0.015163 0.000000 0.005511 0.000000 0.042095 0.000000 0.000000 0.000000 0.028599 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 90.00 109.98 90.00 65.949 23.756 37.204 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/pdb1nt8/pdb pdb_00001nt8 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 2002-05-16 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.811 1.0 X11 EMBL/DESY, HAMBURG 0.811 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 3045.992 5'-d(CpCpGpGpTpApCpCpGpG)-3' 2 syn polymer 40.078 CALCIUM ION 2 syn non-polymer 18.015 water 37 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 2.15 42.70 VAPOR DIFFUSION, HANGING DROP 6.5 MPD, Calcium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K 290 -6.419 1 19 A 1 B 20 -2.443 A_DC1:DG20_B 1 -12.651 0.234 0.355 -0.259 0.629 1 19 A 2 B 19 -8.176 A_DC2:DG19_B 2 -5.970 -0.166 0.244 -0.122 7.214 1 19 A 3 B 18 -0.987 A_DG3:DC18_B 3 7.598 -0.334 0.328 -0.160 1.689 1 19 A 4 B 17 0.022 A_DG4:DC17_B 4 -19.638 -0.409 0.249 -0.098 -13.410 1 20 A 5 B 16 -3.981 A_DT5:DA16_B 5 -11.556 -0.585 0.136 0.314 7.637 1 20 A 6 B 15 -2.690 A_DA6:DT15_B 6 -13.589 0.013 0.252 -0.040 3.500 34.665 A A 1 2 5.747 B B 20 19 3.379 3.403 -0.225 2.294 AA_DC1DC2:DG19DG20_BB 1 5.848 -9.874 34.018 3.296 1.332 3.002 39.635 A A 2 3 -4.904 B B 19 18 3.241 -3.319 0.246 2.542 AA_DC2DG3:DC18DG19_BB 2 -2.732 4.037 39.410 4.121 -0.669 3.885 38.542 A A 3 4 10.673 B B 18 17 3.583 6.998 -1.257 1.449 AA_DG3DG4:DC17DC18_BB 3 -3.839 5.855 37.737 1.196 1.356 3.570 38.033 A A 4 5 -8.018 B B 17 16 3.674 -5.208 0.503 0.682 AA_DG4DT5:DA16DC17_BB 4 1.717 -2.643 37.650 1.783 -0.529 3.116 35.259 A A 5 6 11.381 B B 16 15 2.927 6.850 0.022 1.301 AA_DT5DA6:DT15DA16_BB 5 -1.664 2.764 34.569 1.200 -0.266 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 2003-02-11 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_asym_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Holliday junction formed by the sequence TCGGTACCGA in the presence of one calcium ion Holliday junction formed by TCGGTACCGA in presence of Na and Ca ions Holliday junction formed by TCGGTACCGA with a spine of Sr ions Holliday junction formed by CCGGTACCGG in the more symmetrical form Holliday junction formed by CCGGTACmCGG with a methylated base Holliay junction formed by CCGGTACGG in presnece of a Na ion RCSB Y RCSB 2003-01-29 REL REL CA CALCIUM ION HOH water Chemically synthesized sample CA 2 2 CA CA 102 A CA 1 2 CA CA 101 B HOH 5 3 HOH HOH 103 A HOH 8 3 HOH HOH 104 A HOH 9 3 HOH HOH 105 A HOH 11 3 HOH HOH 106 A HOH 12 3 HOH HOH 107 A HOH 13 3 HOH HOH 108 A HOH 15 3 HOH HOH 109 A HOH 16 3 HOH HOH 110 A HOH 17 3 HOH HOH 111 A HOH 29 3 HOH HOH 112 A HOH 45 3 HOH HOH 113 A HOH 53 3 HOH HOH 114 A HOH 54 3 HOH HOH 115 A HOH 55 3 HOH HOH 116 A HOH 57 3 HOH HOH 117 A HOH 59 3 HOH HOH 118 A HOH 1 3 HOH HOH 102 B HOH 4 3 HOH HOH 103 B HOH 6 3 HOH HOH 104 B HOH 7 3 HOH HOH 105 B HOH 20 3 HOH HOH 106 B HOH 22 3 HOH HOH 107 B HOH 23 3 HOH HOH 108 B HOH 26 3 HOH HOH 109 B HOH 28 3 HOH HOH 110 B HOH 30 3 HOH HOH 111 B HOH 34 3 HOH HOH 112 B HOH 35 3 HOH HOH 113 B HOH 38 3 HOH HOH 114 B HOH 41 3 HOH HOH 115 B HOH 42 3 HOH HOH 116 B HOH 49 3 HOH HOH 117 B HOH 52 3 HOH HOH 118 B HOH 56 3 HOH HOH 119 B HOH 61 3 HOH HOH 120 B HOH 62 3 HOH HOH 121 B HOH 63 3 HOH HOH 122 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 A HOH 103 E O HOH 1_555 A CA 102 C CA CA 1_555 A HOH 114 E O HOH 1_555 58.5 A HOH 103 E O HOH 1_555 A CA 102 C CA CA 1_555 A HOH 115 E O HOH 1_555 82.4 A HOH 114 E O HOH 1_555 A CA 102 C CA CA 1_555 A HOH 115 E O HOH 1_555 75.0 A HOH 103 E O HOH 1_555 A CA 102 C CA CA 1_555 A HOH 116 E O HOH 1_555 83.4 A HOH 114 E O HOH 1_555 A CA 102 C CA CA 1_555 A HOH 116 E O HOH 1_555 141.5 A HOH 115 E O HOH 1_555 A CA 102 C CA CA 1_555 A HOH 116 E O HOH 1_555 96.5 A HOH 103 E O HOH 1_555 A CA 102 C CA CA 1_555 B HOH 103 F O HOH 1_555 101.8 A HOH 114 E O HOH 1_555 A CA 102 C CA CA 1_555 B HOH 103 F O HOH 1_555 111.0 A HOH 115 E O HOH 1_555 A CA 102 C CA CA 1_555 B HOH 103 F O HOH 1_555 173.9 A HOH 116 E O HOH 1_555 A CA 102 C CA CA 1_555 B HOH 103 F O HOH 1_555 79.7 B HOH 102 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 104 F O HOH 1_555 131.6 B HOH 102 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 105 F O HOH 1_555 110.4 B HOH 104 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 105 F O HOH 1_555 113.9 B HOH 102 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 110 F O HOH 1_555 80.7 B HOH 104 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 110 F O HOH 1_555 140.6 B HOH 105 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 110 F O HOH 1_555 57.6 B HOH 102 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 118 F O HOH 1_555 54.7 B HOH 104 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 118 F O HOH 1_555 129.0 B HOH 105 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 118 F O HOH 1_555 68.3 B HOH 110 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 118 F O HOH 1_555 86.1 B HOH 102 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 119 F O HOH 1_555 58.0 B HOH 104 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 119 F O HOH 1_555 76.5 B HOH 105 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 119 F O HOH 1_555 136.6 B HOH 110 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 119 F O HOH 1_555 138.7 B HOH 118 F O HOH 1_555 B CA 101 D CA CA 1_555 B HOH 119 F O HOH 1_555 73.1 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 110 E HOH 1 2.43 0.30 108.30 110.73 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 -5.68 0.90 105.70 100.02 A A A O5' P OP2 DC DC DC 2 2 2 N 1 -3.01 0.40 104.50 101.49 A A A O4' C4' C3' DC DC DC 2 2 2 N 1 -5.09 0.80 102.40 97.31 A A A C3' C2' C1' DC DC DC 2 2 2 N 1 -6.72 0.80 105.90 99.18 A A A O4' C1' C2' DC DC DC 2 2 2 N 1 -10.81 0.70 108.00 97.19 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 5.41 0.50 119.90 125.31 A A A C2 N3 C4 DC DC DC 2 2 2 N 1 -2.80 0.40 104.50 101.70 A A A O4' C4' C3' DG DG DG 3 3 3 N 1 -4.51 0.70 108.00 103.49 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 -3.37 0.40 104.50 101.13 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 -5.80 0.70 108.00 102.20 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -4.56 0.50 111.90 107.34 A A A C2 N3 C4 DG DG DG 4 4 4 N 1 4.11 0.40 110.80 114.91 A A A C4 C5 N7 DG DG DG 4 4 4 N 1 3.06 0.40 106.40 109.46 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 -4.53 0.40 105.40 100.87 A A A N9 C4 C5 DG DG DG 4 4 4 N 1 -5.88 0.60 130.40 124.52 A A A C6 C5 N7 DG DG DG 4 4 4 N 1 -9.45 0.90 116.20 106.75 A A A N1 C2 N2 DG DG DG 4 4 4 N 1 8.90 0.70 119.90 128.80 A A A N3 C2 N2 DG DG DG 4 4 4 N 1 -5.78 0.80 109.40 103.62 A A A O5' C5' C4' DT DT DT 5 5 5 N 1 5.79 0.30 108.30 114.09 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 4.82 0.60 119.00 123.82 A A A C4 C5 C7 DT DT DT 5 5 5 N 1 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 -15.09 1.90 104.00 88.91 A A A O3' P O5' DT DA DA 5 6 6 Y 1 3.00 0.30 108.30 111.30 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 4.11 0.60 118.60 122.71 A A A C6 N1 C2 DA DA DA 6 6 6 N 1 3.52 0.50 110.70 114.22 A A A C4 C5 N7 DA DA DA 6 6 6 N 1 -3.75 0.50 103.90 100.15 A A A C5 N7 C8 DA DA DA 6 6 6 N 1 -3.70 0.40 105.80 102.10 A A A N9 C4 C5 DA DA DA 6 6 6 N 1 5.33 0.30 108.30 113.63 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 -9.84 1.20 119.70 109.86 A A A C3' O3' P DC DC DC 7 7 8 Y 1 -5.40 0.80 105.90 100.50 A A A O4' C1' C2' DC DC DC 8 8 8 N 1 4.69 0.70 119.90 124.59 A A A N3 C2 N2 DG DG DG 9 9 9 N 1 -5.14 0.60 119.90 114.76 A A A N1 C6 O6 DG DG DG 9 9 9 N 1 5.52 0.60 128.60 134.12 A A A C5 C6 O6 DG DG DG 9 9 9 N 1 10.28 1.20 119.70 129.98 A A A C3' O3' P DG DG DG 9 9 10 Y 1 9.79 1.50 119.60 129.39 A A A OP1 P OP2 DG DG DG 10 10 10 N 1 -7.58 1.00 110.10 102.52 B B B C1' O4' C4' DC DC DC 11 11 11 N 1 -6.78 0.70 108.00 101.22 B B B O4' C1' N1 DC DC DC 11 11 11 N 1 4.71 0.40 120.30 125.01 B B B C6 N1 C2 DC DC DC 11 11 11 N 1 4.03 0.40 121.90 125.93 B B B N3 C4 C5 DC DC DC 11 11 11 N 1 -3.35 0.50 121.00 117.65 B B B C5 C6 N1 DC DC DC 11 11 11 N 1 5.18 0.60 118.90 124.08 B B B N1 C2 O2 DC DC DC 11 11 11 N 1 -6.33 0.90 105.70 99.36 B B B O5' P OP2 DC DC DC 12 12 12 N 1 4.62 0.40 120.30 124.92 B B B C6 N1 C2 DC DC DC 12 12 12 N 1 -3.48 0.50 119.90 116.42 B B B C2 N3 C4 DC DC DC 12 12 12 N 1 4.37 0.40 121.90 126.27 B B B N3 C4 C5 DC DC DC 12 12 12 N 1 4.27 0.70 121.90 126.17 B B B N3 C2 O2 DC DC DC 12 12 12 N 1 -7.42 0.70 120.20 112.78 B B B C5 C4 N4 DC DC DC 12 12 12 N 1 11.30 1.50 119.60 130.90 B B B OP1 P OP2 DG DG DG 13 13 13 N 1 -3.28 0.50 111.90 108.62 B B B C2 N3 C4 DG DG DG 13 13 13 N 1 3.82 0.60 119.90 123.72 B B B N1 C6 O6 DG DG DG 13 13 13 N 1 -4.15 0.60 128.60 124.45 B B B C5 C6 O6 DG DG DG 13 13 13 N 1 10.66 1.50 119.60 130.26 B B B OP1 P OP2 DG DG DG 14 14 14 N 1 -6.81 0.90 105.70 98.89 B B B O5' P OP1 DG DG DG 14 14 14 N 1 7.84 1.20 110.70 118.54 B B B O5' P OP2 DG DG DG 14 14 14 N 1 8.63 1.10 109.80 118.43 B B B C5' C4' O4' DG DG DG 14 14 14 N 1 1.89 0.30 108.30 110.19 B B B O4' C1' N9 DG DG DG 14 14 14 N 1 -4.57 0.60 123.90 119.33 B B B N1 C2 N3 DG DG DG 14 14 14 N 1 3.44 0.50 111.90 115.34 B B B C2 N3 C4 DG DG DG 14 14 14 N 1 -2.62 0.40 106.40 103.78 B B B C8 N9 C4 DG DG DG 14 14 14 N 1 7.92 1.20 119.70 127.62 B B B C3' O3' P DG DG DT 14 14 15 Y 1 2.49 0.30 108.30 110.79 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 -5.17 0.60 122.30 117.13 B B B N3 C2 O2 DT DT DT 15 15 15 N 1 4.47 0.60 119.00 123.47 B B B C4 C5 C7 DT DT DT 15 15 15 N 1 -6.61 0.60 122.90 116.29 B B B C6 C5 C7 DT DT DT 15 15 15 N 1 4.97 0.30 108.30 113.27 B B B O4' C1' N9 DA DA DA 16 16 16 N 1 10.95 1.50 119.60 130.55 B B B OP1 P OP2 DC DC DC 17 17 17 N 1 4.60 0.50 119.90 124.50 B B B C2 N3 C4 DC DC DC 17 17 17 N 1 5.74 0.60 118.90 124.64 B B B N1 C2 O2 DC DC DC 17 17 17 N 1 -4.57 0.70 118.00 113.43 B B B N3 C4 N4 DC DC DC 17 17 17 N 1 4.89 0.70 120.20 125.09 B B B C5 C4 N4 DC DC DC 17 17 17 N 1 -8.16 0.90 105.70 97.54 B B B O5' P OP1 DG DG DG 19 19 19 N 1 7.79 1.20 110.70 118.49 B B B O5' P OP2 DG DG DG 19 19 19 N 1 2.92 0.40 110.80 113.72 B B B C4 C5 N7 DG DG DG 19 19 19 N 1 3.82 0.60 126.00 129.82 B B B N3 C4 N9 DG DG DG 19 19 19 N 1 -5.38 0.60 130.40 125.02 B B B C6 C5 N7 DG DG DG 19 19 19 N 1 7.56 0.60 119.90 127.46 B B B N1 C6 O6 DG DG DG 19 19 19 N 1 -9.83 0.60 128.60 118.77 B B B C5 C6 O6 DG DG DG 19 19 19 N 1 2.92 0.30 108.30 111.22 B B B O4' C1' N9 DG DG DG 20 20 20 N 1 4.04 0.50 111.90 115.94 B B B C2 N3 C4 DG DG DG 20 20 20 N 1 -5.04 0.40 110.80 105.76 B B B C4 C5 N7 DG DG DG 20 20 20 N 1 -4.80 0.40 106.40 101.60 B B B C8 N9 C4 DG DG DG 20 20 20 N 1 6.65 0.40 105.40 112.05 B B B N9 C4 C5 DG DG DG 20 20 20 N 1 -5.34 0.60 126.00 120.66 B B B N3 C4 N9 DG DG DG 20 20 20 N 1 5.48 0.60 130.40 135.88 B B B C6 C5 N7 DG DG DG 20 20 20 N 1 7.74 0.90 116.20 123.94 B B B N1 C2 N2 DG DG DG 20 20 20 N 1 -7.65 0.70 119.90 112.25 B B B N3 C2 N2 DG DG DG 20 20 20 N 1 9.13 1.30 127.00 136.13 B B B C8 N9 C1' DG DG DG 20 20 20 N 1 A A C2 N3 DC DC 2 2 -0.049 0.008 1.353 1.304 N 1 A A O3' C3' DT DT 5 5 -0.062 0.006 1.419 1.357 N 1 A A N3 C4 DA DA 6 6 0.053 0.006 1.344 1.397 N 1 A A N9 C4 DA DA 6 6 0.036 0.006 1.374 1.410 N 1 A A N3 C4 DG DG 10 10 0.043 0.007 1.350 1.393 N 1 B B O3' C3' DC DC 11 11 -0.062 0.006 1.419 1.357 N 1 B B O3' P DC DC 11 12 -0.082 0.012 1.607 1.525 Y 1 B B C4 N4 DC DC 12 12 -0.072 0.009 1.335 1.263 N 1 B B N1 C2 DG DG 13 13 0.048 0.008 1.373 1.421 N 1 B B O3' C3' DG DG 14 14 -0.106 0.006 1.419 1.313 N 1 B B N7 C8 DG DG 14 14 0.043 0.006 1.305 1.348 N 1 B B C1' N1 DT DT 15 15 0.091 0.013 1.488 1.579 N 1 B B N1 C2 DT DT 15 15 0.078 0.008 1.376 1.454 N 1 B B O3' C3' DA DA 16 16 -0.038 0.006 1.419 1.381 N 1 B B C6 O6 DG DG 19 19 0.064 0.009 1.237 1.301 N 34.530 -1.19 0.00 -0.77 2.84 0.00 -2.17 0.939 0.925 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.28262 0.24659 0.24834 2.00 34.92 167 4940 3539 4.5 97.37 4.868 0.136 RANDOM 1 THROUGHOUT 1.0 1.0 MOLECULAR REPLACEMENT 0.253 0.205 0.80 0.80 1.40 MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 2.00 34.92 37 443 2 404 0 0.024 0.021 452 0.002 0.020 186 3.768 3.000 694 1.779 3.000 472 0.117 0.200 60 0.020 0.020 210 0.000 0.020 2 0.170 0.200 51 0.227 0.200 194 0.117 0.200 109 0.282 0.200 22 0.043 0.200 3 0.204 0.200 26 0.378 0.200 16 0.128 0.200 10 3.613 3.000 452 4.770 4.500 694 0.207 0.233 2.052 9 248 20 34.53 1.91 34.92 1NT8 6058 4276 1.0 1.0 0.103 0.106 1 4.18 4.0 97.6 0.849 1.91 2.01 0.8 624 0.849 3.9 97.4 refinement REFMAC 5.1.24 data reduction MOSFLM data scaling CCP4 (SCALA) refinement XTALVIEW The structure is the more symmetrical form of the Holliday Junction with two calcium ions present Structural Characterisation of the Holliday junction formed by the sequence CCGGTACCGG at 2.00 A 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N metalc 3.017 A CA 102 C CA CA 1_555 A HOH 103 E O HOH 1_555 metalc 2.604 A CA 102 C CA CA 1_555 A HOH 114 E O HOH 1_555 metalc 2.474 A CA 102 C CA CA 1_555 A HOH 115 E O HOH 1_555 metalc 2.408 A CA 102 C CA CA 1_555 A HOH 116 E O HOH 1_555 metalc 2.852 A CA 102 C CA CA 1_555 B HOH 103 F O HOH 1_555 metalc 2.414 B CA 101 D CA CA 1_555 B HOH 102 F O HOH 1_555 metalc 2.735 B CA 101 D CA CA 1_555 B HOH 104 F O HOH 1_555 metalc 3.242 B CA 101 D CA CA 1_555 B HOH 105 F O HOH 1_555 metalc 2.630 B CA 101 D CA CA 1_555 B HOH 110 F O HOH 1_555 metalc 2.443 B CA 101 D CA CA 1_555 B HOH 118 F O HOH 1_555 metalc 2.568 B CA 101 D CA CA 1_555 B HOH 119 F 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 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 1NT8 PDB 1 1NT8 1 10 1NT8 1 10 1NT8 A 1 1 10 11 20 1NT8 11 20 1NT8 B 1 1 10 BINDING SITE FOR RESIDUE CA B 101 B CA 101 Software 5 BINDING SITE FOR RESIDUE CA A 102 A CA 102 Software 5 B HOH 102 F HOH 5 1_555 B HOH 104 F HOH 5 1_555 B HOH 110 F HOH 5 1_555 B HOH 118 F HOH 5 1_555 B HOH 119 F HOH 5 1_555 A HOH 103 E HOH 5 1_555 A HOH 114 E HOH 5 1_555 A HOH 115 E HOH 5 1_555 A HOH 116 E HOH 5 1_555 B HOH 103 F HOH 5 1_555 5 C 1 2 1