0.013867 0.000000 0.005783 0.000000 0.042282 0.000000 0.000000 0.000000 0.029946 0.00000 0.00000 0.00000 Eichman, B.F. Mooers, B.H.M. Alberti, M. Hearst, J.E. Ho, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 112.64 90.00 72.116 23.651 36.182 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 C15 H14 O4 258.269 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN 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 Y 147 N O Y 148 N C Y 149 N C Y 150 N C Y 151 N C Y 152 N C Y 153 N C Y 154 N C Y 155 N C Y 156 N C Y 157 N C Y 158 N C Y 159 N O N 160 N O N 161 N C N 162 N C N 163 N O N 164 N C N 165 N C 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 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 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 Y 152 N sing Y 153 N sing Y 154 N sing N 155 N doub Y 156 N doub N 157 N sing Y 158 N sing N 159 N sing Y 160 N doub Y 161 N sing N 162 N sing Y 163 N sing Y 164 N sing Y 165 N doub Y 166 N sing Y 167 N sing N 168 N sing Y 169 N doub Y 170 N doub N 171 N sing Y 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 308 15 26 10.1006/jmbi.2001.4567 11302703 The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions. 2001 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 97 3971 3976 10.1073/pnas.97.8.3971 The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions 2000 10.2210/pdb1fhz/pdb pdb_00001fhz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.0 1 CCD 1999-10-08 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 1.100 1.0 5.0.2 ALS 1.100 SYNCHROTRON ALS BEAMLINE 5.0.2 DNA IS CROSS-LINKED BY PSORALEN 3045.992 DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3') 2 syn polymer 258.269 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN 1 syn non-polymer 18.015 water 43 nat water no no (DC)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG) CCGGTACCGG A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.23 44.89 VAPOR DIFFUSION, SITTING DROP 7 sodium cacodylate, MgCl2, MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 sodium cacodylate 1 MgCl2 1 MPD 1 MgCl2 2 MPD 2 -45.332 1 20 A 6 B 15 13.809 A_DA6:DT15_B 1 -16.125 -0.348 -0.898 0.310 -4.755 1 19 A 7 B 14 -0.696 A_DC7:DG14_B 2 -2.384 0.089 0.181 -0.083 10.732 1 19 A 8 B 13 4.540 A_DC8:DG13_B 3 -6.969 0.554 -0.175 -0.080 8.416 1 19 A 9 B 12 1.511 A_DG9:DC12_B 4 -6.914 -0.183 0.253 0.014 2.192 1 19 A 10 B 11 1.475 A_DG10:DC11_B 5 -17.746 -0.285 0.030 -0.158 2.543 25.594 A A 6 7 9.166 B B 15 14 2.386 3.799 -0.811 1.029 AA_DA6DC7:DG14DT15_BB 1 -14.754 35.600 20.626 1.419 -1.678 2.943 41.353 A A 7 8 -0.021 B B 14 13 2.960 -0.015 0.165 2.171 AA_DC7DC8:DG13DG14_BB 2 7.506 -10.684 40.696 3.076 0.498 3.352 37.626 A A 8 9 -1.057 B B 13 12 3.407 -0.682 0.180 3.080 AA_DC8DG9:DC12DG13_BB 3 -0.164 0.254 37.620 4.867 -0.301 3.911 42.529 A A 9 10 5.382 B B 12 11 3.689 3.894 -0.180 2.681 AA_DG9DG10:DC11DC12_BB 4 -3.627 5.013 42.210 3.236 -0.180 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-04-21 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id native d(CCGGTACCGG) NDB Y NDB 2000-08-02 REL REL PSO 4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN HOH water PSO 21 2 PSO PSO 21 B HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 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 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 38 3 HOH HOH 38 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 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 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 25 3 HOH HOH 25 B HOH 26 3 HOH HOH 26 B HOH 32 3 HOH HOH 32 B HOH 35 3 HOH HOH 35 B HOH 36 3 HOH HOH 36 B HOH 37 3 HOH HOH 37 B HOH 39 3 HOH HOH 39 B HOH 43 3 HOH HOH 43 B HOH 44 3 HOH HOH 44 B HOH 45 3 HOH HOH 45 B HOH 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 B HOH 55 3 HOH HOH 55 B HOH 56 3 HOH HOH 56 B HOH 57 3 HOH HOH 57 B HOH 58 3 HOH HOH 58 B HOH 59 3 HOH HOH 59 B HOH 60 3 HOH HOH 60 B C 1 n 1 DC 1 A C 2 n 2 DC 2 A G 3 n 3 DG 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 C 8 n 8 DC 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A C 11 n 1 DC 11 B C 12 n 2 DC 12 B G 13 n 3 DG 13 B G 14 n 4 DG 14 B T 15 n 5 DT 15 B A 16 n 6 DA 16 B C 17 n 7 DC 17 B C 18 n 8 DC 18 B G 19 n 9 DG 19 B G 20 n 10 DG 20 B author_defined_assembly 4 tetrameric 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_655 -x+1,y,-z crystal symmetry operation 72.1160000000 0.0000000000 0.0000000000 1 A HOH 62 D HOH 1 A B C6 C4 DT PSO 5 21 2.10 1 B B C5 C5' DT PSO 15 21 2.16 1 B DT 15 0.084 SIDE CHAIN 1 -5.85 0.60 123.70 117.85 A A A C5 C6 N1 DT DT DT 5 5 5 N 1 -11.18 0.60 119.00 107.82 A A A C4 C5 C7 DT DT DT 5 5 5 N 1 -15.32 0.60 122.90 107.58 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 -5.98 0.60 123.70 117.72 B B B C5 C6 N1 DT DT DT 15 15 15 N 1 -10.92 0.60 119.00 108.08 B B B C4 C5 C7 DT DT DT 15 15 15 N 1 -15.05 0.60 122.90 107.85 B B B C6 C5 C7 DT DT DT 15 15 15 N 1 A A C4 C5 DT DT 5 5 0.056 0.009 1.445 1.501 N 1 A A C5 C6 DT DT 5 5 0.199 0.007 1.339 1.538 N 1 A A C6 N1 DT DT 5 5 0.063 0.007 1.378 1.441 N 1 B B C4 C5 DT DT 15 15 0.054 0.009 1.445 1.499 N 1 B B C5 C6 DT DT 15 15 0.199 0.007 1.339 1.538 N 1 B B C6 N1 DT DT 15 15 0.073 0.007 1.378 1.451 N -8.0249 0.0000 -0.0139 13.3859 0.0000 -5.3610 ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS 0.311 0.228 0.236 0.236 2.20 33.39 305 2891 2891 10.5 96.5 random 1 THROUGHOUT 0.0 MOLECULAR REPLACEMENT Parkinson et al. 2.20 33.39 43 466 19 404 0 0.015 1.594 2.20 33.39 1FHZ 2900 2900 -3 0.067 1 12.3 3.3 96.7 0.1 2.20 2.28 284 3.3 98.3 data reduction DENZO data scaling SCALEPACK model building X-PLOR refinement X-PLOR 3.851 phasing X-PLOR PSORALEN CROSS-LINKED D(CCGGTACCGG) FORMS HOLLIDAY JUNCTION 1 N N 1 N N 2 N N 3 N N 3 N N A four-way junction is a dimer constructed from chains A and B and a symmetry partner generated by the two-fold covale 1.559 none A DT 5 A C5 DT 5 1_555 B PSO 21 C C4 PSO 1_555 covale 1.560 none A DT 5 A C6 DT 5 1_555 B PSO 21 C C3 PSO 1_555 covale 1.553 none B DT 15 B C5 DT 5 1_555 B PSO 21 C C4' PSO 1_555 covale 1.566 none B DT 15 B C6 DT 5 1_555 B PSO 21 C C5' PSO 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 15 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 15 B O4 DT 5 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 14 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 14 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 14 B N2 DG 4 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 13 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 13 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 13 B N2 DG 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 12 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 12 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 12 B N4 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 11 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 11 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 11 B N4 DC 1 1_555 DNA psoralen, cross-linked DNA, Holliday junction, DNA-drug complex, DNA 1FHZ PDB 1 1FHZ 1 10 1FHZ 1 10 1FHZ A 1 1 10 11 20 1FHZ 11 20 1FHZ B 1 1 10 BINDING SITE FOR RESIDUE PSO B 21 B PSO 21 Software 4 A DT 5 A DT 5 4 1_555 A DA 6 A DA 6 4 1_555 B DT 15 B DT 5 4 1_555 B DA 16 B DA 6 4 1_555 5 monoclinic C 1 2 1