0.021432 0.000000 0.000000 0.000000 0.021004 0.000000 0.000000 0.000000 0.018505 0.00000 0.00000 0.00000 Sudarsanakumar, C. Xiong, Y. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.0 90.0 90.0 46.66 47.61 54.04 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA 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 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 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 N 84 N N N 85 N C N 86 N O N 87 N N N 88 N C N 89 N O N 90 N C N 91 N C N 92 N C N 93 N H 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 R C N 119 N O 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 H N 148 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 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 doub N 66 N sing N 67 N doub N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N doub N 101 N sing N 102 N sing N 103 N sing N 104 N doub N 105 N sing 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 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 N 135 N sing Y 136 N sing Y 137 N sing Y 138 N doub N 139 N sing Y 140 N sing N 141 N sing Y 142 N doub N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 299 103 112 10.1006/jmbi.2000.3730 10860725 Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag). 2000 10.2210/pdb1efo/pdb pdb_00001efo 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 297 1 IMAGE PLATE 1999-07-22 RIGAKU RAXIS IIC SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 2617.723 DNA (5'-D(*CP*TP*CP*CP*TP*CP*TP*TP*C)-3') 1 syn polymer 3327.100 RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3') 1 syn polymer 18.015 water 23 nat water no no (DC)(DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC) CTCCTCTTC A polydeoxyribonucleotide no no GAAGAGAGAG GAAGAGAGAG B polyribonucleotide n n n n n n n n n n n n n n n n n n n 1 2.49 50.62 VAPOR DIFFUSION, HANGING DROP 6.0 MPD, LITHIUM CHLORIDE, SPERMINE TETRACHLORIDE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 SPERMINE TETRACHLORIDE 1 CACODYLATE 1 LICL 1 MPD 1 LICL 2 MPD 2 -9.099 1 19 A 1 B 19 0.561 A_DC1:G19_B 1 0.527 0.463 0.245 -0.357 10.510 1 20 A 2 B 18 2.003 A_DT2:A18_B 2 -5.910 0.248 -0.035 -0.240 11.155 1 19 A 3 B 17 7.133 A_DC3:G17_B 3 -9.044 1.077 -0.201 -0.279 3.697 1 19 A 4 B 15 5.100 A_DC4:G15_B 4 -7.725 0.071 -0.052 0.010 12.821 1 20 A 5 B 14 7.429 A_DT5:A14_B 5 -11.543 -0.397 -0.060 -0.027 10.339 1 19 A 6 B 13 0.974 A_DC6:G13_B 6 -10.329 0.903 -0.060 -0.400 6.136 1 20 A 7 B 12 10.038 A_DT7:A12_B 7 -17.095 0.198 -0.052 -0.362 6.486 1 20 A 8 B 11 3.365 A_DT8:A11_B 8 -11.057 0.287 0.186 -0.285 5.302 1 19 A 9 B 10 7.221 A_DC9:G10_B 9 -13.089 0.382 0.098 -0.146 2.937 25.062 A A 1 2 -2.410 B B 19 18 2.870 -1.046 -0.393 -1.882 AA_DC1DT2:A18G19_BB 1 0.465 -1.071 25.036 -4.061 1.027 3.368 35.280 A A 2 3 1.500 B B 18 17 3.422 0.909 0.443 -1.736 AA_DT2DC3:G17A18_BB 2 -0.739 1.219 35.261 -3.005 -0.845 3.256 27.757 A A 3 4 7.474 B B 17 15 3.512 3.575 -0.451 -1.953 AA_DC3DC4:G15G17_BB 3 -1.448 3.028 27.493 -4.966 0.577 2.944 28.292 A A 4 5 9.272 B B 15 14 3.233 4.504 -0.173 -1.585 AA_DC4DT5:A14G15_BB 4 -3.242 6.675 27.754 -4.238 -0.363 2.882 35.453 A A 5 6 17.484 B B 14 13 3.413 10.475 -0.888 -1.615 AA_DT5DC6:G13A14_BB 5 -3.984 6.650 33.689 -4.172 0.881 2.809 32.343 A A 6 7 16.745 B B 13 12 3.304 9.182 1.025 -1.673 AA_DC6DT7:A12G13_BB 6 3.975 -7.250 30.795 -4.561 -1.167 2.662 29.133 A A 7 8 18.275 B B 12 11 3.351 9.043 -0.962 -1.888 AA_DT7DT8:A11A12_BB 7 -1.546 3.124 27.681 -5.619 1.594 3.280 35.245 A A 8 9 0.413 B B 11 10 3.300 0.250 0.086 -1.337 AA_DT8DC9:G10A11_BB 8 -2.053 3.392 35.186 -2.245 -0.450 software chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references 1 0 2000-05-29 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2000-02-09 REL REL HOH water WAT 103 3 HOH HOH 103 A WAT 106 3 HOH HOH 106 A WAT 113 3 HOH HOH 113 A WAT 117 3 HOH HOH 117 A WAT 118 3 HOH HOH 118 A WAT 120 3 HOH HOH 120 A WAT 121 3 HOH HOH 121 A WAT 101 3 HOH HOH 101 B WAT 102 3 HOH HOH 102 B WAT 104 3 HOH HOH 104 B WAT 105 3 HOH HOH 105 B WAT 107 3 HOH HOH 107 B WAT 108 3 HOH HOH 108 B WAT 109 3 HOH HOH 109 B WAT 110 3 HOH HOH 110 B WAT 111 3 HOH HOH 111 B WAT 112 3 HOH HOH 112 B WAT 114 3 HOH HOH 114 B WAT 115 3 HOH HOH 115 B WAT 116 3 HOH HOH 116 B WAT 119 3 HOH HOH 119 B WAT 122 3 HOH HOH 122 B WAT 123 3 HOH HOH 123 B C 1 n 1 DC 1 A T 2 n 2 DT 2 A C 3 n 3 DC 3 A C 4 n 4 DC 4 A T 5 n 5 DT 5 A C 6 n 6 DC 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A G 10 n 1 G 10 B A 11 n 2 A 11 B A 12 n 3 A 12 B G 13 n 4 G 13 B A 14 n 5 A 14 B G 15 n 6 G 15 B A 16 n 7 A 16 B G 17 n 8 G 17 B A 18 n 9 A 18 B G 19 n 10 G 19 B author_defined_assembly 2 dimeric 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 0.2220000 0.1990000 0.1990000 2.30 10.0 237 2578 2486 9 91.4 RANDOM 1 THROUGHOUT 2.0 1.0 2.30 10.0 23 417 0 394 0 0.007 1.2 2.3 10.0 1EFO 2880 2486 2.0 1.0 0.0700000 1 5.6 91.4 0.0800000 2.30 2.38 4.0 71.3 phasing AMoRE refinement CNS data scaling SCALEPACK CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG) 1 N N 2 N N 3 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B G 19 B N1 G 10 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B G 19 B O6 G 10 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B G 19 B N2 G 10 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B A 18 B N1 A 9 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B A 18 B N6 A 9 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B G 17 B N1 G 8 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B G 17 B O6 G 8 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B G 17 B N2 G 8 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B G 15 B N1 G 6 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B G 15 B O6 G 6 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B G 15 B N2 G 6 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B A 14 B N1 A 5 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B A 14 B N6 A 5 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B G 13 B N1 G 4 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B G 13 B O6 G 4 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B G 13 B N2 G 4 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B A 12 B N1 A 3 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B A 12 B N6 A 3 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B A 11 B N1 A 2 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B A 11 B N6 A 2 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B G 10 B N1 G 1 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B G 10 B O6 G 1 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B G 10 B N2 G 1 1_555 DNA-RNA HYBRID A-FORM CONFORMATION, HYBRID, ADENINE BULGE, LOOPED OUT, DNA-RNA COMPLEX, DNA-RNA HYBRID 1EFO PDB 1 1EFO 1EFO PDB 2 1EFO 1 9 1EFO 1 9 1EFO A 1 1 9 10 19 1EFO 10 19 1EFO B 2 1 10 23 orthorhombic I 2 2 2