0.024033 0.000000 0.000000 0.000000 0.024033 0.000000 0.000000 0.000000 0.041570 0.00000 0.00000 0.00000 Zhang, W. Sheng, J. Huang, Z. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 41.609 41.609 24.056 C11 H17 N2 O8 P Se 415.195 n 5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE) DNA linking Cl -1 35.453 CHLORIDE 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 H2 O 18.015 WATER 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 N N 7 N C N 8 N C N 9 N O N 10 N N N 11 N C N 12 N O N 13 N C N 14 N C N 15 R C N 16 N C N 17 R C N 18 N O N 19 R C N 20 R C N 21 N SE N 22 N C N 23 N O 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 H N 39 N H N 40 N H N 41 N CL N 42 N O N 43 N P N 44 N O N 45 N O N 46 N O N 47 N C N 48 R C N 49 N O N 50 S C N 51 N O N 52 N C N 53 R C Y 54 N N Y 55 N C Y 56 N N Y 57 N C Y 58 N C N 59 N N Y 60 N N Y 61 N C Y 62 N N Y 63 N C 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 H N 76 N H N 77 N H N 78 N O N 79 N P N 80 N O N 81 N O N 82 N O N 83 N C N 84 R C N 85 N O N 86 S C N 87 N O N 88 N C N 89 R C N 90 N N N 91 N C N 92 N O N 93 N N N 94 N C N 95 N N N 96 N C N 97 N C 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 H N 110 N H N 111 N H N 112 N O N 113 N P N 114 N O N 115 N O N 116 N O N 117 N C N 118 R C N 119 N O N 120 S C N 121 N O N 122 N C N 123 R C Y 124 N N Y 125 N C Y 126 N N Y 127 N C N 128 N C N 129 N O N 130 N N N 131 N C N 132 N N N 133 N N Y 134 N C 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 H N 147 N H N 148 N H N 149 N O N 150 N H N 151 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 doub N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N doub 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 sing 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 sing N 42 N sing N 43 N sing N 44 N doub 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 sing Y 65 N sing Y 66 N sing Y 67 N doub N 68 N sing Y 69 N sing Y 70 N sing Y 71 N doub N 72 N sing Y 73 N doub N 74 N sing N 75 N sing Y 76 N sing Y 77 N doub N 78 N sing Y 79 N sing N 80 N sing N 81 N sing N 82 N doub 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 sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N doub 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 Y 138 N sing Y 139 N sing Y 140 N doub N 141 N sing Y 142 N sing N 143 N sing Y 144 N doub N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing TO BE PUBLISHED 0353 DNA octamer d(gtggccac) with 2'-se modification 10.2210/pdb4fp6/pdb pdb_00004fp6 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 CCD ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 0.98 1.0 12.3.1 ALS 0.98 SYNCHROTRON ALS BEAMLINE 12.3.1 2520.592 DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3') 1 syn polymer 35.453 CHLORIDE ION 1 syn non-polymer 18.015 water 60 nat water no yes (DG)(2ST)(DG)(DG)(DC)(DC)(DA)(DC) GTGGCCAC A polydeoxyribonucleotide n n n n n n n n 2.07 40.45 -19.859 1 19 A 1 A 8 -0.260 A_DG1:DC8_A 1 -6.395 -0.295 -0.350 -0.019 -8.267 1 20 A 2 A 7 0.745 A_2ST2:DA7_A 2 -9.212 -0.082 0.074 -0.133 -2.654 1 19 A 3 A 6 -1.082 A_DG3:DC6_A 3 -10.881 -0.185 0.133 -0.178 -6.885 1 19 A 4 A 5 0.585 A_DG4:DC5_A 4 -16.892 -0.187 -0.056 -0.084 6.885 1 19 A 5 A 4 0.585 A_DC5:DG4_A 5 -16.892 0.187 -0.056 -0.084 2.654 1 19 A 6 A 3 -1.082 A_DC6:DG3_A 6 -10.881 0.185 0.133 -0.178 8.267 1 20 A 7 A 2 0.745 A_DA7:2ST2_A 7 -9.212 0.082 0.074 -0.133 19.859 1 19 A 8 A 1 -0.260 A_DC8:DG1_A 8 -6.395 0.295 -0.350 -0.019 2.657 31.675 A A 1 2 18.903 A A 8 7 3.120 10.138 -0.006 -0.963 AA_DG12ST2:DA7DC8_AA 1 -1.947 3.631 29.986 -3.464 -0.315 2.534 30.916 A A 2 3 17.757 A A 7 6 3.058 9.325 0.334 -1.316 AA_2ST2DG3:DC6DA7_AA 2 0.062 -0.117 29.509 -4.050 -0.616 2.998 36.392 A A 3 4 11.695 A A 6 5 3.341 7.250 0.267 -1.512 AA_DG3DG4:DC5DC6_AA 3 2.932 -4.730 35.569 -3.410 -0.028 2.724 30.257 A A 4 5 12.487 A A 5 4 2.943 6.470 0.000 -0.737 AA_DG4DC5:DG4DC5_AA 4 0.000 0.000 29.573 -2.560 0.000 2.998 36.392 A A 5 6 11.695 A A 4 3 3.341 7.250 -0.267 -1.512 AA_DC5DC6:DG3DG4_AA 5 -2.932 4.730 35.569 -3.410 0.028 2.534 30.916 A A 6 7 17.757 A A 3 2 3.058 9.325 -0.334 -1.316 AA_DC6DA7:2ST2DG3_AA 6 -0.062 0.117 29.509 -4.050 0.616 2.657 31.675 A A 7 8 18.903 A A 2 1 3.120 10.138 0.006 -0.963 AA_DA7DC8:DG12ST2_AA 7 1.947 -3.631 29.986 -3.464 0.315 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Data collection Database references Derived calculations 1 0 2012-08-15 1 1 2024-02-28 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2012-06-21 REL REL CL CHLORIDE ION HOH water CL 1 2 CL CL 101 A HOH 1 3 HOH HOH 201 A HOH 2 3 HOH HOH 202 A HOH 3 3 HOH HOH 203 A HOH 4 3 HOH HOH 204 A HOH 5 3 HOH HOH 205 A HOH 6 3 HOH HOH 206 A HOH 7 3 HOH HOH 207 A HOH 8 3 HOH HOH 208 A HOH 9 3 HOH HOH 209 A HOH 10 3 HOH HOH 210 A HOH 11 3 HOH HOH 211 A HOH 12 3 HOH HOH 212 A HOH 13 3 HOH HOH 213 A HOH 14 3 HOH HOH 214 A HOH 15 3 HOH HOH 215 A HOH 16 3 HOH HOH 216 A HOH 17 3 HOH HOH 217 A HOH 19 3 HOH HOH 218 A HOH 20 3 HOH HOH 219 A HOH 22 3 HOH HOH 220 A HOH 25 3 HOH HOH 221 A HOH 26 3 HOH HOH 222 A HOH 27 3 HOH HOH 223 A HOH 28 3 HOH HOH 224 A HOH 42 3 HOH HOH 225 A HOH 44 3 HOH HOH 226 A HOH 45 3 HOH HOH 227 A HOH 46 3 HOH HOH 228 A HOH 47 3 HOH HOH 229 A HOH 48 3 HOH HOH 230 A HOH 49 3 HOH HOH 231 A HOH 50 3 HOH HOH 232 A HOH 51 3 HOH HOH 233 A HOH 52 3 HOH HOH 234 A HOH 53 3 HOH HOH 235 A HOH 54 3 HOH HOH 236 A HOH 55 3 HOH HOH 237 A HOH 56 3 HOH HOH 238 A HOH 57 3 HOH HOH 239 A HOH 58 3 HOH HOH 240 A HOH 63 3 HOH HOH 241 A HOH 65 3 HOH HOH 242 A HOH 66 3 HOH HOH 243 A HOH 67 3 HOH HOH 244 A HOH 68 3 HOH HOH 245 A HOH 69 3 HOH HOH 246 A HOH 74 3 HOH HOH 247 A HOH 75 3 HOH HOH 248 A HOH 77 3 HOH HOH 249 A HOH 78 3 HOH HOH 250 A HOH 79 3 HOH HOH 251 A HOH 81 3 HOH HOH 252 A HOH 82 3 HOH HOH 253 A HOH 83 3 HOH HOH 254 A HOH 84 3 HOH HOH 255 A HOH 85 3 HOH HOH 256 A HOH 86 3 HOH HOH 257 A HOH 87 3 HOH HOH 258 A HOH 88 3 HOH HOH 259 A HOH 89 3 HOH HOH 260 A G 1 n 1 DG 1 A 2ST 2 n 2 2ST 2 A G 3 n 3 DG 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A C 6 n 6 DC 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A author_and_software_defined_assembly PISA 2 dimeric 2240 -14 2820 A 2ST 2 A 2ST 2 DT 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 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8_554 -y,-x,-z-1/2 crystal symmetry operation 0.0000000000 0.0000000000 -12.0280000000 1 A A O O HOH HOH 247 248 1.77 1 A A O O HOH HOH 209 211 2.18 1 A DC 8 0.075 SIDE CHAIN 1 -3.02 0.50 128.60 125.58 A A A N3 C4 C5 DG DG DG 1 1 1 N 1 -4.74 0.40 104.50 99.76 A A A O4' C4' C3' DG DG DG 3 3 3 N 1 2.82 0.30 108.30 111.12 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 3.33 0.50 104.30 107.63 A A A C5 N7 C8 DG DG DG 3 3 3 N 1 -3.11 0.50 113.10 109.99 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 -4.05 0.40 104.50 100.45 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 3.65 0.40 110.80 114.45 A A A C4 C5 N7 DG DG DG 4 4 4 N 1 -4.87 0.50 104.30 99.43 A A A C5 N7 C8 DG DG DG 4 4 4 N 1 -15.12 1.90 104.00 88.88 A A A O3' P O5' DG DC DC 4 5 5 Y 1 6.91 1.10 110.50 117.41 A A A O3' P OP2 DG DC DC 4 5 5 Y 1 -5.82 0.90 105.70 99.88 A A A O5' P OP1 DC DC DC 5 5 5 N 1 10.16 1.20 110.70 120.86 A A A O5' P OP2 DC DC DC 5 5 5 N 1 16.29 1.60 120.90 137.19 A A A P O5' C5' DC DC DC 5 5 5 N 1 -3.33 0.40 104.50 101.17 A A A O4' C4' C3' DC DC DC 5 5 5 N 1 -3.05 0.40 104.50 101.45 A A A O4' C4' C3' DA DA DA 7 7 7 N 1 3.69 0.60 118.60 122.29 A A A C6 N1 C2 DA DA DA 7 7 7 N 1 4.68 0.40 105.80 110.48 A A A C8 N9 C4 DA DA DA 7 7 7 N 1 3.90 0.60 118.60 122.50 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 -2.84 0.40 104.50 101.66 A A A O4' C4' C3' DC DC DC 8 8 8 N 1 1.85 0.30 108.30 110.15 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 4.56 0.40 120.30 124.86 A A A C6 N1 C2 DC DC DC 8 8 8 N 1 -5.08 0.70 119.20 114.12 A A A N1 C2 N3 DC DC DC 8 8 8 N 1 6.67 0.50 117.40 124.07 A A A C4 C5 C6 DC DC DC 8 8 8 N 1 -7.90 0.50 121.00 113.10 A A A C5 C6 N1 DC DC DC 8 8 8 N 1 A A C4 C5 DG DG 3 3 -0.042 0.007 1.379 1.337 N 1 A A P OP2 DC DC 5 5 -0.108 0.017 1.485 1.377 N 1 A A O5' C5' DC DC 5 5 -0.189 0.025 1.418 1.229 N 1 A A P OP2 DC DC 6 6 -0.113 0.017 1.485 1.372 N 1 A A N1 C6 DC DC 6 6 0.040 0.006 1.367 1.407 N 1 A A P O5' DC DC 8 8 -0.079 0.010 1.593 1.514 N 1 A A N1 C2 DC DC 8 8 0.093 0.010 1.397 1.490 N 1 A A N1 C6 DC DC 8 8 -0.040 0.006 1.367 1.327 N 1 A A N3 C4 DC DC 8 8 -0.068 0.007 1.335 1.267 N 18.639 0.00 0.00 0.00 0.00 0.00 0.00 0.966 0.955 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.22110 0.18967 0.19101 1.28 29.42 263 5489 4.6 98.59 0.977 0.041 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.055 0.058 0.80 0.80 1.40 MAXIMUM LIKELIHOOD MASK 1.28 29.42 60 224 1 163 0 0.039 0.021 180 3.521 3.000 271 0.435 0.200 32 0.040 0.020 84 2.306 3.000 180 2.580 4.500 271 0.337 0.357 1.311 17 366 20 89.70 1.28 29.42 4FP6 5489 5890 1 refinement REFMAC 5.5.0110 DNA octamer d(gtggccac) with 2'-se modification 1 N N 2 N N 3 N N covale 1.644 both A DG 1 A O3' DG 1 1_555 A 2ST 2 A P 2ST 2 1_555 covale 1.661 both A 2ST 2 A O3' 2ST 2 1_555 A DG 3 A P DG 3 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 8 A N3 DC 8 8_554 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 8 A O2 DC 8 8_554 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 8 A N4 DC 8 8_554 hydrog WATSON-CRICK A 2ST 2 A N3 2ST 2 1_555 A DA 7 A N1 DA 7 8_554 hydrog WATSON-CRICK A 2ST 2 A O4 2ST 2 1_555 A DA 7 A N6 DA 7 8_554 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 A DC 6 A N3 DC 6 8_554 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 A DC 6 A O2 DC 6 8_554 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 A DC 6 A N4 DC 6 8_554 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 5 A N3 DC 5 8_554 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 5 A O2 DC 5 8_554 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 5 A N4 DC 5 8_554 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 4 A N1 DG 4 8_554 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 4 A O6 DG 4 8_554 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 4 A N2 DG 4 8_554 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 3 A N1 DG 3 8_554 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 3 A O6 DG 3 8_554 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 3 A N2 DG 3 8_554 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 A 2ST 2 A N3 2ST 2 8_554 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 A 2ST 2 A O4 2ST 2 8_554 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 A DG 1 A N1 DG 1 8_554 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 A DG 1 A O6 DG 1 8_554 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 A DG 1 A N2 DG 1 8_554 DNA 2'-SE-THYMIDINE DNA, DNA 4FP6 PDB 1 4FP6 1 8 4FP6 1 8 4FP6 A 1 1 8 BINDING SITE FOR RESIDUE CL A 101 A CL 101 Software 7 A HOH 205 C HOH 7 8_554 A HOH 216 C HOH 7 1_555 A HOH 216 C HOH 7 8_554 A HOH 226 C HOH 7 8_554 A HOH 247 C HOH 7 8_554 A HOH 248 C HOH 7 8_554 A HOH 248 C HOH 7 1_555 96 P 43 21 2