0.018605 0.000000 0.005230 0.000000 0.051546 0.000000 0.000000 0.000000 0.022660 0.000000 0.000000 0.000000 Cruse, W. Saludjian, P. Neuman, A. Prange, T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 105.70 90.00 53.730 19.390 45.830 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 F N2 O8 P 326.172 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE 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 N N 138 N C N 139 N N N 140 N C N 141 N C N 142 N C N 143 N O N 144 N O N 145 N F N 146 R C N 147 N C N 148 S C N 149 R C N 150 N O N 151 N O N 152 N C N 153 N O N 154 N P N 155 N O N 156 N O N 157 N O 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 sing 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 sing N 146 N doub N 147 N doub 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 sing N 164 N sing N 165 N sing N 166 N sing N 167 N doub N 168 N sing N 169 N sing 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/pdb1id9/pdb pdb_00001id9 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 Si(111) IMAGE PLATE 1998-10-08 MARRESEARCH curvated Si(111) mirror SINGLE WAVELENGTH M x-ray 1 0.967 1.0 DW32 LURE 0.967 SYNCHROTRON LURE BEAMLINE DW32 2826.694 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3' 2 syn polymer 205.089 RHODIUM HEXAMINE ION 2 syn non-polymer 35.453 CHLORIDE ION 2 syn non-polymer 18.015 water 50 nat water no yes GCUUCGGC(UFP) GCUUCGGCN A,B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n 1 2.03 39.53 VAPOR DIFFUSION, SITTING DROP 6.8 Cacodylate, MPD, rhodium(iii) hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Cacodylate 1 MPD 1 rhodium(iii) hexammine 1 MPD 2 -5.384 1 19 A 1 B 8 -0.423 A_G1:C8_B 1 -12.337 0.060 -0.034 -0.150 -2.206 1 19 A 2 B 7 -1.567 A_C2:G7_B 2 -11.376 0.111 0.056 -0.199 -1.211 28 A 3 B 6 0.714 A_U3:G6_B 3 -7.458 2.418 0.193 -0.533 1.891 A 4 B 5 -41.505 A_U4:C5_B 4 -2.525 -0.564 -0.132 0.126 8.885 A 5 B 4 -39.783 A_C5:U4_B 5 -2.911 0.553 -0.099 0.045 3.444 28 A 6 B 3 -4.135 A_G6:U3_B 6 -9.707 -2.442 -0.083 -0.686 -4.888 1 19 A 7 B 2 -0.400 A_G7:C2_B 7 -13.163 -0.185 0.037 -0.162 -5.646 1 19 A 8 B 1 -0.728 A_C8:G1_B 8 -4.680 0.162 0.221 -0.150 2.792 32.819 A A 1 2 14.895 B B 8 7 3.192 8.317 -0.718 -1.428 AA_G1C2:G7C8_BB 1 -3.074 5.505 31.631 -3.859 0.779 3.081 41.104 A A 2 3 8.571 B B 7 6 3.302 5.998 0.246 -1.377 AA_C2U3:G6G7_BB 2 0.683 -0.976 40.677 -2.599 -0.278 2.664 21.462 A A 3 4 18.361 B B 6 5 3.174 6.720 -3.992 -1.938 AA_U3U4:C5G6_BB 3 -1.377 3.762 20.348 -7.696 10.210 2.928 38.697 A A 4 5 12.722 B B 5 4 3.404 8.364 -0.153 -1.941 AA_U4C5:U4C5_BB 4 -2.221 3.378 37.753 -3.937 -0.037 2.527 26.470 A A 5 6 21.957 B B 4 3 3.443 9.821 3.107 -1.707 AA_C5G6:U3U4_BB 5 -0.462 1.033 24.606 -6.194 -6.902 3.294 40.907 A A 6 7 6.933 B B 3 2 3.540 4.832 0.309 -1.734 AA_G6G7:C2U3_BB 6 -2.716 3.897 40.546 -3.036 -0.754 3.307 33.947 A A 7 8 1.354 B B 2 1 3.354 0.791 0.084 -2.006 AA_G7C8:G1C2_BB 7 -0.315 0.540 33.937 -3.565 -0.195 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 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 2023-08-09 _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 Rhodium hexammine replaced by iridium hexammine RCSB Y RCSB 2001-04-04 REL RHD RHODIUM HEXAMINE ION CL CHLORIDE ION HOH water phosphoramidite method sample 165D pdb entry 165D PDB experimental model RHO 11 2 RHD RHD 11 A RHO 12 2 RHD RHD 12 A CL 32 3 CL CL 32 A CL 31 3 CL CL 31 B HOH 101 4 HOH HOH 101 A HOH 102 4 HOH HOH 102 A HOH 105 4 HOH HOH 105 A HOH 107 4 HOH HOH 107 A HOH 109 4 HOH HOH 109 A HOH 111 4 HOH HOH 111 A HOH 112 4 HOH HOH 112 A HOH 113 4 HOH HOH 113 A HOH 115 4 HOH HOH 115 A HOH 116 4 HOH HOH 116 A HOH 117 4 HOH HOH 117 A HOH 118 4 HOH HOH 118 A HOH 119 4 HOH HOH 119 A HOH 121 4 HOH HOH 121 A HOH 124 4 HOH HOH 124 A HOH 125 4 HOH HOH 125 A HOH 126 4 HOH HOH 126 A HOH 127 4 HOH HOH 127 A HOH 128 4 HOH HOH 128 A HOH 129 4 HOH HOH 129 A HOH 130 4 HOH HOH 130 A HOH 131 4 HOH HOH 131 A HOH 134 4 HOH HOH 134 A HOH 136 4 HOH HOH 136 A HOH 137 4 HOH HOH 137 A HOH 138 4 HOH HOH 138 A HOH 139 4 HOH HOH 139 A HOH 141 4 HOH HOH 141 A HOH 143 4 HOH HOH 143 A HOH 145 4 HOH HOH 145 A HOH 147 4 HOH HOH 147 A HOH 149 4 HOH HOH 149 A HOH 103 4 HOH HOH 103 B HOH 104 4 HOH HOH 104 B HOH 106 4 HOH HOH 106 B HOH 108 4 HOH HOH 108 B HOH 110 4 HOH HOH 110 B HOH 114 4 HOH HOH 114 B HOH 120 4 HOH HOH 120 B HOH 122 4 HOH HOH 122 B HOH 123 4 HOH HOH 123 B HOH 132 4 HOH HOH 132 B HOH 133 4 HOH HOH 133 B HOH 135 4 HOH HOH 135 B HOH 140 4 HOH HOH 140 B HOH 142 4 HOH HOH 142 B HOH 144 4 HOH HOH 144 B HOH 146 4 HOH HOH 146 B HOH 148 4 HOH HOH 148 B HOH 150 4 HOH HOH 150 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 UFP 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 UFP 9 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 1 4.17 0.50 119.90 124.07 A A A C2 N3 C4 C C C 2 2 2 N 1 -3.34 0.40 121.90 118.56 A A A N3 C4 C5 C C C 2 2 2 N 1 3.55 0.50 121.00 124.55 A A A C5 C6 N1 C C C 2 2 2 N 1 -5.26 0.60 127.00 121.74 A A A C2 N3 C4 U U U 3 3 3 N 1 4.19 0.60 114.60 118.79 A A A N3 C4 C5 U U U 3 3 3 N 1 -5.64 0.60 125.90 120.26 A A A C5 C4 O4 U U U 3 3 3 N 1 -5.11 0.80 109.40 104.29 A A A O5' C5' C4' U U U 4 4 4 N 1 3.80 0.60 114.90 118.70 A A A N1 C2 N3 U U U 4 4 4 N 1 -4.10 0.60 127.00 122.90 A A A C2 N3 C4 U U U 4 4 4 N 1 -4.85 0.60 125.90 121.05 A A A C5 C4 O4 U U U 4 4 4 N 1 -2.44 0.40 121.90 119.46 A A A N3 C4 C5 C C C 5 5 5 N 1 -4.13 0.60 118.80 114.67 A A A C4 C5 C6 G G G 6 6 6 N 1 4.61 0.50 111.50 116.11 A A A C5 C6 N1 G G G 6 6 6 N 1 -7.33 0.60 128.60 121.27 A A A C5 C6 O6 G G G 6 6 6 N 1 3.20 0.50 111.50 114.70 A A A C5 C6 N1 G G G 7 7 7 N 1 -2.41 0.40 121.90 119.49 A A A N3 C4 C5 C C C 8 8 8 N 1 9.58 1.20 119.70 129.28 A A A C3' O3' P C C UFP 8 8 9 Y 1 -3.89 0.60 125.10 121.21 B B B C6 N1 C2 G G G 1 1 1 N 1 -3.32 0.40 121.90 118.58 B B B N3 C4 C5 C C C 2 2 2 N 1 3.25 0.50 121.00 124.25 B B B C5 C6 N1 C C C 2 2 2 N 1 -3.75 0.60 121.00 117.25 B B B C6 N1 C2 U U U 3 3 3 N 1 3.88 0.60 114.90 118.78 B B B N1 C2 N3 U U U 3 3 3 N 1 -3.90 0.60 127.00 123.10 B B B C2 N3 C4 U U U 4 4 4 N 1 -3.76 0.60 125.90 122.14 B B B C5 C4 O4 U U U 4 4 4 N 1 -9.12 1.50 119.60 110.48 B B B OP1 P OP2 C C C 5 5 5 N 1 -3.24 0.40 121.90 118.66 B B B N3 C4 C5 C C C 5 5 5 N 1 -6.02 0.80 109.40 103.38 B B B O5' C5' C4' G G G 6 6 6 N 1 -2.63 0.40 121.90 119.27 B B B N3 C4 C5 C C C 8 8 8 N Last fluoro-uracil (chain B) refined as a two-position disorder 0.195 0.156 0.155 0.153 1.6 11 410 4425 4339 98 RANDOM 1 Isotropic, the rhodium atoms were anisotropically refined THROUGHOUT 2 4 MOLECULAR REPLACEMENT pdb entry 165D personal dictionary from small molecules 1.6 11 50 454 19 385 0 0.013 0.027 0.074 0.02 0.2 0.02 0.181 1.7 64 76.9 0.198 0.02 0.166 1.8 65 74.8 0.195 0.02 0.165 2 95 77.6 0.19 0.02 0.156 3 135 69.1 0.2 0.02 0.117 5 42 54.4 0.22 0.02 0.13 11 9 42.2 18 1.6 11 1ID9 4425 4339 2 4 0.041 0.045 1 21 9 98 0.141 1.6 1.7 4.1 786 0.16 5 76 data reduction MOSFLM data scaling SCALA phasing AMoRE refinement SHELXL-97 data scaling CCP4 (SCALA) STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]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 covale 1.594 both A C 8 A O3' C 8 1_555 A UFP 9 A P UFP 9 1_555 covale 1.616 both B C 8 B O3' C 8 1_555 B UFP 9 B P UFP 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, FLUORO URACIL, RHODIUM(III) HEXAMMINE, C-U MISMATCH, G-U mismatch, DNA-RNA COMPLEX 1ID9 PDB 1 1ID9 1 9 1ID9 1 9 1ID9 A 1 1 9 1 9 1ID9 1 9 1ID9 B 1 1 9 BINDING SITE FOR RESIDUE RHD A 11 A RHD 11 Software 5 BINDING SITE FOR RESIDUE RHD A 12 A RHD 12 Software 5 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 117 G HOH 5 1_555 A HOH 119 G HOH 5 1_555 A C 5 A C 5 5 4_545 A G 7 A G 7 5 1_545 A C 8 A C 8 5 1_545 A HOH 126 G HOH 5 4_545 B C 5 B C 5 5 4_545 5 C 1 2 1