0.030506 0.000000 0.000000 0.000000 0.030506 0.000000 0.000000 0.000000 0.009756 0.00000 0.00000 0.00000 Xiong, Y. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.0 90.0 90.0 32.78 32.78 102.5 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 C9 H13 N2 O9 P 324.181 y URIDINE-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 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 O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 R C N 125 N O N 126 R C N 127 N N N 128 N C N 129 N O N 130 N N N 131 N C N 132 N O N 133 N C N 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 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 doub 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 sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N doub N 151 N sing N 152 N sing UK RNA RNARFU 2122 1355-8382 6 1316 1324 10.1017/S135583820000090X 10999608 Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge. 2000 10.2210/pdb1dqh/pdb pdb_00001dqh 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 263 1 IMAGE PLATE RIGAKU RAXIS IIC SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU300 2806.735 RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3') HELIX II OF 5S RRNA 1 syn polymer 3231.988 RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3') 1 syn polymer 18.015 water 57 nat water no no GCCACCCUG GCCACCCUG A polyribonucleotide no no CAGGGUCGGC CAGGGUCGGC B polyribonucleotide n n n n n n n n n n n n n n n n n n n 1 2.28 46.05 VAPOR DIFFUSION, HANGING DROP 6.0 MGCL2, CACL2, CACODYLATE, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 MGCL2 1 CACL2 1 CACODYLATE 1 MPD 1 MPD 2 -1.806 1 19 A 1 B 19 0.072 A_G1:C19_B 1 -9.823 -0.273 0.185 -0.127 0.018 1 19 A 2 B 18 -1.095 A_C2:G18_B 2 -14.895 0.304 0.239 -0.226 -1.435 1 19 A 3 B 17 -2.191 A_C3:G17_B 3 -11.965 0.067 0.300 -0.128 10.217 1 20 A 4 B 15 1.003 A_A4:U15_B 4 -5.123 -0.117 0.271 -0.114 13.201 1 19 A 5 B 14 -2.123 A_C5:G14_B 5 -10.938 0.423 -0.070 -0.116 7.330 1 19 A 6 B 13 -0.668 A_C6:G13_B 6 -16.022 0.185 0.005 -0.236 1.426 1 19 A 7 B 12 -0.584 A_C7:G12_B 7 -10.165 0.233 0.004 -0.185 0.191 1 20 A 8 B 11 6.545 A_U8:A11_B 8 -14.295 0.097 0.046 -0.159 -5.036 1 19 A 9 B 10 0.161 A_G9:C10_B 9 -10.958 -0.103 0.055 -0.142 3.052 38.738 A A 1 2 8.322 B B 19 18 3.227 5.499 -0.716 -1.323 AA_G1C2:G18C19_BB 1 -2.385 3.610 38.289 -2.645 0.798 3.015 35.465 A A 2 3 10.524 B B 18 17 3.229 6.378 0.346 -0.983 AA_C2C3:G17G18_BB 2 0.791 -1.305 34.897 -2.514 -0.456 2.971 33.862 A A 3 4 2.149 B B 17 15 3.047 1.251 0.528 -1.255 AA_C3A4:U15G17_BB 3 -1.698 2.917 33.798 -2.341 -1.158 3.113 33.190 A A 4 5 8.305 B B 15 14 3.351 4.728 -0.402 -1.467 AA_A4C5:G14U15_BB 4 0.205 -0.360 32.860 -3.355 0.737 2.997 34.300 A A 5 6 12.084 B B 14 13 3.397 7.078 0.621 -1.720 AA_C5C6:G13G14_BB 5 0.820 -1.400 33.574 -4.015 -0.925 2.783 30.669 A A 6 7 15.728 B B 13 12 3.432 8.219 -0.412 -2.075 AA_C6C7:G12G13_BB 6 -1.398 2.675 29.540 -5.492 0.512 2.740 32.844 A A 7 8 16.247 B B 12 11 3.219 9.066 0.731 -1.495 AA_C7U8:A11G12_BB 7 2.268 -4.064 31.521 -4.090 -0.932 2.543 33.996 A A 8 9 21.264 B B 11 10 3.293 12.172 -0.071 -1.555 AA_U8G9:C10A11_BB 8 0.417 -0.728 31.800 -4.456 0.183 chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Other Data collection Database references 1 0 2000-11-13 1 1 2008-04-27 1 2 2011-07-13 1 3 2012-07-25 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2000-01-04 REL REL HOH water WAT 103 3 HOH HOH 103 A WAT 107 3 HOH HOH 107 A WAT 108 3 HOH HOH 108 A WAT 124 3 HOH HOH 124 A WAT 126 3 HOH HOH 126 A WAT 127 3 HOH HOH 127 A WAT 131 3 HOH HOH 131 A WAT 132 3 HOH HOH 132 A WAT 133 3 HOH HOH 133 A WAT 135 3 HOH HOH 135 A WAT 140 3 HOH HOH 140 A WAT 141 3 HOH HOH 141 A WAT 142 3 HOH HOH 142 A WAT 145 3 HOH HOH 145 A WAT 151 3 HOH HOH 151 A WAT 153 3 HOH HOH 153 A WAT 155 3 HOH HOH 155 A WAT 156 3 HOH HOH 156 A WAT 100 3 HOH HOH 100 B 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 106 3 HOH HOH 106 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 113 3 HOH HOH 113 B WAT 114 3 HOH HOH 114 B WAT 115 3 HOH HOH 115 B WAT 116 3 HOH HOH 116 B WAT 117 3 HOH HOH 117 B WAT 118 3 HOH HOH 118 B WAT 119 3 HOH HOH 119 B WAT 120 3 HOH HOH 120 B WAT 121 3 HOH HOH 121 B WAT 122 3 HOH HOH 122 B WAT 123 3 HOH HOH 123 B WAT 125 3 HOH HOH 125 B WAT 128 3 HOH HOH 128 B WAT 129 3 HOH HOH 129 B WAT 130 3 HOH HOH 130 B WAT 134 3 HOH HOH 134 B WAT 136 3 HOH HOH 136 B WAT 137 3 HOH HOH 137 B WAT 138 3 HOH HOH 138 B WAT 139 3 HOH HOH 139 B WAT 143 3 HOH HOH 143 B WAT 144 3 HOH HOH 144 B WAT 146 3 HOH HOH 146 B WAT 147 3 HOH HOH 147 B WAT 148 3 HOH HOH 148 B WAT 149 3 HOH HOH 149 B WAT 150 3 HOH HOH 150 B WAT 152 3 HOH HOH 152 B WAT 154 3 HOH HOH 154 B G 1 n 1 G 1 A C 2 n 2 C 2 A C 3 n 3 C 3 A A 4 n 4 A 4 A C 5 n 5 C 5 A C 6 n 6 C 6 A C 7 n 7 C 7 A U 8 n 8 U 8 A G 9 n 9 G 9 A C 10 n 1 C 10 B A 11 n 2 A 11 B G 12 n 3 G 12 B G 13 n 4 G 13 B G 14 n 5 G 14 B U 15 n 6 U 15 B C 16 n 7 C 16 B G 17 n 8 G 17 B G 18 n 9 G 18 B C 19 n 10 C 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 0.2430000 0.2020000 0.2020000 1.7 10.0 653 6645 6022 10.8 90.6 RANDOM 1 THROUGHOUT 2.0 MOLECULAR REPLACEMENT CNS 1.7 10.0 57 456 0 399 0 0.008 1.26 1.7 22.59 1DQH 6696 6070 2.0 1.0 0.0790000 1 20.2 4.9 90.7 phasing AMoRE refinement CNS 0.9 data reduction DENZO data scaling SCALEPACK CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS 1 N N 2 N N 3 N N 3 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 19 B N3 C 10 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 19 B O2 C 10 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 19 B N4 C 10 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B G 18 B N1 G 9 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 18 B O6 G 9 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 18 B N2 G 9 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B G 17 B N1 G 8 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B G 17 B O6 G 8 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B G 17 B N2 G 8 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 B U 15 B N3 U 6 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 B U 15 B O4 U 6 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 B G 14 B N1 G 5 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 B G 14 B O6 G 5 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 B G 14 B N2 G 5 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 B G 13 B N1 G 4 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 B G 13 B O6 G 4 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 B G 13 B N2 G 4 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 B G 12 B N1 G 3 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 B G 12 B O6 G 3 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 B G 12 B N2 G 3 1_555 hydrog WATSON-CRICK A U 8 A N3 U 8 1_555 B A 11 B N1 A 2 1_555 hydrog WATSON-CRICK A U 8 A O4 U 8 1_555 B A 11 B N6 A 2 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 B C 10 B N3 C 1 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 B C 10 B O2 C 1 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 B C 10 B N4 C 1 1_555 RNA DOUBLE HELIX, CYTOSINE BULGE, RNA 1DQH PDB 1 1DQH 1DQH PDB 2 1DQH 1 9 1DQH 1 9 1DQH A 1 1 9 10 19 1DQH 10 19 1DQH B 2 1 10 96 tetragonal P 43 21 2