0.015035 0.000000 0.005475 0.000000 0.041358 0.000000 0.000000 0.000000 0.028760 0.00000 0.00000 0.00000 Hays, F.A. Vargason, J.M. Ho, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.0 110.010 90.0 66.513 24.179 37.004 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 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 N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C N 21 N H 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 H N 35 N O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N N Y 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 H N 74 N H N 75 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 N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub 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 N 58 N sing Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing N 64 N sing Y 65 N doub 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 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/pdb1p4y/pdb pdb_00001p4y 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 IMAGE PLATE 2003-01-24 RIGAKU RAXIS IV NI FILTER SINGLE WAVELENGTH M x-ray 1 1.542 1.0 1.542 ROTATING ANODE RIGAKU RU300 3046.980 5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3' 2 syn polymer 22.990 SODIUM ION 4 syn non-polymer 18.015 water 108 nat water no no (DC)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DG) CCGGCGCCGG A,B polydeoxyribonucleotide n n n n n n n n n n 1 1.94 35.95 7.00 0.5mM DNA, 25mM sodium cacodylate, 7.5mM CaCl2, 0.1mM SPERMINE TETRAHYDROCHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 298 sodium cacodylate 1 CaCl2 1 SPERMINE TETRAHYDROCHLORIDE 1 H2O 1 sodium cacodylate 2 CaCl2 2 SPERMINE TETRAHYDROCHLORIDE 2 H2O 2 -4.913 1 19 A 1 B 20 0.007 A_DC1:DG20_B 1 -7.931 0.293 -0.028 -0.111 1.298 1 19 A 2 B 19 5.301 A_DC2:DG19_B 2 -1.726 0.116 -0.281 0.100 2.223 1 19 A 3 B 18 -0.414 A_DG3:DC18_B 3 5.867 -0.399 0.153 -0.179 -2.849 1 19 A 4 B 17 -0.780 A_DG4:DC17_B 4 -25.438 -0.077 0.368 -0.140 -21.163 1 19 A 5 B 16 -6.733 A_DC5:DG16_B 5 6.011 -0.436 0.938 0.049 -0.618 1 19 A 6 B 15 -2.019 A_DG6:DC15_B 6 -11.453 -0.172 0.100 -0.138 3.794 38.136 A A 1 2 9.619 B B 20 19 3.431 6.244 0.397 2.433 AA_DC1DC2:DG19DG20_BB 1 4.588 -7.068 37.369 2.842 0.039 3.389 35.095 A A 2 3 -0.491 B B 19 18 3.402 -0.295 -0.264 2.728 AA_DC2DG3:DC18DG19_BB 2 -3.669 6.096 34.907 4.570 -0.135 3.759 40.534 A A 3 4 0.499 B B 18 17 3.664 0.345 -1.195 1.809 AA_DG3DG4:DC17DC18_BB 3 -3.205 4.631 40.411 2.567 1.319 3.742 38.783 A A 4 5 -2.682 B B 17 16 3.863 -1.775 0.458 0.520 AA_DG4DC5:DG16DC17_BB 4 -5.310 8.022 38.393 1.036 -1.447 3.045 30.035 A A 5 6 9.296 B B 16 15 3.035 4.789 0.017 0.408 AA_DC5DG6:DC15DG16_BB 5 3.273 -6.354 29.483 -0.136 0.598 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn 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 2003-09-02 1 1 2008-04-29 1 2 2011-07-13 1 3 2024-02-14 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _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 1DCW UD0008 PDB experimental model N 21 2 NA NA 21 A N 36 2 NA NA 36 A N 49 2 NA NA 49 A N 55 2 NA NA 55 B W 22 3 HOH HOH 22 A W 24 3 HOH HOH 24 A W 25 3 HOH HOH 25 A W 26 3 HOH HOH 26 A W 27 3 HOH HOH 27 A W 32 3 HOH HOH 32 A W 33 3 HOH HOH 33 A W 34 3 HOH HOH 34 A W 37 3 HOH HOH 37 A W 38 3 HOH HOH 38 A W 39 3 HOH HOH 39 A W 41 3 HOH HOH 41 A W 43 3 HOH HOH 43 A W 46 3 HOH HOH 46 A W 47 3 HOH HOH 47 A W 48 3 HOH HOH 48 A W 51 3 HOH HOH 51 A W 54 3 HOH HOH 54 A W 56 3 HOH HOH 56 A W 58 3 HOH HOH 58 A W 59 3 HOH HOH 59 A W 62 3 HOH HOH 62 A W 67 3 HOH HOH 67 A W 70 3 HOH HOH 70 A W 71 3 HOH HOH 71 A W 72 3 HOH HOH 72 A W 78 3 HOH HOH 78 A W 80 3 HOH HOH 80 A W 81 3 HOH HOH 81 A W 82 3 HOH HOH 82 A W 84 3 HOH HOH 84 A W 85 3 HOH HOH 85 A W 86 3 HOH HOH 86 A W 87 3 HOH HOH 87 A W 88 3 HOH HOH 88 A W 90 3 HOH HOH 90 A W 95 3 HOH HOH 95 A W 97 3 HOH HOH 97 A W 98 3 HOH HOH 98 A W 101 3 HOH HOH 101 A W 103 3 HOH HOH 103 A W 105 3 HOH HOH 105 A W 107 3 HOH HOH 107 A W 109 3 HOH HOH 109 A W 110 3 HOH HOH 110 A W 115 3 HOH HOH 115 A W 116 3 HOH HOH 116 A W 119 3 HOH HOH 119 A W 120 3 HOH HOH 120 A W 121 3 HOH HOH 121 A W 122 3 HOH HOH 122 A W 123 3 HOH HOH 123 A W 125 3 HOH HOH 125 A W 127 3 HOH HOH 127 A W 130 3 HOH HOH 130 A W 131 3 HOH HOH 131 A W 132 3 HOH HOH 132 A W 23 3 HOH HOH 23 B W 28 3 HOH HOH 28 B W 29 3 HOH HOH 29 B W 30 3 HOH HOH 30 B W 31 3 HOH HOH 31 B W 35 3 HOH HOH 35 B W 40 3 HOH HOH 40 B W 42 3 HOH HOH 42 B W 44 3 HOH HOH 44 B W 45 3 HOH HOH 45 B W 50 3 HOH HOH 50 B W 52 3 HOH HOH 52 B W 53 3 HOH HOH 53 B W 57 3 HOH HOH 57 B W 60 3 HOH HOH 60 B W 61 3 HOH HOH 61 B W 63 3 HOH HOH 63 B W 64 3 HOH HOH 64 B W 65 3 HOH HOH 65 B W 66 3 HOH HOH 66 B W 68 3 HOH HOH 68 B W 69 3 HOH HOH 69 B W 73 3 HOH HOH 73 B W 74 3 HOH HOH 74 B W 75 3 HOH HOH 75 B W 76 3 HOH HOH 76 B W 77 3 HOH HOH 77 B W 79 3 HOH HOH 79 B W 83 3 HOH HOH 83 B W 89 3 HOH HOH 89 B W 91 3 HOH HOH 91 B W 92 3 HOH HOH 92 B W 93 3 HOH HOH 93 B W 94 3 HOH HOH 94 B W 96 3 HOH HOH 96 B W 99 3 HOH HOH 99 B W 100 3 HOH HOH 100 B W 102 3 HOH HOH 102 B W 104 3 HOH HOH 104 B W 106 3 HOH HOH 106 B W 108 3 HOH HOH 108 B W 111 3 HOH HOH 111 B W 112 3 HOH HOH 112 B W 113 3 HOH HOH 113 B W 114 3 HOH HOH 114 B W 117 3 HOH HOH 117 B W 118 3 HOH HOH 118 B W 124 3 HOH HOH 124 B W 126 3 HOH HOH 126 B W 128 3 HOH HOH 128 B W 129 3 HOH HOH 129 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 C 5 n 5 DC 5 A G 6 n 6 DG 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 C 15 n 5 DC 15 B G 16 n 6 DG 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 A DC 1 A O5' DC 1 1_555 A NA 36 D NA NA 1_555 A HOH 82 G O HOH 1_555 121.7 A DG 10 A N3 DG 10 1_555 A NA 49 E NA NA 1_555 A HOH 56 G O HOH 1_555 101.5 A HOH 24 G O HOH 1_555 A NA 21 C NA NA 1_555 A HOH 25 G O HOH 1_555 77.2 A HOH 24 G O HOH 1_555 A NA 21 C NA NA 1_555 A HOH 56 G O HOH 1_555 83.5 A HOH 25 G O HOH 1_555 A NA 21 C NA NA 1_555 A HOH 56 G O HOH 1_555 147.8 A HOH 24 G O HOH 1_555 A NA 21 C NA NA 1_555 A HOH 109 G O HOH 1_555 134.8 A HOH 25 G O HOH 1_555 A NA 21 C NA NA 1_555 A HOH 109 G O HOH 1_555 143.1 A HOH 56 G O HOH 1_555 A NA 21 C NA NA 1_555 A HOH 109 G O HOH 1_555 66.6 B DG 19 B O4' DG 9 1_555 B NA 55 F NA NA 1_555 B HOH 75 H O HOH 1_555 57.0 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_556 -x,y,-z+1 crystal symmetry operation -12.6621821170 0.0000000000 34.7701763015 8.7 0.26 0.012 0.229 0.229 1.70 22.50 490 4940 4436 10 77.1 RANDOM 1 THROUGHOUT 2.000 MOLECULAR REPLACEMENT UD0008 0.26 0.21 5.00 0.10 0.03 1.70 22.50 108 516 4 404 0 0.007 1.2 18.5 1.57 0.285 0.046 0.209 1.81 39 374 6 9.4 40.8 1.6 1.650 22.550 1P4Y 4940 0.000 0.048 1 74.0 0.279 1.65 1.71 2.140 21.7 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 1 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS A AND B. THE FULL FOUR STRANDED HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING: matrix= ( -1.00000 -0.00046 -0.00015 ) ( -0.00046 1.00000 0.00072 ) ( 0.00015 0.00072 -1.00000 ) translation= (-12.65734 -0.02663 34.77174) metalc 2.475 A DC 1 A O5' DC 1 1_555 A NA 36 D NA NA 1_555 metalc 2.945 A DG 10 A N3 DG 10 1_555 A NA 49 E NA NA 1_555 metalc 2.810 A NA 21 C NA NA 1_555 A HOH 24 G O HOH 1_555 metalc 2.470 A NA 21 C NA NA 1_555 A HOH 25 G O HOH 1_555 metalc 2.716 A NA 21 C NA NA 1_555 A HOH 56 G O HOH 1_555 metalc 2.476 A NA 21 C NA NA 1_555 A HOH 109 G O HOH 1_555 metalc 2.638 A NA 36 D NA NA 1_555 A HOH 82 G O HOH 1_555 metalc 2.560 A NA 49 E NA NA 1_555 A HOH 56 G O HOH 1_555 metalc 2.634 B DG 19 B O4' DG 9 1_555 B NA 55 F NA NA 1_555 metalc 2.806 B NA 55 F NA NA 1_555 B HOH 75 H O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 20 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 20 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 20 B N2 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 19 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 19 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 19 B N2 DG 9 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 18 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 18 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 18 B N4 DC 8 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 17 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 17 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 17 B N4 DC 7 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 16 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 16 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 16 B N2 DG 6 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 15 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 15 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 15 B N4 DC 5 1_555 DNA Holliday Junction, DNA Four-Way Junction, DNA 1P4Y PDB 1 1P4Y 1 10 1P4Y 1 10 1P4Y A 1 1 10 11 20 1P4Y 11 20 1P4Y B 1 1 10 BINDING SITE FOR RESIDUE NA A 21 A NA 21 Software 6 BINDING SITE FOR RESIDUE NA A 36 A NA 36 Software 4 BINDING SITE FOR RESIDUE NA A 49 A NA 49 Software 3 BINDING SITE FOR RESIDUE NA B 55 B NA 55 Software 2 A HOH 24 G HOH 6 1_555 A HOH 25 G HOH 6 1_555 A NA 49 E NA 6 1_555 A HOH 56 G HOH 6 1_555 A HOH 109 G HOH 6 1_555 B HOH 76 H HOH 6 2_556 A DC 1 A DC 1 4 1_555 A DC 2 A DC 2 4 1_555 A HOH 82 G HOH 4 1_555 B DG 14 B DG 4 4 2_557 A DG 10 A DG 10 3 1_555 A NA 21 C NA 3 1_555 A HOH 56 G HOH 3 1_555 B DG 19 B DG 9 2 1_555 B HOH 75 H HOH 2 1_555 5 C 1 2 1