0.018587 0.000000 0.006729 0.000000 0.051546 0.000000 0.000000 0.000000 0.021211 0.00000 0.00000 0.00000 THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED (NAMED RHD), TWO WITH FULL OCCUPANCY FACTORS (RESIDUES 19 AND 20) AND TWO WITH PARTIAL OCCUPANCIES (RESIDUES 21 AND 22). Cruse, W. Saludjian, P. Biala, E. Strazewski, P. Prange, T. Kennard, O. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 109.90 90.00 53.800 19.400 50.140 C9 H12 Br N2 O8 P 387.078 n 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE DNA 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 H18 N6 Rh 3 205.089 RHODIUM HEXAMINE ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N O N 8 N O N 9 N BR N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O N 22 N H 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 O N 35 N P N 36 N O N 37 N O N 38 N O N 39 N C N 40 R C N 41 N O N 42 S C N 43 N O N 44 R C N 45 N O N 46 R C N 47 N N N 48 N C N 49 N O N 50 N N N 51 N C N 52 N N N 53 N C N 54 N C N 55 N H N 56 N H 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 O N 70 N P N 71 N O N 72 N O N 73 N O N 74 N C N 75 R C N 76 N O N 77 S C N 78 N O N 79 R C N 80 N O N 81 R C Y 82 N N Y 83 N C Y 84 N N Y 85 N C N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N N Y 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 O N 108 N H N 109 N H N 110 N RH N 111 N N N 112 N N N 113 N N N 114 N N N 115 N N N 116 N N N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H 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 O N 136 N P N 137 N O N 138 N O N 139 N O N 140 N C N 141 R C N 142 N O N 143 S C N 144 N O N 145 R C N 146 N O N 147 R C N 148 N N N 149 N C N 150 N O N 151 N N N 152 N C N 153 N O N 154 N C N 155 N C N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N sing N 9 N doub N 10 N doub 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 N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub 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 doub 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 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 doub N 62 N sing N 63 N doub N 64 N sing N 65 N sing N 66 N sing 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 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 Y 95 N sing Y 96 N sing Y 97 N doub N 98 N sing Y 99 N sing N 100 N sing Y 101 N doub N 102 N doub N 103 N sing N 104 N sing 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 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 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 doub 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 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 doub N 164 N sing N 165 N sing N 166 N sing N 167 N doub N 168 N sing N 169 N doub N 170 N sing N 171 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 91 4160 4164 10.1073/pnas.91.10.4160 7514296 Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure. 1994 10.2210/pdb165d/pdb pdb_0000165d 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 1 IMAGE PLATE MARRESEARCH DIFFRACTOMETER ENRAF-NONIUS FAST M x-ray 1 M x-ray 2 1.0 1.0 LURE SYNCHROTRON LURE 2887.600 DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3') 2 syn polymer 205.089 RHODIUM HEXAMINE ION 4 syn non-polymer 18.015 water 54 nat water no yes GCUUCGGC(BRU) GCUUCGGCU A,B polyribonucleotide n n n n n n n n n 2.13 42.26 VAPOR DIFFUSION, SITTING DROP 6.30 pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K 277.00 WATER 1 LI CACODYLATE 1 [RH(NH3)6]CL3 1 0.915 1 19 A 1 B 17 1.089 A_G1:C17_B 1 -13.439 -0.507 -0.271 -0.379 5.509 1 19 A 2 B 16 1.106 A_C2:G16_B 2 -11.964 0.162 -0.027 -0.263 4.776 28 A 3 B 15 -1.858 A_U3:G15_B 3 -10.255 2.233 -0.124 -0.490 2.026 A 4 B 14 -40.981 A_U4:C14_B 4 2.784 -0.638 0.220 0.206 7.013 A 5 B 13 -39.828 A_C5:U13_B 5 -3.734 0.733 -0.397 0.119 -0.232 1 28 A 6 B 12 -1.239 A_G6:U12_B 6 -12.882 -2.244 -0.180 -0.601 -4.817 1 19 A 7 B 11 1.012 A_G7:C11_B 7 -12.774 -0.178 -0.160 -0.118 -3.779 1 19 A 8 B 10 -0.871 A_C8:G10_B 8 -6.718 0.445 0.090 -0.195 3.012 35.993 A A 1 2 7.535 B B 17 16 3.238 4.640 -0.228 -1.669 AA_G1C2:G16C17_BB 1 -2.718 4.415 35.602 -3.335 -0.002 3.163 38.323 A A 2 3 8.177 B B 16 15 3.377 5.349 -0.023 -1.320 AA_C2U3:G15G16_BB 2 2.142 -3.275 37.904 -2.684 0.305 3.479 22.320 A A 3 4 17.641 B B 15 14 3.406 6.663 -3.926 -1.958 AA_U3U4:C14G15_BB 3 -5.163 13.668 20.686 -7.783 8.032 3.164 39.169 A A 4 5 9.174 B B 14 13 3.489 6.124 0.004 -1.867 AA_U4C5:U13C14_BB 4 2.016 -3.019 38.655 -3.536 0.241 2.344 27.932 A A 5 6 25.709 B B 13 12 3.434 12.018 3.202 -1.635 AA_C5G6:U12U13_BB 5 -0.651 1.393 25.252 -6.047 -6.779 3.103 40.218 A A 6 7 11.075 B B 12 11 3.456 7.573 0.186 -1.616 AA_G6G7:C11U12_BB 6 -0.690 1.009 39.522 -3.219 -0.350 3.497 35.346 A A 7 8 -1.251 B B 11 10 3.462 -0.759 0.107 -1.732 AA_G7C8:G10C11_BB 7 -0.073 0.121 35.338 -2.734 -0.187 diffrn_detector chem_comp_atom chem_comp_bond database_2 pdbx_struct_special_symmetry struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Data collection Database references Derived calculations 1 0 1994-08-31 1 1 2008-05-22 1 2 2011-07-13 1 3 2018-04-18 1 4 2024-02-07 _diffrn_detector.detector _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 BNL Y NDB 1994-03-21 REL RHD RHODIUM HEXAMINE ION HOH water RHD 19 2 RHD RHD 19 A RHD 20 2 RHD RHD 20 A RHD 22 2 RHD RHD 22 A RHD 21 2 RHD RHD 21 B HOH 23 3 HOH HOH 23 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 33 3 HOH HOH 33 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 41 3 HOH HOH 41 A HOH 43 3 HOH HOH 43 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 A HOH 51 3 HOH HOH 51 A HOH 53 3 HOH HOH 53 A HOH 54 3 HOH HOH 54 A HOH 56 3 HOH HOH 56 A HOH 57 3 HOH HOH 57 A HOH 59 3 HOH HOH 59 A HOH 60 3 HOH HOH 60 A HOH 61 3 HOH HOH 61 A HOH 63 3 HOH HOH 63 A HOH 64 3 HOH HOH 64 A HOH 65 3 HOH HOH 65 A HOH 66 3 HOH HOH 66 A HOH 73 3 HOH HOH 73 A HOH 74 3 HOH HOH 74 A HOH 24 3 HOH HOH 24 B HOH 32 3 HOH HOH 32 B HOH 34 3 HOH HOH 34 B HOH 39 3 HOH HOH 39 B HOH 40 3 HOH HOH 40 B HOH 42 3 HOH HOH 42 B HOH 44 3 HOH HOH 44 B HOH 45 3 HOH HOH 45 B HOH 46 3 HOH HOH 46 B HOH 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 B HOH 52 3 HOH HOH 52 B HOH 55 3 HOH HOH 55 B HOH 58 3 HOH HOH 58 B HOH 62 3 HOH HOH 62 B HOH 67 3 HOH HOH 67 B HOH 68 3 HOH HOH 68 B HOH 69 3 HOH HOH 69 B HOH 70 3 HOH HOH 70 B HOH 71 3 HOH HOH 71 B HOH 72 3 HOH HOH 72 B HOH 75 3 HOH HOH 75 B HOH 76 3 HOH HOH 76 B G 1 n 1 G 1 A C 2 n 2 C 2 A U 3 n 3 U 3 A U 4 n 4 U 4 A C 5 n 5 C 5 A G 6 n 6 G 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A +U 9 n 9 BRU 9 A G 10 n 1 G 10 B C 11 n 2 C 11 B U 12 n 3 U 12 B U 13 n 4 U 13 B C 14 n 5 C 14 B G 15 n 6 G 15 B G 16 n 7 G 16 B C 17 n 8 C 17 B +U 18 n 9 BRU 18 B author_defined_assembly 2 dimeric A BRU 9 A BRU 9 DU B BRU 18 B BRU 9 DU 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 B BRU 18 B BRU 9 1 A A O O HOH HOH 51 61 1.43 1 B B O O HOH HOH 50 71 2.05 1 A G 1 0.075 SIDE CHAIN 1 A G 7 0.073 SIDE CHAIN 1 B C 11 0.072 SIDE CHAIN 1 -4.37 0.70 122.20 117.83 A A A N3 C2 O2 U U U 3 3 3 N 1 7.03 1.10 110.50 117.53 A A A O3' P OP2 U U U 3 4 4 Y 1 5.02 0.70 108.50 113.52 B B B O4' C1' N1 U U U 13 13 13 N 1 -11.63 1.90 104.00 92.37 B B B O3' P O5' C G G 14 15 15 Y 1 18.09 1.10 110.50 128.59 B B B O3' P OP2 C G G 14 15 15 Y 1 6.74 1.10 110.50 117.24 B B B O3' P OP2 G G G 15 16 16 Y 1 13.40 1.10 110.50 123.90 B B B O3' P OP2 C BRU BRU 17 18 18 A A Y 1 -28.72 2.20 105.20 76.48 B B B O3' P OP2 C BRU BRU 17 18 18 B B Y 1 16.67 1.10 110.50 127.17 B B B O3' P OP1 C BRU BRU 17 18 18 B B Y 0.18 0.18 1.550 10.000 6098 1 2.000 1.550 10.000 54 474 31 389 0 0.017 0.030 2.10 1.600 165D 6093 2.000 1,2 refinement X-PLOR THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N covale 1.584 both A C 8 A O3' C 8 1_555 A BRU 9 A P BRU 9 1_555 covale 1.617 both A B C 17 B O3' C 8 1_555 B BRU 18 B P BRU 9 1_555 covale 1.632 both B B C 17 B O3' C 8 1_555 B BRU 18 B P BRU 9 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 17 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 17 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 17 B N4 C 8 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B G 16 B N1 G 7 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 16 B O6 G 7 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 16 B N2 G 7 1_555 hydrog TYPE_28_PAIR A U 3 A N3 U 3 1_555 B G 15 B O6 G 6 1_555 hydrog TYPE_28_PAIR A U 3 A O2 U 3 1_555 B G 15 B N1 G 6 1_555 hydrog U-C MISPAIR A U 4 A O4 U 4 1_555 B C 14 B N4 C 5 1_555 hydrog C-U MISPAIR A C 5 A N4 C 5 1_555 B U 13 B O4 U 4 1_555 hydrog TYPE_28_PAIR A G 6 A N1 G 6 1_555 B U 12 B O2 U 3 1_555 hydrog TYPE_28_PAIR A G 6 A O6 G 6 1_555 B U 12 B N3 U 3 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 11 B N3 C 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 11 B O2 C 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 11 B N4 C 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 10 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 10 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 10 B N2 G 1 1_555 DNA-RNA HYBRID A-DNA/RNA, DOUBLE HELIX, OVERHANGING BASES, MODIFIED, MISMATCHED, DNA-RNA HYBRID 165D PDB 1 165D 1 9 165D 1 9 165D A 1 1 9 10 18 165D 10 18 165D B 1 1 9 BINDING SITE FOR RESIDUE RHD A 19 A RHD 19 Software 5 BINDING SITE FOR RESIDUE RHD A 20 A RHD 20 Software 5 BINDING SITE FOR RESIDUE RHD B 21 B RHD 21 Software 5 BINDING SITE FOR RESIDUE RHD A 22 A RHD 22 Software 6 A C 5 A C 5 5 1_555 A G 6 A G 6 5 1_555 A G 7 A G 7 5 1_555 A HOH 26 G HOH 5 1_555 B HOH 72 H HOH 5 1_555 A C 5 A C 5 5 4_546 A G 7 A G 7 5 1_545 A C 8 A C 8 5 1_545 B C 14 B C 5 5 4_546 B HOH 45 H HOH 5 4_546 A U 3 A U 3 5 1_555 B G 15 B G 6 5 1_555 B G 16 B G 7 5 1_555 B HOH 34 H HOH 5 1_555 B HOH 46 H HOH 5 1_555 A C 2 A C 2 6 2_566 A U 3 A U 3 6 2_566 A BRU 9 A BRU 9 6 1_555 B C 11 B C 2 6 2_556 B U 12 B U 3 6 2_556 B HOH 32 H HOH 6 2_556 5 C 1 2 1