0.039730 0.000000 0.000000 0.000000 0.023381 0.000000 0.000000 0.000000 0.022134 0.00000 0.00000 0.00000 Teplova, M. Wallace, S.T. Tereshko, V. Minasov, G. Simons, A.M. Cook, P.D. Manoharan, M. Egli, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.17 42.77 45.18 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 C12 H20 N3 O9 P 381.276 n 2'-O-3-AMINOPROPYL 2'-DEOXYURIDINE-5'-MONOPHOSPHATE RNA 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 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H 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 O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C N 94 N H 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 O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H 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 O N 145 N H N 146 N H N 147 N P N 148 N O N 149 N O N 150 N O N 151 N O N 152 N C N 153 R C N 154 N O N 155 R C N 156 N O N 157 R C N 158 N O N 159 R C N 160 N N N 161 N C N 162 N O N 163 N N N 164 N C N 165 N O N 166 N C N 167 N C N 168 N C N 169 N C N 170 N C N 171 N N 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 H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 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 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 sing N 177 N sing N 178 N doub N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 96 14240 14245 10.1073/pnas.96.25.14240 10588690 Structural origins of the exonuclease resistance of a zwitterionic RNA 1999 10.2210/pdb1d9h/pdb pdb_00001d9h 120 1 IMAGE PLATE RIGAKU RAXIS IIC SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 3104.073 DNA/RNA (5'-D(*GP*CP*GP*TP*AP)-R(*(U31)P)-D(*AP*CP*GP*C)-3') 2 syn polymer 18.015 water 145 nat water no yes (DG)(DC)(DG)(DT)(DA)(U31)(DA)(DC)(DG)(DC) GCGTAUACGC A,B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n 1 1.88 34.61 VAPOR DIFFUSION, HANGING DROP 7.0 MPD, POTASSIUN CACODYLATE, KCL, SPERMINE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K 295 POTASSIUN CACODYLATE 1 KCL 1 SPERMINE 1 MPD 1 MPD 2 4.541 1 19 A 1 B 20 -2.047 A_DG1:DC20_B 1 -3.235 -0.124 0.214 -0.194 7.522 1 19 A 2 B 19 1.562 A_DC2:DG19_B 2 -15.057 0.151 0.002 -0.153 -6.899 1 19 A 3 B 18 1.062 A_DG3:DC18_B 3 -15.327 -0.348 0.132 -0.182 -3.221 1 20 A 4 B 17 0.857 A_DT4:DA17_B 4 -18.412 -0.134 -0.043 -0.131 2.168 1 20 A 5 B 16 -4.550 A_DA5:U3116_B 5 -14.224 0.204 0.215 -0.100 3.017 1 20 A 6 B 15 4.924 A_U316:DA15_B 6 -13.930 0.053 0.339 -0.053 1.854 1 20 A 7 B 14 0.566 A_DA7:DT14_B 7 -9.970 0.081 0.032 -0.204 8.475 1 19 A 8 B 13 1.441 A_DC8:DG13_B 8 -12.857 0.197 -0.256 -0.192 -1.851 1 19 A 9 B 12 1.738 A_DG9:DC12_B 9 -8.354 -0.242 0.135 -0.121 0.653 1 19 A 10 B 11 -1.433 A_DC10:DG11_B 10 2.322 0.475 -0.063 -0.218 3.147 37.701 A A 1 2 1.902 B B 20 19 3.198 1.229 0.197 -1.720 AA_DG1DC2:DG19DC20_BB 1 1.346 -2.083 37.659 -2.816 -0.136 2.568 28.906 A A 2 3 19.977 B B 19 18 3.446 9.781 0.031 -2.046 AA_DC2DG3:DC18DG19_BB 2 -1.031 2.106 27.215 -6.158 -0.278 2.893 37.285 A A 3 4 7.376 B B 18 17 3.065 4.704 -0.985 -1.370 AA_DG3DT4:DA17DC18_BB 3 -0.711 1.115 36.990 -2.712 1.455 1.621 34.342 A A 4 5 36.990 B B 17 16 3.043 20.459 0.604 -1.486 AA_DT4DA5:U3116DA17_BB 4 1.223 -2.210 27.705 -5.064 -0.871 2.873 33.016 A A 5 6 12.767 B B 16 15 3.187 7.200 0.842 -1.175 AA_DA5U316:DA15U3116_BB 5 0.339 -0.600 32.241 -3.214 -1.427 2.302 33.993 A A 6 7 22.620 B B 15 14 3.076 12.908 -0.195 -1.478 AA_U316DA7:DT14DA15_BB 6 1.184 -2.075 31.492 -4.295 0.496 3.077 31.354 A A 7 8 4.430 B B 14 13 3.196 2.387 0.412 -1.827 AA_DA7DC8:DG13DT14_BB 7 3.654 -6.783 31.056 -3.813 -0.099 2.542 29.249 A A 8 9 22.156 B B 13 12 3.502 10.917 -0.237 -1.976 AA_DC8DG9:DC12DG13_BB 8 -2.277 4.621 27.083 -6.187 -0.005 3.206 36.401 A A 9 10 2.838 B B 12 11 3.286 1.770 0.107 -1.532 AA_DG9DC10:DG11DC12_BB 9 3.564 -5.715 36.190 -2.697 0.322 chem_comp_atom chem_comp_bond database_2 struct_conn struct_ref_seq repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1999-12-02 1 1 2008-01-03 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end RCSB Y RCSB 1999-10-27 REL REL HOH water HOH 1 2 HOH HOH 11 A HOH 2 2 HOH HOH 12 A HOH 3 2 HOH HOH 13 A HOH 4 2 HOH HOH 14 A HOH 5 2 HOH HOH 15 A HOH 6 2 HOH HOH 16 A HOH 7 2 HOH HOH 17 A HOH 8 2 HOH HOH 18 A HOH 9 2 HOH HOH 19 A HOH 10 2 HOH HOH 20 A HOH 11 2 HOH HOH 21 A HOH 12 2 HOH HOH 22 A HOH 13 2 HOH HOH 23 A HOH 14 2 HOH HOH 24 A HOH 15 2 HOH HOH 25 A HOH 16 2 HOH HOH 26 A HOH 17 2 HOH HOH 27 A HOH 18 2 HOH HOH 28 A HOH 19 2 HOH HOH 29 A HOH 20 2 HOH HOH 30 A HOH 21 2 HOH HOH 31 A HOH 22 2 HOH HOH 32 A HOH 23 2 HOH HOH 33 A HOH 24 2 HOH HOH 34 A HOH 25 2 HOH HOH 35 A HOH 26 2 HOH HOH 36 A HOH 27 2 HOH HOH 37 A HOH 28 2 HOH HOH 38 A HOH 29 2 HOH HOH 39 A HOH 30 2 HOH HOH 40 A HOH 31 2 HOH HOH 41 A HOH 32 2 HOH HOH 42 A HOH 33 2 HOH HOH 43 A HOH 34 2 HOH HOH 44 A HOH 35 2 HOH HOH 45 A HOH 36 2 HOH HOH 46 A HOH 37 2 HOH HOH 47 A HOH 38 2 HOH HOH 48 A HOH 39 2 HOH HOH 49 A HOH 40 2 HOH HOH 50 A HOH 41 2 HOH HOH 51 A HOH 42 2 HOH HOH 52 A HOH 43 2 HOH HOH 53 A HOH 44 2 HOH HOH 54 A HOH 45 2 HOH HOH 55 A HOH 46 2 HOH HOH 56 A HOH 47 2 HOH HOH 57 A HOH 48 2 HOH HOH 58 A HOH 49 2 HOH HOH 59 A HOH 50 2 HOH HOH 60 A HOH 51 2 HOH HOH 61 A HOH 52 2 HOH HOH 62 A HOH 53 2 HOH HOH 63 A HOH 54 2 HOH HOH 64 A HOH 55 2 HOH HOH 65 A HOH 56 2 HOH HOH 66 A HOH 57 2 HOH HOH 67 A HOH 58 2 HOH HOH 68 A HOH 59 2 HOH HOH 69 A HOH 60 2 HOH HOH 70 A HOH 61 2 HOH HOH 71 A HOH 62 2 HOH HOH 72 A HOH 63 2 HOH HOH 73 A HOH 64 2 HOH HOH 74 A HOH 65 2 HOH HOH 75 A HOH 66 2 HOH HOH 76 A HOH 67 2 HOH HOH 77 A HOH 1 2 HOH HOH 21 B HOH 2 2 HOH HOH 22 B HOH 3 2 HOH HOH 23 B HOH 4 2 HOH HOH 24 B HOH 5 2 HOH HOH 25 B HOH 6 2 HOH HOH 26 B HOH 7 2 HOH HOH 27 B HOH 8 2 HOH HOH 28 B HOH 9 2 HOH HOH 29 B HOH 10 2 HOH HOH 30 B HOH 11 2 HOH HOH 31 B HOH 12 2 HOH HOH 32 B HOH 13 2 HOH HOH 33 B HOH 14 2 HOH HOH 34 B HOH 15 2 HOH HOH 35 B HOH 16 2 HOH HOH 36 B HOH 17 2 HOH HOH 37 B HOH 18 2 HOH HOH 38 B HOH 19 2 HOH HOH 39 B HOH 20 2 HOH HOH 40 B HOH 21 2 HOH HOH 41 B HOH 22 2 HOH HOH 42 B HOH 23 2 HOH HOH 43 B HOH 24 2 HOH HOH 44 B HOH 25 2 HOH HOH 45 B HOH 26 2 HOH HOH 46 B HOH 27 2 HOH HOH 47 B HOH 28 2 HOH HOH 48 B HOH 29 2 HOH HOH 49 B HOH 30 2 HOH HOH 50 B HOH 31 2 HOH HOH 51 B HOH 32 2 HOH HOH 52 B HOH 33 2 HOH HOH 53 B HOH 34 2 HOH HOH 54 B HOH 35 2 HOH HOH 55 B HOH 36 2 HOH HOH 56 B HOH 37 2 HOH HOH 57 B HOH 38 2 HOH HOH 58 B HOH 39 2 HOH HOH 59 B HOH 40 2 HOH HOH 60 B HOH 41 2 HOH HOH 61 B HOH 42 2 HOH HOH 62 B HOH 43 2 HOH HOH 63 B HOH 44 2 HOH HOH 64 B HOH 45 2 HOH HOH 65 B HOH 46 2 HOH HOH 66 B HOH 47 2 HOH HOH 67 B HOH 48 2 HOH HOH 68 B HOH 49 2 HOH HOH 69 B HOH 50 2 HOH HOH 70 B HOH 51 2 HOH HOH 71 B HOH 52 2 HOH HOH 72 B HOH 53 2 HOH HOH 73 B HOH 54 2 HOH HOH 74 B HOH 55 2 HOH HOH 75 B HOH 56 2 HOH HOH 76 B HOH 57 2 HOH HOH 77 B HOH 58 2 HOH HOH 78 B HOH 59 2 HOH HOH 79 B HOH 60 2 HOH HOH 80 B HOH 61 2 HOH HOH 81 B HOH 62 2 HOH HOH 82 B HOH 63 2 HOH HOH 83 B HOH 64 2 HOH HOH 84 B HOH 65 2 HOH HOH 85 B HOH 66 2 HOH HOH 86 B HOH 67 2 HOH HOH 87 B HOH 68 2 HOH HOH 88 B HOH 69 2 HOH HOH 89 B HOH 70 2 HOH HOH 90 B HOH 71 2 HOH HOH 91 B HOH 72 2 HOH HOH 92 B HOH 73 2 HOH HOH 93 B HOH 74 2 HOH HOH 94 B HOH 75 2 HOH HOH 95 B HOH 76 2 HOH HOH 96 B HOH 77 2 HOH HOH 97 B HOH 78 2 HOH HOH 98 B DG 1 n 1 DG 1 A DC 2 n 2 DC 2 A DG 3 n 3 DG 3 A DT 4 n 4 DT 4 A DA 5 n 5 DA 5 A U31 6 n 6 U31 6 A DA 7 n 7 DA 7 A DC 8 n 8 DC 8 A DG 9 n 9 DG 9 A DC 10 n 10 DC 10 A DG 1 n 1 DG 11 B DC 2 n 2 DC 12 B DG 3 n 3 DG 13 B DT 4 n 4 DT 14 B DA 5 n 5 DA 15 B U31 6 n 6 U31 16 B DA 7 n 7 DA 17 B DC 8 n 8 DC 18 B DG 9 n 9 DG 19 B DC 10 n 10 DC 20 B author_defined_assembly 2 dimeric A U31 6 A U31 6 U B U31 16 B U31 6 U 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 A O O HOH HOH 49 59 1.82 0.243 0.187 0.187 1.60 8.0 6234 RANDOM 1 THROUGHOUT 2.0 1.60 8.0 435 901 8 458 0 0.007 1.07 1.60 30.0 1D9H 6444 6444 0.086 1 94.8 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement X-PLOR Structural origins of the exonuclease resistance of a zwitterionic RNA 1 N N 1 N N 2 N N 2 N N covale 1.599 both A DA 5 A O3' DA 5 1_555 A U31 6 A P U31 6 1_555 covale 1.601 one A U31 6 A O3' U31 6 1_555 A DA 7 A P DA 7 1_555 covale 1.601 both B DA 15 B O3' DA 5 1_555 B U31 16 B P U31 6 1_555 covale 1.603 one B U31 16 B O3' U31 6 1_555 B DA 17 B P DA 7 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 20 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 20 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 20 B N4 DC 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 DT 4 A N3 DT 4 1_555 B DA 17 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 17 B N6 DA 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B U31 16 B N3 U31 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B U31 16 B O4 U31 6 1_555 hydrog WATSON-CRICK A U31 6 A N3 U31 6 1_555 B DA 15 B N1 DA 5 1_555 hydrog WATSON-CRICK A U31 6 A O4 U31 6 1_555 B DA 15 B N6 DA 5 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 14 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 14 B O4 DT 4 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 13 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 13 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 13 B N2 DG 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 12 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 12 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 12 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 11 B N2 DG 1 1_555 DNA, RNA EXONUCLEASE RESISTANCE, A-DNA, DNA, RNA 1D9H PDB 1 1 1D9H 1 10 1D9H 1 10 1D9H A 1 1 10 11 20 1D9H 11 20 1D9H B 1 1 10 19 orthorhombic P 21 21 21