0.018580 0.000000 0.006726 0.000000 0.051600 0.000000 0.000000 0.000000 0.021143 0.000000 0.000000 0.000000 Cruse, W. Saludjian, P. Neuman, A. Prange, T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 109.90 90.00 53.820 19.380 50.300 C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking Cl -1 35.453 CHLORIDE ION non-polymer 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 C9 H12 Cl N2 O8 P 342.627 n 5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN 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 N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N N N 20 N C N 21 N C 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 H N 35 N H N 36 N CL 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 R C N 48 N O N 49 R C Y 50 N N Y 51 N C Y 52 N N Y 53 N C N 54 N C N 55 N O N 56 N N N 57 N C N 58 N N N 59 N N Y 60 N C 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 H N 74 N H N 75 N O N 76 N H N 77 N H N 78 N RH N 79 N N N 80 N N N 81 N N N 82 N N N 83 N N N 84 N N N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H 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 O N 104 N P N 105 N O N 106 N O N 107 N O N 108 N C N 109 R C N 110 N O N 111 S C N 112 N O N 113 R C N 114 N O N 115 R C N 116 N N N 117 N C N 118 N O N 119 N N N 120 N C N 121 N O N 122 N C N 123 N C 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 H N 136 N H N 137 N O N 138 N P N 139 N O N 140 N O N 141 N O N 142 N C N 143 R C N 144 N O N 145 S C N 146 N O N 147 N C N 148 R C N 149 N N N 150 N C N 151 N O N 152 N N N 153 N C N 154 N O N 155 N C N 156 N C N 157 N CL 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 169 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 N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N doub N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N doub 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 Y 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N sing N 66 N sing Y 67 N doub 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 N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing 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 doub N 130 N sing N 131 N sing N 132 N sing N 133 N doub N 134 N sing N 135 N doub 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 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 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 57 1609 1613 10.1107/S0907444901012318 11679725 Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues 2001 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 91 4160 4164 Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure 1994 10.2210/pdb1idw/pdb pdb_00001idw 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 277 1 mirrors DIFFRACTOMETER 1997-03-20 ENRAF-NONIUS FAST GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE ENRAF-NONIUS FR571 2843.149 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3' 2 syn polymer 205.089 RHODIUM HEXAMINE ION 2 syn non-polymer 35.453 CHLORIDE ION 2 syn non-polymer 18.015 water 46 nat water no yes GCUUCGGC(UCL) GCUUCGGCU A,B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n 1 2.18 43.66 VAPOR DIFFUSION, SITTING DROP 6.8 cacodylate buffer, MPD, Rhodium-hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 cacodylate buffer 1 MPD 1 rhodium-hexammine 1 MPD 2 0.213 1 19 A 1 B 8 -3.177 A_G1:C8_B 1 -7.216 -0.689 0.220 -0.341 3.982 1 19 A 2 B 7 -1.020 A_C2:G7_B 2 -13.355 0.123 -0.027 -0.139 0.295 28 A 3 B 6 -1.163 A_U3:G6_B 3 -8.164 2.396 0.168 -0.531 2.194 A 4 B 5 -43.178 A_U4:C5_B 4 0.772 -0.552 0.004 0.232 7.951 A 5 B 4 -40.763 A_C5:U4_B 5 -4.351 0.664 -0.444 0.070 -1.934 28 A 6 B 3 -1.535 A_G6:U3_B 6 -11.060 -2.353 -0.282 -0.576 -5.396 1 19 A 7 B 2 -1.176 A_G7:C2_B 7 -11.113 -0.268 -0.043 -0.175 -4.870 1 19 A 8 B 1 -0.551 A_C8:G1_B 8 -5.215 0.307 0.279 -0.147 3.186 35.926 A A 1 2 1.964 B B 8 7 3.248 1.211 -0.127 -1.818 AA_G1C2:G7C8_BB 1 0.335 -0.543 35.904 -3.117 0.252 3.221 41.049 A A 2 3 9.818 B B 7 6 3.481 6.855 0.071 -1.349 AA_C2U3:G6G7_BB 2 0.271 -0.388 40.496 -2.693 -0.071 3.518 20.414 A A 3 4 11.728 B B 6 5 3.289 4.106 -4.109 -1.956 AA_U3U4:C5G6_BB 3 -3.710 10.597 19.658 -7.466 9.833 2.996 38.987 A A 4 5 12.959 B B 5 4 3.481 8.582 -0.095 -1.892 AA_U4C5:U4C5_BB 4 1.290 -1.948 38.045 -3.876 0.298 2.516 27.328 A A 5 6 25.875 B B 4 3 3.612 11.833 3.175 -1.532 AA_C5G6:U3U4_BB 5 -0.842 1.841 24.663 -6.145 -6.926 3.210 39.743 A A 6 7 6.803 B B 3 2 3.444 4.609 0.200 -1.625 AA_G6G7:C2U3_BB 6 -3.719 5.489 39.317 -2.939 -0.737 3.365 34.828 A A 7 8 0.417 B B 2 1 3.380 0.250 0.199 -1.910 AA_G7C8:G1C2_BB 7 -0.201 0.336 34.826 -3.230 -0.364 software diffrn_detector chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Version format compliance Refinement description Data collection Data collection Database references Derived calculations Refinement description 1 0 2001-04-12 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2018-04-18 1 5 2023-08-09 _software.name _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 A fluoro-Uracil replaces the chloro-uracil at position #9 RCSB Y RCSB 2001-04-05 REL RHD RHODIUM HEXAMINE ION CL CHLORIDE ION HOH water phosphoramidite method sample 165D PDB ENTRY 165D PDB experimental model RHD 11 2 RHD RHD 11 A RHD 12 2 RHD RHD 12 A CL 32 3 CL CL 32 A CL 31 3 CL CL 31 B HOH 102 4 HOH HOH 102 A HOH 103 4 HOH HOH 103 A HOH 104 4 HOH HOH 104 A HOH 105 4 HOH HOH 105 A HOH 106 4 HOH HOH 106 A HOH 107 4 HOH HOH 107 A HOH 108 4 HOH HOH 108 A HOH 110 4 HOH HOH 110 A HOH 111 4 HOH HOH 111 A HOH 113 4 HOH HOH 113 A HOH 114 4 HOH HOH 114 A HOH 115 4 HOH HOH 115 A HOH 117 4 HOH HOH 117 A HOH 118 4 HOH HOH 118 A HOH 119 4 HOH HOH 119 A HOH 120 4 HOH HOH 120 A HOH 121 4 HOH HOH 121 A HOH 122 4 HOH HOH 122 A HOH 125 4 HOH HOH 125 A HOH 131 4 HOH HOH 131 A HOH 132 4 HOH HOH 132 A HOH 134 4 HOH HOH 134 A HOH 137 4 HOH HOH 137 A HOH 138 4 HOH HOH 138 A HOH 142 4 HOH HOH 142 A HOH 143 4 HOH HOH 143 A HOH 144 4 HOH HOH 144 A HOH 145 4 HOH HOH 145 A HOH 101 4 HOH HOH 101 B HOH 109 4 HOH HOH 109 B HOH 112 4 HOH HOH 112 B HOH 116 4 HOH HOH 116 B HOH 123 4 HOH HOH 123 B HOH 124 4 HOH HOH 124 B HOH 126 4 HOH HOH 126 B HOH 127 4 HOH HOH 127 B HOH 128 4 HOH HOH 128 B HOH 129 4 HOH HOH 129 B HOH 130 4 HOH HOH 130 B HOH 133 4 HOH HOH 133 B HOH 135 4 HOH HOH 135 B HOH 136 4 HOH HOH 136 B HOH 139 4 HOH HOH 139 B HOH 140 4 HOH HOH 140 B HOH 141 4 HOH HOH 141 B HOH 146 4 HOH HOH 146 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 UCL 9 A G 1 n 1 G 1 B C 2 n 2 C 2 B U 3 n 3 U 3 B U 4 n 4 U 4 B C 5 n 5 C 5 B G 6 n 6 G 6 B G 7 n 7 G 7 B C 8 n 8 C 8 B +U 9 n 9 UCL 9 B author_defined_assembly 2 dimeric A UCL 9 A UCL 9 DU B UCL 9 B UCL 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 C4' UCL 9 PLANAR B 1 -3.64 0.60 125.10 121.46 A A A C6 N1 C2 G G G 1 1 1 N 1 4.15 0.60 114.90 119.05 A A A N1 C2 N3 U U U 3 3 3 N 1 -4.72 0.60 127.00 122.28 A A A C2 N3 C4 U U U 3 3 3 N 1 -3.93 0.60 125.90 121.97 A A A C5 C4 O4 U U U 3 3 3 N 1 -4.93 0.60 125.90 120.97 A A A C5 C4 O4 U U U 4 4 4 N 1 -2.40 0.40 121.90 119.50 A A A N3 C4 C5 C C C 5 5 5 N 1 3.02 0.50 111.50 114.52 A A A C5 C6 N1 G G G 6 6 6 N 1 -6.23 0.80 109.40 103.17 A A A O5' C5' C4' G G G 7 7 7 N 1 -4.81 0.60 125.10 120.29 B B B C6 N1 C2 G G G 1 1 1 N 1 -4.10 0.60 119.90 115.80 B B B N1 C6 O6 G G G 1 1 1 N 1 -4.34 0.60 125.90 121.56 B B B C5 C4 O4 U U U 3 3 3 N 1 -4.25 0.60 127.00 122.75 B B B C2 N3 C4 U U U 4 4 4 N 1 -6.15 0.80 109.40 103.25 B B B O5' C5' C4' G G G 6 6 6 N 1 -6.42 0.80 108.20 101.78 B B B O4' C1' N1 C C C 8 8 8 N 1 -12.39 1.20 119.70 107.31 B B B C3' O3' P C C UCL 8 8 9 A Y 1 -8.59 1.20 119.70 111.11 B B B C3' O3' P C C UCL 8 8 9 B Y 1 17.68 1.90 104.00 121.68 B B B O3' P O5' C UCL UCL 8 9 9 A A Y 1 12.75 1.90 104.00 116.75 B B B O3' P O5' C UCL UCL 8 9 9 B B Y 18.4 Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. One chlorine atom is disordered. 0.202 0.172 0.176 0.172 1.8 6.0 311 3738 3641 95 RANDOM 1 isotropic THROUGHOUT 2 4 FOURIER SYNTHESIS PDB ENTRY 165D personal dictionary from small molecules 1.8 6.0 46 455 20 389 0 0.011 0.032 0.097 0.071 0.21 0.02 0.169 2.0 40 43.2 0.191 0.02 0.164 2.3 93 98.5 0.211 0.02 0.176 2.7 80 98.7 0.187 0.02 0.168 3.5 69 96.8 0.19 0.02 0.195 6.0 30 76.5 16.4 1.81 6 1IDW 3738 3641 2 4 0.039 0.041 1 18 3.5 97 0.212 1.8 2. 3.0 517 0.206 2.5 43.2 data collection MADNESS data reduction ROTAVATA phasing AMoRE refinement SHELXL-97 data reduction MADNESS data scaling CCP4 (AGROVATA data scaling ROTAVATA STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF RH(NH3)6+++ 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N 4 N N 4 N N The second strand of the dimer is not symmetric covale 1.589 both A C 8 A O3' C 8 1_555 A UCL 9 A P UCL 9 1_555 covale 1.591 both A B C 8 B O3' C 8 1_555 B UCL 9 B P UCL 9 1_555 covale 1.559 both B B C 8 B O3' C 8 1_555 B UCL 9 B P UCL 9 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B G 7 B N1 G 7 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 7 B O6 G 7 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 7 B N2 G 7 1_555 hydrog TYPE_28_PAIR A U 3 A N3 U 3 1_555 B G 6 B O6 G 6 1_555 hydrog TYPE_28_PAIR A U 3 A O2 U 3 1_555 B G 6 B N1 G 6 1_555 hydrog U-C MISPAIR A U 4 A O4 U 4 1_555 B C 5 B N4 C 5 1_555 hydrog C-U MISPAIR A C 5 A N4 C 5 1_555 B U 4 B O4 U 4 1_555 hydrog TYPE_28_PAIR A G 6 A N1 G 6 1_555 B U 3 B O2 U 3 1_555 hydrog TYPE_28_PAIR A G 6 A O6 G 6 1_555 B U 3 B N3 U 3 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 2 B N3 C 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 2 B O2 C 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 2 B N4 C 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 1 B N2 G 1 1_555 DNA/RNA RNA/DNA HYBRID, RHODIUM HEXAMMINE, C-U MISMATCH, G-U MISMATCH, DNA-RNA COMPLEX 1IDW PDB 1 1IDW 1 9 1IDW 1 9 1IDW A 1 1 9 1 9 1IDW 1 9 1IDW B 1 1 9 BINDING SITE FOR RESIDUE RHD A 11 A RHD 11 Software 4 BINDING SITE FOR RESIDUE RHD A 12 A RHD 12 Software 5 A C 5 A C 5 4 1_555 A G 6 A G 6 4 1_555 A G 7 A G 7 4 1_555 A HOH 106 G HOH 4 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 5 B C 5 5 4_546 B HOH 126 H HOH 5 4_546 5 C 1 2 1