0.015266 0.000000 0.005558 0.000000 0.040479 0.000000 0.000000 0.000000 0.028782 0.00000 0.00000 0.00000 Vargason, J.M. Ho, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 110.01 90.00 65.503 24.704 36.975 C10 H16 N3 O7 P 321.224 n 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking 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 N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N C N 8 N O N 9 N N N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O 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 H N 36 N H N 37 N H N 38 N CA N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 N C N 50 R C Y 51 N N Y 52 N C Y 53 N N Y 54 N C Y 55 N C N 56 N N Y 57 N N Y 58 N C Y 59 N N Y 60 N C 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 H N 73 N H N 74 N H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 N C N 86 R C N 87 N N N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N C N 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 Y 121 N N Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N N Y 131 N C 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 H N 146 N O N 147 N P N 148 N O N 149 N O N 150 N O N 151 N C N 152 R C N 153 N O N 154 S C N 155 N O N 156 N C N 157 R C N 158 N N N 159 N C N 160 N O N 161 N N N 162 N C N 163 N O N 164 N C N 165 N C N 166 N C 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 180 N H N 181 N H N 182 N O N 183 N H N 184 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N doub N 7 N sing N 8 N sing N 9 N sing N 10 N doub 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 sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 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 Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N sing Y 67 N sing Y 68 N doub N 69 N sing Y 70 N doub N 71 N sing N 72 N sing Y 73 N sing Y 74 N doub N 75 N sing Y 76 N sing N 77 N sing N 78 N sing N 79 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing 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 doub N 115 N sing 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 Y 135 N sing Y 136 N sing Y 137 N doub N 138 N sing Y 139 N sing N 140 N sing Y 141 N doub N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N doub N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing US J.Biol.Chem. JBCHA3 0071 0021-9258 277 21041 21049 10.1074/jbc.M201357200 11919197 The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution. 2002 10.2210/pdb1l6b/pdb pdb_00001l6b 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 2001-01-22 ADSC QUANTUM 4 Si 111 Chanel SINGLE WAVELENGTH M x-ray 1 1.150 1.0 5.0.2 ALS 1.150 SYNCHROTRON ALS BEAMLINE 5.0.2 3060.020 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3' 2 syn polymer 40.078 CALCIUM ION 1 syn non-polymer 18.015 water 95 nat water no yes (DC)(DC)(DG)(DG)(DT)(DA)(DC)(5CM)(DG)(DG) CCGGTACCGG A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.45 49.84 VAPOR DIFFUSION, SITTING DROP 7.0 Sodium Cacodylate, CaCl2, Spermine tetrahydrochloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 Sodium Cacodylate 1 CaCl2 1 Spermine tetrahydrochloride 1 CaCl2 2 -3.619 1 19 A 1 B 20 2.943 A_DC1:DG20_B 1 -12.774 0.644 0.088 -0.082 -0.676 1 19 A 2 B 19 -0.141 A_DC2:DG19_B 2 -2.438 0.289 0.159 -0.222 2.922 1 19 A 3 B 18 -6.680 A_DG3:5CM18_B 3 -1.025 -0.328 0.141 -0.286 0.230 1 19 A 4 B 17 4.350 A_DG4:DC17_B 4 -12.149 -0.203 0.111 0.006 -2.699 1 20 A 5 B 16 1.008 A_DT5:DA16_B 5 -16.581 0.063 0.062 -0.080 -2.500 1 20 A 6 B 15 2.117 A_DA6:DT15_B 6 -10.310 0.030 0.105 -0.164 3.837 38.045 A A 1 2 8.777 B B 20 19 3.507 5.693 0.155 2.546 AA_DC1DC2:DG19DG20_BB 1 3.728 -5.747 37.453 3.086 0.298 3.201 37.042 A A 2 3 -1.609 B B 19 18 3.269 -1.022 0.018 2.488 AA_DC2DG3:5CM18DG19_BB 2 0.021 -0.034 37.028 4.052 -0.025 3.678 38.477 A A 3 4 5.616 B B 18 17 3.500 3.688 -0.579 1.623 AA_DG3DG4:DC175CM18_BB 3 -4.596 6.999 38.041 1.957 0.249 3.399 37.589 A A 4 5 -2.171 B B 17 16 3.429 -1.398 -0.302 0.618 AA_DG4DT5:DA16DC17_BB 4 0.655 -1.017 37.559 1.149 0.557 3.359 41.550 A A 5 6 1.536 B B 16 15 3.295 1.089 0.897 1.353 AA_DT5DA6:DT15DA16_BB 5 1.597 -2.252 41.507 1.790 -1.092 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_conn_type struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-08-07 1 1 2008-04-28 1 2 2011-07-13 1 3 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _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_conn_type.id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2002-03-08 REL REL CA CALCIUM ION HOH water The sequence is chemically synthesized. sample CA 21 2 CA CA 21 B HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 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 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 39 3 HOH HOH 39 A HOH 40 3 HOH HOH 40 A HOH 54 3 HOH HOH 54 A HOH 61 3 HOH HOH 61 A HOH 64 3 HOH HOH 64 A HOH 65 3 HOH HOH 65 A HOH 67 3 HOH HOH 67 A HOH 68 3 HOH HOH 68 A HOH 70 3 HOH HOH 70 A HOH 75 3 HOH HOH 75 A HOH 78 3 HOH HOH 78 A HOH 85 3 HOH HOH 85 A HOH 86 3 HOH HOH 86 A HOH 87 3 HOH HOH 87 A HOH 88 3 HOH HOH 88 A HOH 90 3 HOH HOH 90 A HOH 91 3 HOH HOH 91 A HOH 93 3 HOH HOH 93 A HOH 94 3 HOH HOH 94 A HOH 96 3 HOH HOH 96 A HOH 99 3 HOH HOH 99 A HOH 100 3 HOH HOH 100 A HOH 101 3 HOH HOH 101 A HOH 102 3 HOH HOH 102 A HOH 103 3 HOH HOH 103 A HOH 108 3 HOH HOH 108 A HOH 109 3 HOH HOH 109 A HOH 110 3 HOH HOH 110 A HOH 113 3 HOH HOH 113 A HOH 114 3 HOH HOH 114 A HOH 115 3 HOH HOH 115 A HOH 25 3 HOH HOH 25 B HOH 26 3 HOH HOH 26 B HOH 27 3 HOH HOH 27 B HOH 37 3 HOH HOH 37 B HOH 38 3 HOH HOH 38 B HOH 41 3 HOH HOH 41 B HOH 42 3 HOH HOH 42 B HOH 43 3 HOH HOH 43 B HOH 44 3 HOH HOH 44 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 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 B HOH 51 3 HOH HOH 51 B HOH 52 3 HOH HOH 52 B HOH 53 3 HOH HOH 53 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 HOH 62 3 HOH HOH 62 B HOH 63 3 HOH HOH 63 B HOH 66 3 HOH HOH 66 B HOH 69 3 HOH HOH 69 B HOH 71 3 HOH HOH 71 B HOH 72 3 HOH HOH 72 B HOH 73 3 HOH HOH 73 B HOH 74 3 HOH HOH 74 B HOH 76 3 HOH HOH 76 B HOH 77 3 HOH HOH 77 B HOH 79 3 HOH HOH 79 B HOH 80 3 HOH HOH 80 B HOH 81 3 HOH HOH 81 B HOH 82 3 HOH HOH 82 B HOH 83 3 HOH HOH 83 B HOH 84 3 HOH HOH 84 B HOH 89 3 HOH HOH 89 B HOH 92 3 HOH HOH 92 B HOH 95 3 HOH HOH 95 B HOH 97 3 HOH HOH 97 B HOH 98 3 HOH HOH 98 B HOH 104 3 HOH HOH 104 B HOH 105 3 HOH HOH 105 B HOH 106 3 HOH HOH 106 B HOH 107 3 HOH HOH 107 B HOH 111 3 HOH HOH 111 B HOH 112 3 HOH HOH 112 B HOH 116 3 HOH HOH 116 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 5CM 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 5CM 18 B G 19 n 9 DG 19 B G 20 n 10 DG 20 B 39.6562 -65.3704 -3.5173 65.7801 -27.2352 -30.5233 -0.0841 -0.9030 -0.5051 0.3513 0.1557 0.6348 1.1211 -0.8730 -0.0716 0.2193 -0.0509 0.0226 0.2019 -0.0111 0.2009 refined -23.5496 -4.0210 31.5800 X-RAY DIFFRACTION 19.0929 -34.1174 6.4047 7.7498 -3.7460 19.3486 -0.3929 0.5998 0.2261 0.1842 -0.5138 -0.2891 -0.4788 0.9031 0.9067 0.2135 -0.0682 -0.0104 0.2145 -0.0163 0.2316 refined -24.3518 -2.2437 27.4043 X-RAY DIFFRACTION 73.6440 29.7510 -34.8349 -31.1825 -7.8896 12.6152 0.3110 -0.7572 -0.5078 0.9600 -1.0112 -0.4549 0.0084 0.5481 0.7002 0.2822 -0.0708 0.0029 0.2112 0.0620 0.3076 refined -20.2174 -7.0259 31.7428 X-RAY DIFFRACTION 31.8458 -16.4704 -17.2257 60.7766 26.7388 15.3935 -0.3105 0.0076 -0.1267 0.0063 -0.1597 -0.6120 0.1935 -0.2728 0.4701 0.1780 -0.0714 0.0054 0.2284 0.0183 0.2290 refined -19.7853 -2.7001 29.4324 X-RAY DIFFRACTION 25.8388 31.5804 -38.8855 140.7212 -1.7557 -49.6423 -1.0436 -2.1748 -2.3502 -1.1715 -0.0225 -2.8706 -0.2093 1.0938 1.0661 0.1361 0.0018 0.0531 0.1811 0.1867 0.5998 refined -15.0534 -8.6311 29.9965 X-RAY DIFFRACTION 19.3127 -18.7803 27.7757 31.9537 -18.5586 39.3974 0.0925 -0.0749 0.2600 0.1104 0.0654 -0.0749 0.5252 0.3620 -0.1580 0.1474 -0.0708 0.0213 0.2107 0.0077 0.2390 refined -15.7179 -3.6051 28.5235 X-RAY DIFFRACTION -33.2176 35.6873 21.4316 97.4899 8.6115 9.6956 -0.4664 -0.8486 -0.6343 0.0611 1.8361 -0.9404 0.6118 0.1238 -1.3697 0.1127 0.0185 0.2925 0.0525 -0.0218 0.8587 refined -11.8014 -8.9161 24.7459 X-RAY DIFFRACTION -15.6948 6.3589 -5.6967 -1.1890 12.8826 17.7216 0.4353 0.2259 0.1550 -0.2832 -0.5064 -0.0562 0.4219 0.4380 0.0712 0.1603 -0.0487 0.0251 0.2080 0.0105 0.2461 refined -12.2614 -3.8573 26.3341 X-RAY DIFFRACTION 10.1295 -5.6539 -56.9417 -170.7949 130.6918 39.3911 -0.8956 -0.3819 -1.8019 4.3522 -1.9174 2.0470 1.4498 -0.1603 2.8130 0.2247 -0.1052 0.0578 0.2145 -0.1042 0.4111 refined -9.8904 -5.4184 20.2105 X-RAY DIFFRACTION 86.2189 -61.8312 116.8995 142.9202 -175.8928 172.1028 1.5859 -0.1292 0.1968 -0.3509 -1.6707 -1.1169 1.1662 -0.0665 0.0848 0.1104 -0.1023 0.0036 0.1680 -0.0212 0.2505 refined -8.8316 -3.2726 24.3849 X-RAY DIFFRACTION 31.9197 24.2335 36.3879 -3.2971 -29.4735 37.5881 1.4370 -0.4494 -0.3081 -0.6766 -1.5241 -0.7593 1.5704 -0.0925 0.0871 0.2338 -0.0041 0.0037 0.2439 -0.0464 0.1803 refined -8.7296 0.1935 18.4519 X-RAY DIFFRACTION -18.6331 -13.4605 -29.3996 27.9050 13.8058 31.9223 -0.1392 0.0019 0.0260 0.0020 -0.0358 -0.2992 0.2906 0.1245 0.1749 0.1604 -0.0896 -0.0044 0.2620 -0.0031 0.2816 refined -6.3843 -0.5946 23.3958 X-RAY DIFFRACTION 37.7508 14.6060 -13.7286 4.5721 -32.8983 127.2733 0.8822 -0.5793 0.3741 0.2324 -0.1017 0.2333 -1.0202 0.6222 -0.7804 0.1646 0.0241 -0.0357 0.2349 -0.0592 0.2170 refined -8.1580 4.9250 15.2207 X-RAY DIFFRACTION -32.7401 11.3623 11.3356 55.2677 -12.4559 27.8329 0.0751 0.1836 -0.4812 -0.4189 -0.3610 0.1893 -0.1083 -0.0029 0.2859 0.1904 0.0547 -0.0007 0.2589 -0.0179 0.2635 refined -8.9181 1.5595 11.8048 X-RAY DIFFRACTION 12.6731 -22.8190 -0.3025 42.1537 -45.6118 40.4101 -1.2262 1.3317 0.1101 1.9541 0.6642 -0.2658 -1.1482 1.4436 0.5620 0.2141 0.0013 -0.1155 0.1596 -0.0377 0.2842 refined -8.7823 9.0508 11.5989 X-RAY DIFFRACTION 5.5263 10.7363 -24.5397 8.9619 33.2917 -59.8856 0.3400 -0.5365 -0.1510 0.1242 -0.3654 0.1300 0.2653 0.3460 0.0254 0.2353 0.0110 -0.0382 0.2294 0.0237 0.2299 refined -11.9075 5.3907 12.2875 X-RAY DIFFRACTION -8.0511 2.0084 -29.3745 2.3787 -0.4330 -38.5842 0.1117 -0.6018 0.0702 -0.2074 -0.7694 -0.7221 0.3514 0.0497 0.6577 0.3115 -0.0269 -0.0631 0.1570 0.0400 0.2908 refined -12.1175 11.6276 7.4152 X-RAY DIFFRACTION 0.3359 4.8936 6.5259 3.5442 -2.4547 7.9459 -0.1593 0.0172 -0.0179 0.0270 0.3810 -0.3305 -0.1823 0.5346 -0.2217 0.2187 0.0208 -0.0081 0.2276 0.0094 0.2407 refined -14.7532 7.8645 9.7921 X-RAY DIFFRACTION 14.6766 10.3688 -13.2883 57.6915 -0.2695 -6.0534 -0.2504 -1.0129 -0.7037 -1.1069 -0.8841 -1.5993 -1.2908 -1.2208 1.1345 0.2728 0.0084 -0.0414 0.2118 0.0882 0.2113 refined -15.8403 10.9027 2.8171 X-RAY DIFFRACTION -15.4863 -8.6937 -1.4508 61.2629 -19.7220 31.9492 -0.3364 0.1117 -0.1955 0.0340 0.4591 -0.2928 -0.2823 0.1434 -0.1227 0.1664 0.0389 -0.0065 0.2276 0.0002 0.2463 refined -17.8822 9.2521 7.4232 X-RAY DIFFRACTION 27.0270 -16.3273 -73.2060 -78.9518 26.9969 64.0552 0.1635 0.0307 0.0330 0.1312 -0.0225 0.4782 1.1582 0.3953 -0.1409 0.2593 -0.0886 -0.0099 0.2301 -0.0165 0.2168 refined 7.4001 2.1815 21.4797 X-RAY DIFFRACTION -26.6266 -19.5159 -3.5969 84.4258 -21.6730 48.1060 -0.0233 0.2363 0.3677 0.4446 -0.2828 -0.2385 -0.0441 -0.1182 0.3061 0.1629 -0.0792 -0.0027 0.2372 0.0083 0.2497 refined 6.0313 6.4583 22.4479 X-RAY DIFFRACTION -38.2354 28.7267 31.0678 25.7498 -4.4404 -8.0421 -1.5383 0.6958 -0.3909 0.1941 0.9944 0.1001 0.4676 0.4919 0.5439 0.2241 0.0043 0.0379 0.2499 -0.0342 0.1960 refined 6.3693 -0.7713 24.8018 X-RAY DIFFRACTION -9.1722 -22.2466 -13.2270 21.3942 -26.4130 109.1286 -0.2350 0.2918 0.1452 0.5085 -0.2768 0.5082 -0.2947 0.1974 0.5119 0.1606 -0.0568 -0.0007 0.2508 -0.0243 0.2377 refined 3.0774 2.5364 23.1817 X-RAY DIFFRACTION -37.0645 6.1146 18.2591 2.3341 16.3855 -18.4106 -0.7110 -0.6349 -0.1565 -0.3906 0.6335 -0.2130 1.2969 0.6083 0.0775 0.3833 0.0119 0.0861 0.1887 0.0383 0.2222 refined 2.8543 -2.5424 28.9653 X-RAY DIFFRACTION 6.8665 3.6303 15.8893 2.6342 -7.4169 -0.0140 -0.2463 0.2643 -0.1261 0.0614 0.3957 -0.1924 0.2585 0.7660 -0.1493 0.2269 -0.0339 0.0229 0.2339 0.0085 0.2251 refined 0.1425 0.6967 25.7545 X-RAY DIFFRACTION -10.1660 -2.5773 7.4818 -24.2274 8.3416 47.9807 -0.7835 0.0564 -0.3690 0.1475 0.1313 -0.0198 0.1707 -0.6070 0.6523 0.2729 -0.0380 0.0321 0.2531 0.0577 0.1649 refined -1.2412 -0.5688 33.1204 X-RAY DIFFRACTION -3.7392 7.7900 1.0676 30.5541 -26.9825 50.4288 -0.3723 -0.0949 -0.3595 -0.0542 0.4762 0.6386 0.6481 -0.4029 -0.1039 0.1950 -0.0334 -0.0068 0.2160 0.0024 0.2190 refined -3.0786 0.1943 28.2931 X-RAY DIFFRACTION -16.0032 6.9011 -13.9362 3.4182 23.8670 -96.1209 -2.1464 -1.5257 -1.1615 0.8624 1.5533 0.4565 -1.0846 -0.7243 0.5931 0.3068 0.0557 0.0141 0.3860 0.0562 0.1338 refined -6.1684 2.4174 33.3546 X-RAY DIFFRACTION -1.2355 -39.6528 -24.7245 185.3272 12.4874 -7.8355 -0.2890 0.0847 0.0267 0.7800 0.0739 -0.8428 0.6503 -0.3484 0.2151 0.1800 -0.0669 -0.0044 0.2647 0.0120 0.2290 refined -6.3392 -0.7438 29.3206 X-RAY DIFFRACTION 22.5462 -13.5500 36.6988 99.1579 -0.6837 8.0557 -1.0118 -1.1386 0.1943 0.1334 1.5176 0.0263 -1.2568 -0.3291 -0.5059 0.0939 -0.0736 0.0032 0.3073 -0.0715 0.1915 refined -10.6693 5.5166 30.8363 X-RAY DIFFRACTION 5.0488 -44.3188 -17.9444 92.0636 17.8953 86.4322 -0.0407 0.0734 -0.1095 -0.0767 0.0550 0.1749 -0.0788 -0.5013 -0.0143 0.0834 -0.0804 -0.0113 0.2167 -0.0094 0.2562 refined -10.5029 1.0916 28.2487 X-RAY DIFFRACTION 27.1955 -26.8394 0.6267 -39.9019 -40.7519 -26.2738 -1.2519 -0.8863 0.0119 -0.4573 -0.1782 2.2497 -0.9802 -0.0979 1.4300 0.1979 -0.0634 -0.0548 0.1369 -0.0060 0.3987 refined -14.4433 6.1379 26.3795 X-RAY DIFFRACTION -17.6817 14.6612 -32.7067 22.6536 30.3165 107.1232 0.1292 -0.5096 0.0630 -0.4661 -0.2052 -0.4721 0.0036 -0.3136 0.0760 0.1066 -0.0720 0.0047 0.2026 -0.0243 0.2755 refined -14.2913 1.3489 27.6848 X-RAY DIFFRACTION 59.6155 71.8881 -9.6549 162.2134 1.5461 -42.6892 -1.4804 1.4455 0.7564 2.2728 1.3931 0.4064 -0.9413 0.3748 0.0873 0.3146 -0.1756 -0.0833 0.2856 0.0802 0.1667 refined -18.0137 3.7555 22.4572 X-RAY DIFFRACTION 8.2776 -19.7388 -2.8114 38.3785 -3.8300 61.2367 -0.2251 -0.2312 0.4469 -0.2035 -0.3202 -0.1867 0.2207 0.3154 0.5453 0.1741 -0.0832 -0.0243 0.2198 0.0199 0.2443 refined -18.3580 1.1795 26.6899 X-RAY DIFFRACTION -41.0798 -31.7196 -17.0197 63.5557 23.7012 57.0608 0.2935 1.0608 0.2487 -0.3870 -1.3218 0.5709 0.6020 -0.2607 1.0284 0.1749 -0.1084 0.0053 0.3344 0.0244 0.1953 refined -20.1023 -0.5850 19.1224 X-RAY DIFFRACTION 4.4227 -14.3141 11.4269 0.9409 -10.5879 26.3161 0.2848 0.1522 -0.0319 -0.1219 -0.5185 -0.1114 -0.4637 0.5255 0.2337 0.2111 -0.0829 0.0173 0.2290 0.0155 0.2570 refined -21.0493 -1.6655 24.0961 X-RAY DIFFRACTION 3.6290 -36.9332 -21.0067 58.3032 9.8516 10.7368 0.5185 -0.5715 0.4547 -2.2513 -0.8048 1.4123 0.7825 0.6165 0.2863 0.2532 -0.0615 -0.0166 0.2330 -0.0118 0.1486 refined -21.5352 -6.4913 17.9436 X-RAY DIFFRACTION 10.6415 -10.2606 4.4836 13.8311 4.8193 45.4219 0.2459 0.0988 0.2733 -0.1429 -0.3695 0.1657 0.2110 0.1296 0.1236 0.1695 -0.0821 0.0259 0.2139 0.0025 0.2417 refined -23.6308 -4.6187 22.2279 X-RAY DIFFRACTION A 1 A 1 A 1 A 1 X-RAY DIFFRACTION 1 A 1 A 1 A 1 A 1 X-RAY DIFFRACTION 2 A 2 A 2 A 2 A 2 X-RAY DIFFRACTION 3 A 2 A 2 A 2 A 2 X-RAY DIFFRACTION 4 A 3 A 3 A 3 A 3 X-RAY DIFFRACTION 5 A 3 A 3 A 3 A 3 X-RAY DIFFRACTION 6 A 4 A 4 A 4 A 4 X-RAY DIFFRACTION 7 A 4 A 4 A 4 A 4 X-RAY DIFFRACTION 8 A 5 A 5 A 5 A 5 X-RAY DIFFRACTION 9 A 5 A 5 A 5 A 5 X-RAY DIFFRACTION 10 A 6 A 6 A 6 A 6 X-RAY DIFFRACTION 11 A 6 A 6 A 6 A 6 X-RAY DIFFRACTION 12 A 7 A 7 A 7 A 7 X-RAY DIFFRACTION 13 A 7 A 7 A 7 A 7 X-RAY DIFFRACTION 14 A 8 A 8 A 8 A 8 X-RAY DIFFRACTION 15 A 8 A 8 A 8 A 8 X-RAY DIFFRACTION 16 A 9 A 9 A 9 A 9 X-RAY DIFFRACTION 17 A 9 A 9 A 9 A 9 X-RAY DIFFRACTION 18 A 10 A 10 A 10 A 10 X-RAY DIFFRACTION 19 A 10 A 10 A 10 A 10 X-RAY DIFFRACTION 20 B 11 B 1 B 11 B 1 X-RAY DIFFRACTION 21 B 11 B 1 B 11 B 1 X-RAY DIFFRACTION 22 B 12 B 2 B 12 B 2 X-RAY DIFFRACTION 23 B 12 B 2 B 12 B 2 X-RAY DIFFRACTION 24 B 13 B 3 B 13 B 3 X-RAY DIFFRACTION 25 B 13 B 3 B 13 B 3 X-RAY DIFFRACTION 26 B 14 B 4 B 14 B 4 X-RAY DIFFRACTION 27 B 14 B 4 B 14 B 4 X-RAY DIFFRACTION 28 B 15 B 5 B 15 B 5 X-RAY DIFFRACTION 29 B 15 B 5 B 15 B 5 X-RAY DIFFRACTION 30 B 16 B 6 B 16 B 6 X-RAY DIFFRACTION 31 B 16 B 6 B 16 B 6 X-RAY DIFFRACTION 32 B 17 B 7 B 17 B 7 X-RAY DIFFRACTION 33 B 17 B 7 B 17 B 7 X-RAY DIFFRACTION 34 B 18 B 8 B 18 B 8 X-RAY DIFFRACTION 35 B 18 B 8 B 18 B 8 X-RAY DIFFRACTION 36 B 19 B 9 B 19 B 9 X-RAY DIFFRACTION 37 B 19 B 9 B 19 B 9 X-RAY DIFFRACTION 38 B 20 B 10 B 20 B 10 X-RAY DIFFRACTION 39 B 20 B 10 B 20 B 10 X-RAY DIFFRACTION 40 author_defined_assembly 4 tetrameric B HOH 43 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 44 E O HOH 1_555 80.4 B HOH 43 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 45 E O HOH 1_555 114.2 B HOH 44 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 45 E O HOH 1_555 76.0 B HOH 43 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 46 E O HOH 1_555 144.1 B HOH 44 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 46 E O HOH 1_555 74.3 B HOH 45 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 46 E O HOH 1_555 84.0 B HOH 43 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 81 E O HOH 1_555 59.1 B HOH 44 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 81 E O HOH 1_555 138.4 B HOH 45 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 81 E O HOH 1_555 127.0 B HOH 46 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 81 E O HOH 1_555 134.7 B HOH 43 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 98 E O HOH 1_555 76.3 B HOH 44 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 98 E O HOH 1_555 132.3 B HOH 45 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 98 E O HOH 1_555 76.6 B HOH 46 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 98 E O HOH 1_555 139.5 B HOH 81 E O HOH 1_555 B CA 21 C CA CA 1_555 B HOH 98 E O HOH 1_555 50.4 A 5CM 8 A 5CM 8 DC B 5CM 18 B 5CM 8 DC 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 -12.6522587768 0.0000000000 34.7429269470 1 A HOH 108 D HOH 1 B HOH 76 E HOH 1 A B O O HOH HOH 70 104 1.76 1 B B O O HOH HOH 81 98 1.89 1 A B O O HOH HOH 96 50 2.01 1 B B OP2 O DG HOH 20 82 2.01 1 -8.10 0.80 105.90 97.80 A A A O4' C1' C2' DC DC DC 2 2 2 N 1 -4.74 0.70 108.00 103.26 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 -4.96 0.70 108.00 103.04 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 -5.23 0.80 105.90 100.67 B B B O4' C1' C2' DC DC DC 12 12 12 N 1 -4.28 0.70 108.00 103.72 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 -4.43 0.70 108.00 103.57 B B B O4' C1' N9 DG DG DG 13 13 13 N 1 -5.81 0.70 108.00 102.19 B B B O4' C1' N9 DG DG DG 14 14 14 N 1 -4.98 0.80 102.40 97.42 B B B C3' C2' C1' DT DT DT 15 15 15 N 1 -6.73 0.70 108.00 101.27 B B B O4' C1' N9 DA DA DA 16 16 16 N 1 -7.28 0.70 108.00 100.72 B B B O4' C1' N1 DC DC DC 17 17 17 N 0.264 0.218 0.223 0.223 1.5 16.28 852 7986 7986 Random UNVERIFIED 1 0.0 MOLECULAR REPLACEMENT G.PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN 1.5 16.28 95 502 3 404 0 0.012 2.08 1.5 16.28 1L6B 7988 7988 0.0 0.0 0.043 1 87.3 0.325 1.5 1.55 39.3 model building X-PLOR Custom Script - Real Space translation/rotation/rigid body/rigid part search refinement REFMAC 5.0 data reduction DENZO data scaling SCALEPACK phasing X-PLOR CUSTOM SCRIPT - REAL SPACE TRANSLATION/ROTATION/RIGID BODY/RIGID PART SEARCH CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG 1 N N 1 N N 2 N N 3 N N 3 N N The second part of the biological assembly is generated by a crystallographic two-fold to give one fully watson-crick basepaired Holliday junction covale 1.591 both A DC 7 A O3' DC 7 1_555 A 5CM 8 A P 5CM 8 1_555 covale 1.598 both A 5CM 8 A O3' 5CM 8 1_555 A DG 9 A P DG 9 1_555 covale 1.572 both B DC 17 B O3' DC 7 1_555 B 5CM 18 B P 5CM 8 1_555 covale 1.606 both B 5CM 18 B O3' 5CM 8 1_555 B DG 19 B P DG 9 1_555 metalc 2.514 B CA 21 C CA CA 1_555 B HOH 43 E O HOH 1_555 metalc 2.427 B CA 21 C CA CA 1_555 B HOH 44 E O HOH 1_555 metalc 2.527 B CA 21 C CA CA 1_555 B HOH 45 E O HOH 1_555 metalc 2.261 B CA 21 C CA CA 1_555 B HOH 46 E O HOH 1_555 metalc 2.121 B CA 21 C CA CA 1_555 B HOH 81 E O HOH 1_555 metalc 2.298 B CA 21 C CA CA 1_555 B HOH 98 E 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 5CM 18 B N3 5CM 8 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B 5CM 18 B O2 5CM 8 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B 5CM 18 B N4 5CM 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, DNA four-way junction, cytosine methylation, DNA 1L6B PDB 1 1L6B 1 10 1L6B 1 10 1L6B A 1 1 10 11 20 1L6B 11 20 1L6B B 1 1 10 BINDING SITE FOR RESIDUE CA B 21 B CA 21 Software 6 B HOH 43 E HOH 6 1_555 B HOH 44 E HOH 6 1_555 B HOH 45 E HOH 6 1_555 B HOH 46 E HOH 6 1_555 B HOH 81 E HOH 6 1_555 B HOH 98 E HOH 6 1_555 5 C 1 2 1