0.022291 0.012870 0.000000 0.000000 0.025740 0.000000 0.000000 0.000000 0.023960 0.00000 0.00000 0.00000 Zhang, W. Huang, Z. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 44.861 44.861 41.736 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer C10 H15 N2 O7 P Se 385.169 n 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one 2-Se-Thymidine-5'-phosphate DNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O 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 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C 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 H N 110 N H N 111 N O N 112 N H N 113 N H N 114 N P N 115 N N N 116 N C N 117 N SE N 118 N N N 119 N C N 120 N O N 121 N C N 122 N C N 123 R C N 124 N O N 125 N C N 126 N O N 127 S C N 128 N O N 129 R C N 130 N O N 131 N C N 132 N O N 133 N C 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 H N 147 N H N 148 N H N 149 N O 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 N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub 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 sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub 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 sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N doub N 127 N sing N 128 N sing N 129 N doub 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 sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub To Be Published 0353 DNA 8mer containing two 2SeT modifications 10.2210/pdb5tgp/pdb pdb_00005tgp 100 1 CCD 2015-10-01 MAR CCD 130 mm SINGLE WAVELENGTH M x-ray 1 0.98 1.0 8.2.1 ALS 0.98 SYNCHROTRON ALS BEAMLINE 8.2.1 2648.537 DNA/RNA (5'-R(*G)-D(P*(2ST))-R(P*G)-D(P*(2ST))-R(P*AP*CP*AP*C)-3') 2 syn polymer 18.015 water 25 nat water no yes G(US3)G(US3)ACAC GTGTACAC A,C polyribonucleotide n n n n n n n n 1 2.29 46.26 VAPOR DIFFUSION, HANGING DROP 7.0 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride, 0.020 M Magnesium chloride hexahydrate 294 -12.200 1 19 A 1 C 8 0.502 A_G1:C8_C 1 -4.682 -0.265 -0.018 -0.087 -10.780 1 20 A 2 C 7 -3.841 A_US32:A7_C 2 -12.192 -0.294 0.126 -0.115 -6.652 1 19 A 3 C 6 0.156 A_G3:C6_C 3 -8.494 -0.168 0.029 -0.140 -2.719 1 20 A 4 C 5 -5.796 A_US34:A5_C 4 -9.800 -0.214 -0.082 -0.109 1.288 1 20 A 5 C 4 -5.229 A_A5:US34_C 5 -8.919 0.359 0.025 -0.076 5.304 1 19 A 6 C 3 -1.985 A_C6:G3_C 6 -9.978 0.249 0.192 -0.165 7.673 1 20 A 7 C 2 -2.550 A_A7:US32_C 7 -12.070 0.154 0.143 -0.172 2.324 1 19 A 8 C 1 -1.937 A_C8:G1_C 8 -0.128 0.212 0.072 -0.192 2.993 33.970 A A 1 2 8.926 C C 8 7 3.340 5.194 -0.054 -2.055 AA_G1US32:A7C8_CC 1 1.401 -2.408 33.554 -4.328 0.312 2.448 30.052 A A 2 3 21.010 C C 7 6 3.129 10.659 0.360 -1.443 AA_US32G3:C6A7_CC 2 1.960 -3.863 28.072 -4.714 -0.339 2.954 34.007 A A 3 4 10.965 C C 6 5 3.266 6.378 -0.819 -1.396 AA_G3US34:A5C6_CC 3 0.123 -0.211 33.421 -3.363 1.419 2.720 33.073 A A 4 5 17.731 C C 5 4 3.216 9.945 0.163 -1.200 AA_US34A5:US34A5_CC 4 -0.441 0.786 31.580 -3.670 -0.356 3.068 34.322 A A 5 6 7.960 C C 4 3 3.308 4.683 0.614 -1.492 AA_A5C6:G3US34_CC 5 -0.715 1.215 34.004 -3.247 -1.150 2.470 30.068 A A 6 7 17.467 C C 3 2 3.084 8.929 0.026 -1.642 AA_C6A7:US32G3_CC 6 -1.131 2.212 28.719 -4.755 -0.252 3.210 35.567 A A 7 8 6.726 C C 2 1 3.486 4.098 -0.089 -2.275 AA_A7C8:G1US32_CC 7 -1.826 2.997 35.292 -4.338 -0.127 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Data collection Database references Refinement description 1 0 2017-10-18 1 1 2023-10-04 _database_2.pdbx_DOI _database_2.pdbx_database_accession N RCSB Y RCSB 2016-09-28 REL REL HOH water 32630 synthetic construct sample 1 8 1DNS PDB experimental model HOH 23 2 HOH HOH 101 A HOH 18 2 HOH HOH 102 A HOH 4 2 HOH HOH 103 A HOH 22 2 HOH HOH 104 A HOH 1 2 HOH HOH 105 A HOH 8 2 HOH HOH 106 A HOH 3 2 HOH HOH 107 A HOH 6 2 HOH HOH 108 A HOH 20 2 HOH HOH 109 A HOH 9 2 HOH HOH 110 A HOH 12 2 HOH HOH 111 A HOH 2 2 HOH HOH 112 A HOH 21 2 HOH HOH 113 A HOH 7 2 HOH HOH 101 C HOH 14 2 HOH HOH 102 C HOH 17 2 HOH HOH 103 C HOH 5 2 HOH HOH 104 C HOH 13 2 HOH HOH 105 C HOH 10 2 HOH HOH 106 C HOH 25 2 HOH HOH 107 C HOH 11 2 HOH HOH 108 C HOH 16 2 HOH HOH 109 C HOH 24 2 HOH HOH 110 C HOH 26 2 HOH HOH 111 C HOH 15 2 HOH HOH 112 C G 1 n 1 G 1 A 2ST 2 n 2 US3 2 A G 3 n 3 G 3 A 2ST 4 n 4 US3 4 A A 5 n 5 A 5 A C 6 n 6 C 6 A A 7 n 7 A 7 A C 8 n 8 C 8 A G 1 n 1 G 1 C 2ST 2 n 2 US3 2 C G 3 n 3 G 3 C 2ST 4 n 4 US3 4 C A 5 n 5 A 5 C C 6 n 6 C 6 C A 7 n 7 A 7 C C 8 n 8 C 8 C author_and_software_defined_assembly PISA 2 dimeric 780 -0 3080 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 A O2' G 1 A O2' G 1 1 Y 1 A O2' G 3 A O2' G 3 1 Y 1 A O2' A 5 A O2' A 5 1 Y 1 A O2' C 6 A O2' C 6 1 Y 1 A O2' A 7 A O2' A 7 1 Y 1 A O2' C 8 A O2' C 8 1 Y 1 C O2' G 1 B O2' G 1 1 Y 1 C O2' G 3 B O2' G 3 1 Y 1 C O2' A 5 B O2' A 5 1 Y 1 C O2' C 6 B O2' C 6 1 Y 1 C O2' A 7 B O2' A 7 1 Y 1 C O2' C 8 B O2' C 8 1 Y 1 A A O5' O G HOH 1 101 2.11 1 14.03 1.20 119.70 133.73 A A A C3' O3' P G G US3 1 1 2 Y 1 -18.14 2.20 105.20 87.06 A A A O3' P OP2 G US3 US3 1 2 2 Y 1 -10.68 1.20 119.70 109.02 A A A C3' O3' P US3 US3 G 2 2 3 Y 1 11.97 1.10 110.50 122.47 A A A O3' P OP2 US3 G G 2 3 3 Y 1 7.40 1.20 119.70 127.10 A A A C3' O3' P G G US3 3 3 4 Y 1 7.13 1.10 110.50 117.63 A A A O3' P OP2 US3 A A 4 5 5 Y 1 -10.50 0.90 105.70 95.20 A A A O5' P OP2 A A A 7 7 7 N 1 -7.77 0.90 105.70 97.93 A A A O5' P OP1 C C C 8 8 8 N 1 13.80 1.20 119.70 133.50 C C C C3' O3' P US3 US3 G 2 2 3 Y 1 -11.80 1.90 104.00 92.20 C C C O3' P O5' US3 G G 2 3 3 Y 1 12.79 1.20 119.70 132.49 C C C C3' O3' P G G US3 3 3 4 Y 1 -23.68 2.20 105.20 81.52 C C C O3' P OP1 G US3 US3 3 4 4 Y 1 A A O3' P US3 G 2 3 0.095 0.012 1.607 1.702 Y 1 A A O3' P US3 A 4 5 0.074 0.012 1.607 1.681 Y 1 C C O3' P G US3 3 4 -0.161 0.012 1.607 1.446 Y 24.167 0.00 0.00 0.00 0.00 0.00 -0.01 0.969 0.954 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.20811 0.18848 0.18948 1.60 38.85 307 5882 5.0 97.36 1.930 0.065 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.086 0.083 0.80 0.80 1.20 1dns 1.60 38.85 25 347 0 322 0 0.026 0.013 352 0.002 0.020 174 3.505 1.576 520 2.950 3.000 406 0.623 0.200 56 0.024 0.020 184 0.003 0.020 76 2.165 2.527 352 2.167 2.527 351 2.944 3.780 520 3.603 25.908 527 3.530 25.822 516 0.292 0.254 1.643 19 381 20 89.89 1.60 38.85 5TGP 6189 0.788 0.057 1 30.9 6.5 97.1 0.351 1.6 1.66 2.13 1 2.6 92.7 refinement REFMAC 5.8.0069 data reduction HKL-2000 1.0 data scaling HKL-2000 1.0 phasing PHASER 1.0 N DNA 8mer containing two 2SeT modifications 1 N N 1 N N 2 N N 2 N N covale 1.547 both A G 1 A O3' G 1 1_555 A US3 2 A P US3 2 1_555 covale 1.702 one A US3 2 A O3' US3 2 1_555 A G 3 A P G 3 1_555 covale 1.589 both A G 3 A O3' G 3 1_555 A US3 4 A P US3 4 1_555 covale 1.681 one A US3 4 A O3' US3 4 1_555 A A 5 A P A 5 1_555 covale 1.675 both C G 1 B O3' G 1 1_555 C US3 2 B P US3 2 1_555 covale 1.638 one C US3 2 B O3' US3 2 1_555 C G 3 B P G 3 1_555 covale 1.446 both C G 3 B O3' G 3 1_555 C US3 4 B P US3 4 1_555 covale 1.595 one C US3 4 B O3' US3 4 1_555 C A 5 B P A 5 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 C C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 C C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 C C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A US3 2 A N3 US3 2 1_555 C A 7 B N1 A 7 1_555 hydrog WATSON-CRICK A US3 2 A O4 US3 2 1_555 C A 7 B N6 A 7 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 C C 6 B N3 C 6 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 C C 6 B O2 C 6 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 C C 6 B N4 C 6 1_555 hydrog WATSON-CRICK A US3 4 A N3 US3 4 1_555 C A 5 B N1 A 5 1_555 hydrog WATSON-CRICK A US3 4 A O4 US3 4 1_555 C A 5 B N6 A 5 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 C US3 4 B N3 US3 4 1_555 hydrog WATSON-CRICK A A 5 A N6 A 5 1_555 C US3 4 B O4 US3 4 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 C G 3 B N1 G 3 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 C G 3 B O6 G 3 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 C G 3 B N2 G 3 1_555 hydrog WATSON-CRICK A A 7 A N1 A 7 1_555 C US3 2 B N3 US3 2 1_555 hydrog WATSON-CRICK A A 7 A N6 A 7 1_555 C US3 2 B O4 US3 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 C G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 C G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 C G 1 B N2 G 1 1_555 DNA DNA, selenium, modification 5TGP PDB 1 1 5TGP 1 8 5TGP 1 8 5TGP A 1 1 8 1 8 5TGP 1 8 5TGP C 1 1 8 169 P 61