeric A 5IU 5 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE A 5IU 5 DU B 5IU 11 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE B 5IU 5 DU 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 -4.82 0.80 109.40 104.58 A A A O5' C5' C4' DC DC DC 1 1 1 N 1 -8.14 0.80 109.40 101.26 A A A O5' C5' C4' DA DA DA 2 2 2 N 1 -5.07 0.70 108.00 102.93 A A A O4' C1' N9 DA DA DA 2 2 2 N 1 -4.06 0.60 118.90 114.84 A A A N1 C2 O2 DC DC DC 3 3 3 N 1 4.58 0.70 121.90 126.48 A A A N3 C2 O2 DC DC DC 3 3 3 N 1 3.02 0.50 111.90 114.92 A A A C2 N3 C4 DG DG DG 4 4 4 N 1 3.06 0.50 113.10 116.16 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 -5.69 0.70 108.00 102.31 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -5.40 0.80 105.90 100.50 B B B O4' C1' C2' DC DC DC 7 7 7 N 1 3.57 0.50 121.00 124.57 B B B C5 C6 N1 DC DC DC 7 7 7 N 1 -4.16 0.40 104.50 100.34 B B B O4' C4' C3' DA DA DA 8 8 8 N 1 -6.30 0.70 108.00 101.70 B B B O4' C1' N9 DA DA DA 8 8 8 N 1 4.23 0.60 118.60 122.83 B B B N1 C6 N6 DA DA DA 8 8 8 N 1 10.97 1.60 120.90 131.87 B B B P O5' C5' DC DC DC 9 9 9 N 1 -5.05 0.70 108.00 102.95 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 3.39 0.50 111.90 115.29 B B B C2 N3 C4 DG DG DG 10 10 10 N 1 4.41 0.70 119.90 124.31 B B B N3 C2 N2 DG DG DG 10 10 10 N 1 8.25 1.20 119.70 127.95 B B B C3' O3' P DG DG 5IU 10 10 11 Y 1 7.53 1.10 110.50 118.03 B B B O3' P OP2 DG 5IU 5IU 10 11 11 Y 1 -4.84 0.70 108.00 103.16 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 -5.63 0.60 125.10 119.47 B B B C6 N1 C2 DG DG DG 12 12 12 N 1 -3.36 0.50 128.60 125.24 B B B N3 C4 C5 DG DG DG 12 12 12 N 1 3.65 0.50 111.50 115.15 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 B B P O5' DG DG 10 10 0.073 0.010 1.593 1.666 N The iodo atoms are refined anisotropically 1.30 20.0 5988 5036 98.2 1 Isotropic 4.0 MOLECULAR REPLACEMENT NDB ENTRY ZDFB51 1.30 20.0 43 297 14 240 0 22.5 1.30 20.0 1OMK 6103 5988 0.062 1 22.9 98.2 0.165 1.30 1.35 903 98.8 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement SHELXL The Crystal Structure of d(CACG(5IU)G) 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N covale 1.591 both A DG 4 A O3' DG 4 1_555 A 5IU 5 A P 5IU 5 1_555 covale 1.628 both A 5IU 5 A O3' 5IU 5 1_555 A DG 6 A P DG 6 1_555 covale 1.577 both B DG 10 B O3' DG 4 1_555 B 5IU 11 B P 5IU 5 1_555 covale 1.629 both B 5IU 11 B O3' 5IU 5 1_555 B DG 12 B P DG 6 1_555 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 5IU 11 B N3 5IU 5 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B 5IU 11 B O4 5IU 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 5IU 5 A N3 5IU 5 1_555 B DA 8 B N1 DA 2 1_555 hydrog WATSON-CRICK A 5IU 5 A O4 5IU 5 1_555 B DA 8 B N6 DA 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, 5-IODO-2'-DEOXYURIDINE, DNA 1OMK PDB 1 1OMK 1 6 1OMK 1 6 1OMK A 1 1 6 7 12 1OMK 7 12 1OMK B 1 1 6 BINDING SITE FOR RESIDUE NCO A 30 A NCO 30 Software 8 BINDING SITE FOR RESIDUE NCO A 31 A NCO 31 Software 7 A DC 3 A DC 3 8 1_455 A DG 4 A DG 4 8 1_455 A DG 4 A DG 4 8 4_465 A 5IU 5 A 5IU 5 8 4_465 A DG 6 A DG 6 8 1_555 A HOH 102 E HOH 8 1_455 A HOH 134 E HOH 8 1_555 B DG 10 B DG 4 8 1_555 A DG 4 A DG 4 7 4_565 A DG 6 A DG 6 7 1_555 A HOH 106 E HOH 7 4_565 A HOH 109 E HOH 7 4_565 A HOH 130 E HOH 7 4_565 B DG 12 B DG 6 7 4_565 B DG 12 B DG 6 7 2_564 19 P 21 21 21