0.029958 0.017296 0.000000 0.000000 0.034593 0.000000 0.000000 0.000000 0.011406 0.00000 0.00000 0.00000 Hays, F.A. Vargason, J.M. Ho, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 33.380 33.380 87.670 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 Na 1 22.990 SODIUM ION 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 NA 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 US Biochemistry BICHAW 0033 0006-2960 42 9586 9597 10.1021/bi0346603 12911300 Effect of Sequence on the Conformation of DNA Holliday Junctions 2003 10.2210/pdb1p4z/pdb pdb_00001p4z 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 103.0 1 BENT CONICAL SI-MIRROR (RH COATING) CCD 2002-07-18 ADSC QUANTUM 4 BENT GE(111) MONOCHROMATOR SINGLE WAVELENGTH M x-ray 1 1.0 1.0 14-BM-C APS 1.0 SYNCHROTRON APS BEAMLINE 14-BM-C 3045.004 5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3' 1 syn polymer 22.990 SODIUM ION 3 syn non-polymer 18.015 water 64 nat water no no (DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DG)(DG) CCAGTACTGG A polydeoxyribonucleotide n n n n n n n n n n 1 1.87 33.78 7.50 0.6mM DNA, 5mM TRIS(HCl), 25mM Ca-Acetate, 7% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50 293 TRIS(HCl) 1 Ca-Acetate 1 MPD 1 H2O 1 Ca-Acetate 2 MPD 2 TRIS(HCl) 2 H2O 2 -13.196 1 19 A 1 A 10 0.642 A_DC1:DG10_A 1 -2.093 -0.650 0.611 0.410 5.008 1 A 2 A 9 10.114 A_DC2:DG9_A 2 -8.075 -0.624 -0.315 0.424 -3.108 1 20 A 3 A 8 1.668 A_DA3:DT8_A 3 -19.925 -0.077 0.342 0.073 12.333 1 19 A 4 A 7 6.043 A_DG4:DC7_A 4 -18.762 -0.869 0.356 -0.147 -13.196 1 19 A 1 A 10 0.642 A_DC1:DG10_A 5 -2.093 -0.650 0.611 0.410 5.008 1 A 2 A 9 10.114 A_DC2:DG9_A 6 -8.075 -0.624 -0.315 0.424 -3.108 1 20 A 3 A 8 1.668 A_DA3:DT8_A 7 -19.925 -0.077 0.342 0.073 12.333 1 19 A 4 A 7 6.043 A_DG4:DC7_A 8 -18.762 -0.869 0.356 -0.147 2.697 27.097 A A 1 2 5.417 A A 10 9 2.750 2.470 0.392 0.197 AA_DC1DC2:DG9DG10_AA 1 10.499 -23.024 24.894 -0.122 1.473 3.516 51.867 A A 2 3 5.007 A A 9 8 3.324 4.375 -0.279 2.516 AA_DC2DA3:DT8DG9_AA 2 -1.108 1.268 51.684 2.569 0.241 3.036 27.255 A A 3 4 8.376 A A 8 7 3.195 3.916 0.731 0.249 AA_DA3DG4:DC7DT8_AA 3 -4.526 9.682 26.602 -0.416 -2.643 2.697 27.097 A A 1 2 5.417 A A 10 9 2.750 2.470 0.392 0.197 AA_DC1DC2:DG9DG10_AA 4 10.499 -23.024 24.894 -0.122 1.473 3.516 51.867 A A 2 3 5.007 A A 9 8 3.324 4.375 -0.279 2.516 AA_DC2DA3:DT8DG9_AA 5 -1.108 1.268 51.684 2.569 0.241 3.036 27.255 A A 3 4 8.376 A A 8 7 3.195 3.916 0.731 0.249 AA_DA3DG4:DC7DT8_AA 6 -4.526 9.682 26.602 -0.416 -2.643 chem_comp_atom chem_comp_bond database_2 struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations Refinement description 1 0 2003-09-02 1 1 2008-04-29 1 2 2011-07-13 1 3 2011-11-16 1 4 2024-02-14 1 5 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 Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions RCSB Y RCSB 2003-04-24 REL REL NA SODIUM ION HOH water DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. sample UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS Other experimental model NA 12 2 NA NA 12 A NA 13 2 NA NA 13 A NA 24 2 NA NA 24 A HOH 11 3 HOH HOH 11 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 16 3 HOH HOH 16 A HOH 17 3 HOH HOH 17 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 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 34 3 HOH HOH 34 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 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 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 51 3 HOH HOH 51 A HOH 52 3 HOH HOH 52 A HOH 53 3 HOH HOH 53 A HOH 54 3 HOH HOH 54 A HOH 55 3 HOH HOH 55 A HOH 56 3 HOH HOH 56 A HOH 57 3 HOH HOH 57 A HOH 58 3 HOH HOH 58 A HOH 59 3 HOH HOH 59 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 64 3 HOH HOH 64 A HOH 65 3 HOH HOH 65 A HOH 66 3 HOH HOH 66 A HOH 67 3 HOH HOH 67 A HOH 68 3 HOH HOH 68 A HOH 69 3 HOH HOH 69 A HOH 70 3 HOH HOH 70 A HOH 71 3 HOH HOH 71 A HOH 72 3 HOH HOH 72 A HOH 73 3 HOH HOH 73 A HOH 74 3 HOH HOH 74 A HOH 75 3 HOH HOH 75 A HOH 76 3 HOH HOH 76 A HOH 77 3 HOH HOH 77 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A T 5 n 5 DT 5 A A 6 n 6 DA 6 A C 7 n 7 DC 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A author_defined_assembly 2 dimeric A DC 2 A OP2 DC 2 1_555 A NA 12 B NA NA 1_555 A HOH 25 E O HOH 1_555 127.0 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 0.5000000000 0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 12_545 x,x-y-1,-z+1/6 crystal symmetry operation 16.6900000000 -28.9079279783 14.6116666667 1 A HOH 11 E HOH 1 A HOH 32 E HOH 1 A HOH 33 E HOH 1 A HOH 43 E HOH 1 A HOH 62 E HOH 1 A A OP1 O DT HOH 8 16 2.04 1 A DC 1 0.081 SIDE CHAIN 1 A DG 9 0.095 SIDE CHAIN 1 A A O3' C3' DG DG 10 10 -0.042 0.006 1.419 1.377 N 7.80 0.268 0.019 0.236 0.236 2.00 17.47 195 2143 2143 9.1 95.1 RANDOM 1 RESTRAINED THROUGHOUT 0.000 MOLECULAR REPLACEMENT UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS 0.33 0.26 5.00 0.23 0.24 2.00 17.47 64 269 3 202 0 0.015 1.7 18.30 2.23 0.251 0.055 0.242 2.13 21 244 6 7.9 74.6 3.6 2.000 17.470 1P4Z 2143 0.000 0.039 1 95.1 0.124 2.00 2.13 2.380 74.6 data reduction DENZO data scaling SCALEPACK phasing EPMR refinement CNS 1.0 Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions 1 N N 2 N N 2 N N 2 N N 3 N N THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE CHAIN. GENERATION OF THE DOUBLE HELIX CAN BE PERFORMED WITH THE FOLLOWING: matrix= (0.50000 0.86603 0.00000 ) (0.86603 -0.50000 0.00000 ) (0.00000 0.00000 -1.00000 ) translation= (16.68855 -28.90537 14.61163) metalc 2.825 A DC 2 A OP2 DC 2 1_555 A NA 12 B NA NA 1_555 metalc 2.944 A DG 4 A OP2 DG 4 1_555 A NA 13 C NA NA 1_555 metalc 2.713 A NA 12 B NA NA 1_555 A HOH 25 E O HOH 1_555 metalc 2.920 A NA 24 D NA NA 1_555 A HOH 42 E O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 10 A N1 DG 10 12_545 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 10 A O6 DG 10 12_545 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 10 A N2 DG 10 12_545 hydrog DC-DG PAIR A DC 2 A O2 DC 2 1_555 A DG 9 A N2 DG 9 12_545 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 8 A N3 DT 8 12_545 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 8 A O4 DT 8 12_545 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 7 A N3 DC 7 12_545 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 7 A O2 DC 7 12_545 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 7 A N4 DC 7 12_545 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 A DG 4 A N1 DG 4 12_545 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 A DG 4 A O6 DG 4 12_545 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 A DG 4 A N2 DG 4 12_545 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 A DA 3 A N1 DA 3 12_545 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 A DA 3 A N6 DA 3 12_545 hydrog DG-DC PAIR A DG 9 A N1 DG 9 1_555 A DC 2 A N3 DC 2 12_545 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 A DC 1 A N3 DC 1 12_545 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 A DC 1 A O2 DC 1 12_545 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 A DC 1 A N4 DC 1 12_545 DNA B-DNA, Double Helix, DNA 1P4Z PDB 1 1P4Z 1 10 1P4Z 1 10 1P4Z A 1 1 10 BINDING SITE FOR RESIDUE NA A 12 A NA 12 Software 2 BINDING SITE FOR RESIDUE NA A 13 A NA 13 Software 1 BINDING SITE FOR RESIDUE NA A 24 A NA 24 Software 2 A DC 2 A DC 2 2 1_555 A HOH 25 E HOH 2 1_555 A DG 4 A DG 4 1 1_555 A DC 7 A DC 7 2 1_555 A HOH 42 E HOH 2 1_555 178 P 61 2 2