0.0153 0.0000 0.0056 0.0000 0.0420 0.0000 0.0000 0.0000 0.0284 0.0000 0.0000 0.0000 Naseer, A. Cardin, C.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.0000 110.0100 90.0000 65.2000 23.8000 37.4100 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 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 108 17610 17614 10.1073/pnas.1108685108 21969542 Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand. 2011 10.2210/pdb3gom/pdb pdb_00003gom 100 1 multigraded optics CCD OXFORD SAPPHIRE CCD SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA Holliday junction structure 3045.992 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3' 2 syn polymer 137.327 BARIUM ION 5 syn non-polymer 18.015 water 36 nat water no no (DT)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DA) TCGGCGCCGA A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.24 45.05 VAPOR DIFFUSION, SITTING DROP 7 BaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K 290 BaCl2 1 MPD 1 Na Cacodylate 1 BaCl2 2 MPD 2 Na Cacodylate 2 -2.410 A 1 B 20 5.979 A_DT1:DA20_B 1 -15.787 0.413 0.290 0.138 5.381 1 19 A 2 B 19 -0.312 A_DC2:DG19_B 2 -7.201 0.043 0.291 -0.115 -3.311 1 19 A 3 B 18 -2.592 A_DG3:DC18_B 3 -12.242 0.136 0.252 -0.238 12.289 1 19 A 4 B 17 -2.291 A_DG4:DC17_B 4 -8.972 0.142 0.769 -0.389 -2.435 1 19 A 5 B 16 -5.603 A_DC5:DG16_B 5 -15.298 -0.942 0.062 -0.023 -0.288 1 19 A 6 B 15 -5.071 A_DG6:DC15_B 6 -14.743 -0.393 0.182 -0.148 3.568 37.728 A A 1 2 8.156 B B 20 19 3.335 5.242 0.102 2.089 AA_DT1DC2:DG19DA20_BB 1 5.301 -8.248 37.010 2.508 0.572 3.493 44.502 A A 2 3 -3.057 B B 19 18 3.585 -2.313 -0.714 2.531 AA_DC2DG3:DC18DG19_BB 2 -2.823 3.732 44.359 3.573 0.661 2.879 29.902 A A 3 4 5.569 B B 18 17 2.927 2.859 0.425 0.651 AA_DG3DG4:DC17DC18_BB 3 -4.537 8.838 29.428 0.731 -1.666 3.428 37.224 A A 4 5 -6.901 B B 17 16 3.592 -4.385 -0.568 0.402 AA_DG4DC5:DG16DC17_BB 4 4.662 -7.337 36.689 1.259 1.560 3.429 37.695 A A 5 6 8.064 B B 16 15 3.354 5.194 0.481 0.746 AA_DC5DG6:DC15DG16_BB 5 0.454 -0.704 37.346 0.454 -0.683 software diffrn_source chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Database references Refinement description Data collection Data collection Database references Derived calculations Refinement description 1 0 2009-04-07 1 1 2011-07-13 1 2 2011-11-02 1 3 2017-11-01 1 4 2018-04-04 1 5 2023-09-06 _software.name _diffrn_source.type _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _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_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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4 Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions RCSB Y RCSB 2009-03-19 REL REL BA BARIUM ION HOH water 1NVY PDB entry 1NVY PDB experimental model BA 21 2 BA BA 21 A BA 23 2 BA BA 23 A BA 22 2 BA BA 22 B BA 25 2 BA BA 25 B BA 49 2 BA BA 49 B 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 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 A HOH 52 3 HOH HOH 52 A HOH 53 3 HOH HOH 53 A HOH 55 3 HOH HOH 55 A HOH 56 3 HOH HOH 56 A HOH 58 3 HOH HOH 58 A HOH 60 3 HOH HOH 60 A HOH 24 3 HOH HOH 24 B HOH 34 3 HOH HOH 34 B HOH 35 3 HOH HOH 35 B HOH 36 3 HOH HOH 36 B HOH 37 3 HOH HOH 37 B HOH 38 3 HOH HOH 38 B HOH 39 3 HOH HOH 39 B HOH 45 3 HOH HOH 45 B HOH 46 3 HOH HOH 46 B HOH 47 3 HOH HOH 47 B HOH 48 3 HOH HOH 48 B HOH 50 3 HOH HOH 50 B HOH 51 3 HOH HOH 51 B HOH 57 3 HOH HOH 57 B HOH 59 3 HOH HOH 59 B HOH 61 3 HOH HOH 61 B HOH 62 3 HOH HOH 62 B HOH 63 3 HOH HOH 63 B HOH 64 3 HOH HOH 64 B HOH 65 3 HOH HOH 65 B T 1 n 1 DT 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 A 10 n 10 DA 10 A T 11 n 1 DT 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 A 20 n 10 DA 20 B author_and_software_defined_assembly PISA 4 tetrameric 5740 -98 6090 A DG 4 A O6 DG 4 1_555 A BA 21 C BA BA 1_555 B HOH 48 I O HOH 1_555 101.5 B HOH 24 I O HOH 1_555 A BA 23 D BA BA 1_555 B HOH 65 I O HOH 1_555 47.7 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_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 B B OP2 O DG HOH 16 51 1.94 1 A B O O HOH HOH 28 48 2.06 1 -5.18 0.80 102.40 97.22 A A A C3' C2' C1' DG DG DG 4 4 4 N 1 2.51 0.30 108.30 110.81 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 2.50 0.30 108.30 110.80 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 -5.95 0.70 108.00 102.05 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 1.82 0.30 108.30 110.12 B B B O4' C1' N1 DC DC DC 18 18 18 N 31.247 -2.250 0.000 -0.970 3.160 0.000 -1.570 0.918 0.860 0.349 0.260 0.264 0.264 2.300 19.956 101 2351 2351 4.300 93.220 13.500 0.291 0.604 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.371 0.800 0.800 1.200 PDB entry 1NVY MASK 2.300 19.956 36 445 5 404 0 0.008 452 0.021 1.822 694 3.000 0.066 78 0.200 0.006 208 0.020 0.193 121 0.200 0.316 259 0.200 0.325 28 0.200 31.247 2.300 19.956 3GOM 26 -28 10 0 16 0 2518 2351 1.00 1.00 0.052 1 2.7 93.220 0.21 2.300 2.360 3.21 461 1 2.6 93.220 refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran http://www.ccp4.ac.uk/main.html REFMAC program data extraction H.Yang sw-help@rcsb.rutgers.edu March 3, 2004 C/C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT program 1.401 data collection CrysalisPro Red data reduction CrysalisPro Red data scaling CrysalisPro Red phasing MOLREP Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N metalc 2.562 A DG 4 A O6 DG 4 1_555 A BA 21 C BA BA 1_555 metalc 2.550 A BA 21 C BA BA 1_555 B HOH 48 I O HOH 1_555 metalc 3.124 A BA 23 D BA BA 1_555 B HOH 24 I O HOH 1_555 metalc 2.508 A BA 23 D BA BA 1_555 B HOH 65 I O HOH 1_555 metalc 2.642 B BA 25 F BA BA 1_555 B HOH 57 I O HOH 1_555 hydrog DT-DA PAIR A DT 1 A N3 DT 1 1_555 B DA 20 B N1 DA 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 DG-DC PAIR A DG 3 A O6 DG 3 1_555 B DC 17 B N4 DC 7 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 structure, DNA 3GOM PDB 1 1 3GOM TCGGCGCCGA 1 10 3GOM 1 10 3GOM A 1 1 10 11 20 3GOM 11 20 3GOM B 1 1 10 BINDING SITE FOR RESIDUE BA A 21 A BA 21 Software 6 BINDING SITE FOR RESIDUE BA A 23 A BA 23 Software 1 BINDING SITE FOR RESIDUE BA B 25 B BA 25 Software 2 BINDING SITE FOR RESIDUE BA B 49 B BA 49 Software 1 A DG 3 A DG 3 6 1_555 A DG 4 A DG 4 6 1_555 A HOH 28 H HOH 6 1_555 A HOH 29 H HOH 6 1_555 A HOH 53 H HOH 6 1_555 B HOH 48 I HOH 6 1_555 B HOH 65 I HOH 1 1_555 B HOH 57 I HOH 2 1_555 B HOH 62 I HOH 2 1_555 B HOH 50 I HOH 1 1_555 5 C 1 2 1