0.015247 0.000000 0.005898 0.000000 0.042323 0.000000 0.000000 0.000000 0.028805 0.00000 0.00000 0.00000 Cardin, C.J. Gale, B.C. Thorpe, J.H. Texieira, S.C.M. Gan, Y. Moraes, M.I.A.A. Brogden, A.L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 111.15 90.00 65.588 23.628 37.223 Ca 2 40.078 CALCIUM 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 CA 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 To be Published 0353 Structural Analysis of two Holliday junctions formed by the sequences TCGGTACCGA and CCGGTACCGG 10.2210/pdb1nqs/pdb pdb_00001nqs 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2002-05-15 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.811 1.0 X11 EMBL/DESY, HAMBURG 0.811 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 3045.005 5'-d(TpCpGpGpTpApCpCpGpA)-3' 2 syn polymer 40.078 CALCIUM ION 1 syn non-polymer 18.015 water 42 nat water no no (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DA) TCGGTACCGA A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.12 41.96 VAPOR DIFFUSION, SITTING DROP 6.5 MPD, calcium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K 290 0.069 1 20 A 1 B 20 3.795 A_DT1:DA20_B 1 -11.987 0.147 0.272 -0.057 1.223 1 19 A 2 B 19 -2.239 A_DC2:DG19_B 2 -2.105 0.210 0.141 -0.183 3.977 1 19 A 3 B 18 -3.466 A_DG3:DC18_B 3 -4.854 -0.463 -0.283 -0.395 0.390 1 19 A 4 B 17 -2.569 A_DG4:DC17_B 4 -12.614 -0.464 0.241 -0.295 -8.288 1 20 A 5 B 16 -1.388 A_DT5:DA16_B 5 -11.199 -0.419 0.059 0.163 1.568 1 20 A 6 B 15 -3.192 A_DA6:DT15_B 6 -10.709 0.055 0.105 -0.095 3.761 40.890 A A 1 2 5.104 B B 20 19 3.559 3.554 0.384 2.329 AA_DT1DC2:DG19DA20_BB 1 4.606 -6.614 40.491 2.895 0.019 3.549 33.492 A A 2 3 6.643 B B 19 18 3.325 3.818 -0.081 2.284 AA_DC2DG3:DC18DG19_BB 2 1.814 -3.156 33.231 3.300 0.456 3.240 43.343 A A 3 4 -3.703 B B 18 17 3.269 -2.723 -0.843 1.883 AA_DG3DG4:DC17DC18_BB 3 -6.855 9.322 42.740 2.816 0.472 3.757 33.731 A A 4 5 3.301 B B 17 16 3.737 1.912 0.172 0.414 AA_DG4DT5:DA16DC17_BB 4 2.565 -4.426 33.583 0.358 0.181 3.028 43.458 A A 5 6 0.947 B B 16 15 3.007 0.701 0.075 1.525 AA_DT5DA6:DT15DA16_BB 5 -0.875 1.182 43.444 1.996 -0.180 chem_comp_atom chem_comp_bond database_2 diffrn_source pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-02-04 1 1 2008-04-29 1 2 2011-07-13 1 3 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _diffrn_source.pdbx_synchrotron_site _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Holliday junction formed by sequence TCGGTACCGA in presence of Na ion and Ca ions Holliday junction formed by TCGGTACCGA with a spine of strontium ions Holliday junction formed by CCGGTACCGG in the more symmetrical form Holliday junction formed by CCGGTACmCGG with a methylated base Holliday junction formed by CCGGTACCGG in presence of a Na ion Holliday junction formed by teh mismatched sequence TCGGGACCGG RCSB Y RCSB 2003-01-22 REL REL CA CALCIUM ION HOH water Chemically synthesized sample CA 101 2 CA CA 101 B HOH 6 3 HOH HOH 11 A HOH 7 3 HOH HOH 12 A HOH 8 3 HOH HOH 13 A HOH 14 3 HOH HOH 14 A HOH 17 3 HOH HOH 15 A HOH 18 3 HOH HOH 16 A HOH 20 3 HOH HOH 17 A HOH 21 3 HOH HOH 18 A HOH 22 3 HOH HOH 19 A HOH 26 3 HOH HOH 20 A HOH 28 3 HOH HOH 21 A HOH 31 3 HOH HOH 22 A HOH 33 3 HOH HOH 23 A HOH 34 3 HOH HOH 24 A HOH 40 3 HOH HOH 25 A HOH 41 3 HOH HOH 26 A HOH 42 3 HOH HOH 27 A HOH 1 3 HOH HOH 102 B HOH 2 3 HOH HOH 103 B HOH 3 3 HOH HOH 104 B HOH 4 3 HOH HOH 105 B HOH 5 3 HOH HOH 106 B HOH 9 3 HOH HOH 107 B HOH 10 3 HOH HOH 108 B HOH 11 3 HOH HOH 109 B HOH 12 3 HOH HOH 110 B HOH 13 3 HOH HOH 111 B HOH 15 3 HOH HOH 112 B HOH 16 3 HOH HOH 113 B HOH 19 3 HOH HOH 114 B HOH 23 3 HOH HOH 115 B HOH 24 3 HOH HOH 116 B HOH 25 3 HOH HOH 117 B HOH 27 3 HOH HOH 118 B HOH 29 3 HOH HOH 119 B HOH 30 3 HOH HOH 120 B HOH 32 3 HOH HOH 121 B HOH 35 3 HOH HOH 122 B HOH 36 3 HOH HOH 123 B HOH 37 3 HOH HOH 124 B HOH 38 3 HOH HOH 125 B HOH 39 3 HOH HOH 126 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 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 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 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 A 20 n 10 DA 20 B author_defined_assembly 4 tetrameric B HOH 102 E O HOH 1_555 B CA 101 C CA CA 1_555 B HOH 109 E O HOH 1_555 81.6 B HOH 102 E O HOH 1_555 B CA 101 C CA CA 1_555 B HOH 117 E O HOH 1_555 96.6 B HOH 109 E O HOH 1_555 B CA 101 C CA CA 1_555 B HOH 117 E O HOH 1_555 76.4 B HOH 102 E O HOH 1_555 B CA 101 C CA CA 1_555 B HOH 118 E O HOH 1_555 95.0 B HOH 109 E O HOH 1_555 B CA 101 C CA CA 1_555 B HOH 118 E O HOH 1_555 79.0 B HOH 117 E O HOH 1_555 B CA 101 C CA CA 1_555 B HOH 118 E O HOH 1_555 150.9 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 A HOH 18 D HOH 1 B HOH 123 E HOH 1 -6.57 0.70 108.00 101.43 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 2.42 0.30 108.30 110.72 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 4.04 0.30 108.30 112.34 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 -4.12 0.60 122.90 118.78 B B B C6 C5 C7 DT DT DT 15 15 15 N 1 2.89 0.30 108.30 111.19 B B B O4' C1' N1 DC DC DC 17 17 17 N 1 B B O3' C3' DT DT 15 15 -0.052 0.006 1.419 1.367 N 39.038 -0.39 0.00 -1.12 2.94 0.00 -3.36 0.959 0.903 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.27779 0.22304 0.22538 1.97 34.71 176 3728 3691 4.6 99.00 RANDOM 1 THROUGHOUT 1.0 1.0 MOLECULAR REPLACEMENT 0.80 MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 1.97 34.71 42 447 1 404 0 0.009 0.021 452 0.003 0.020 192 1.982 3.000 694 1.649 3.000 484 0.065 0.200 60 0.010 0.020 210 0.001 0.020 4 0.153 0.200 51 0.210 0.200 197 0.089 0.200 102 0.241 0.200 28 0.070 0.200 3 0.082 0.200 12 0.339 0.200 18 0.104 0.200 15 2.894 3.000 452 4.414 4.500 694 0.347 0.339 2.021 9 263 20 39.038 1.97 34.71 1NQS 3906 3877 1.0 1.0 0.07 0.07 1 6.1 7.6 99.3 0.296 1.97 2.08 6.1 549 0.296 5.6 100 refinement REFMAC 5.1.24 data reduction MOSFLM data scaling CCP4 (SCALA) refinement XTALVIEW Structural Characterisation of the Holliday Junction formed by the sequence d(TCGGTACCGA) at 1.97 A 1 N N 1 N N 2 N N 3 N N 3 N N metalc 2.374 B CA 101 C CA CA 1_555 B HOH 102 E O HOH 1_555 metalc 2.313 B CA 101 C CA CA 1_555 B HOH 109 E O HOH 1_555 metalc 2.382 B CA 101 C CA CA 1_555 B HOH 117 E O HOH 1_555 metalc 2.492 B CA 101 C CA CA 1_555 B HOH 118 E O HOH 1_555 hydrog WATSON-CRICK A DT 1 A N3 DT 1 1_555 B DA 20 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 1 A O4 DT 1 1_555 B DA 20 B N6 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 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 DT 5 A N3 DT 5 1_555 B DA 16 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 16 B N6 DA 6 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 DNA Holliday Junction, Calcium ion, DNA 1NQS PDB 1 1NQS 1 10 1NQS 1 10 1NQS A 1 1 10 11 20 1NQS 11 20 1NQS B 1 1 10 BINDING SITE FOR RESIDUE CA B 101 B CA 101 Software 4 B HOH 102 E HOH 4 1_555 B HOH 109 E HOH 4 1_555 B HOH 117 E HOH 4 1_555 B HOH 118 E HOH 4 1_555 5 C 1 2 1