0.018587 0.000000 0.006729 0.000000 0.051546 0.000000 0.000000 0.000000 0.021139 0.000000 0.000000 0.000000 Cruse, W.B. Saludjian, P. Neuman, A. Prange, T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 109.90 90.00 53.800 19.400 50.310 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 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 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 CL N 70 N O N 71 N P N 72 N O N 73 N O N 74 N O N 75 N C N 76 R C N 77 N O N 78 S C N 79 N O N 80 R C N 81 N O N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 110 N H N 111 N RH N 112 N N N 113 N N N 114 N N N 115 N N N 116 N N N 117 N N 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 H N 136 N O N 137 N P N 138 N O N 139 N O N 140 N O N 141 N C N 142 R C N 143 N O N 144 S C N 145 N O N 146 R C N 147 N O 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 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 169 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 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/pdb1iha/pdb pdb_00001iha 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 siliciu(111) curvated crystal plus multi-layer curvated mirror IMAGE PLATE 1995-03-05 MARRESEARCH Si(111) SINGLE WAVELENGTH M x-ray 1 1.0 DW32 LURE SYNCHROTRON LURE BEAMLINE DW32 2887.600 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(BRU))-3' 2 syn polymer 205.089 RHODIUM HEXAMINE ION 2 syn non-polymer 35.453 CHLORIDE ION 2 syn non-polymer 18.015 water 61 nat water no yes GCUUCGGC(BRU) GCUUCGGCU A,B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n 1 2.18 43.70 VAPOR DIFFUSION, SITTING DROP 6.5 MPD, Rhodium hexammine, lithium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 MPD 1 Rhodium hexammine 1 lithium cacodylate 1 MPD 2 3.275 1 19 A 1 B 8 0.005 A_G1:C8_B 1 -13.129 -0.380 0.210 -0.193 1.600 1 19 A 2 B 7 -1.406 A_C2:G7_B 2 -11.076 0.042 0.105 -0.203 5.165 28 A 3 B 6 -2.790 A_U3:G6_B 3 -8.150 2.265 -0.065 -0.544 1.796 A 4 B 5 -41.940 A_U4:C5_B 4 2.564 -0.621 0.037 0.186 8.015 A 5 B 4 -41.341 A_C5:U4_B 5 -5.468 0.672 -0.338 0.148 1.264 28 A 6 B 3 -1.960 A_G6:U3_B 6 -9.432 -2.305 -0.201 -0.610 -5.217 1 19 A 7 B 2 -0.148 A_G7:C2_B 7 -13.130 -0.163 -0.066 -0.157 -3.848 1 19 A 8 B 1 -0.711 A_C8:G1_B 8 -4.159 0.239 0.209 -0.174 3.229 34.112 A A 1 2 6.389 B B 8 7 3.452 3.740 -0.184 -1.957 AA_G1C2:G7C8_BB 1 -1.492 2.550 33.880 -3.945 0.071 3.046 40.350 A A 2 3 7.254 B B 7 6 3.227 4.988 0.098 -1.330 AA_C2U3:G6G7_BB 2 2.794 -4.063 39.959 -2.470 0.161 3.351 21.720 A A 3 4 18.284 B B 6 5 3.464 6.738 -3.924 -1.965 AA_U3U4:C5G6_BB 3 -4.022 10.914 20.269 -8.086 8.700 3.091 39.145 A A 4 5 9.415 B B 5 4 3.425 6.283 -0.079 -1.885 AA_U4C5:U4C5_BB 4 0.908 -1.361 38.646 -3.568 0.227 2.356 27.891 A A 5 6 26.633 B B 4 3 3.472 12.403 3.225 -1.667 AA_C5G6:U3U4_BB 5 -0.319 0.685 25.028 -6.245 -6.763 3.213 40.138 A A 6 7 8.933 B B 3 2 3.508 6.106 0.176 -1.658 AA_G6G7:C2U3_BB 6 -2.344 3.430 39.624 -3.135 -0.532 3.268 34.302 A A 7 8 2.335 B B 2 1 3.349 1.376 0.102 -1.887 AA_G7C8:G1C2_BB 7 -1.088 1.846 34.259 -3.418 -0.345 software 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 Database references Derived calculations Refinement description 1 0 2001-05-07 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2023-08-16 _software.name _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 previous refinement using xplor at medium resolution a chloro-uracil replaces the bromo-uracil a fluoro-uracil replaces the bromo-uracil a fluoro-uracil replaces the bromo-uracil and iridium hexammine replaces the rhodium hexammine RCSB Y RCSB 2001-04-19 REL REL RHD RHODIUM HEXAMINE ION CL CHLORIDE ION HOH water phosphoramidite method sample 165D 165D from pdb 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 101 4 HOH HOH 101 A 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 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 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 122 4 HOH HOH 122 A HOH 125 4 HOH HOH 125 A HOH 128 4 HOH HOH 128 A HOH 129 4 HOH HOH 129 A HOH 131 4 HOH HOH 131 A HOH 132 4 HOH HOH 132 A HOH 134 4 HOH HOH 134 A HOH 135 4 HOH HOH 135 A HOH 137 4 HOH HOH 137 A HOH 138 4 HOH HOH 138 A HOH 139 4 HOH HOH 139 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 146 4 HOH HOH 146 A HOH 151 4 HOH HOH 151 A HOH 152 4 HOH HOH 152 A HOH 155 4 HOH HOH 155 A HOH 158 4 HOH HOH 158 A HOH 109 4 HOH HOH 109 B HOH 110 4 HOH HOH 110 B HOH 112 4 HOH HOH 112 B HOH 120 4 HOH HOH 120 B HOH 121 4 HOH HOH 121 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 130 4 HOH HOH 130 B HOH 133 4 HOH HOH 133 B HOH 136 4 HOH HOH 136 B HOH 140 4 HOH HOH 140 B HOH 141 4 HOH HOH 141 B HOH 147 4 HOH HOH 147 B HOH 148 4 HOH HOH 148 B HOH 149 4 HOH HOH 149 B HOH 150 4 HOH HOH 150 B HOH 153 4 HOH HOH 153 B HOH 154 4 HOH HOH 154 B HOH 156 4 HOH HOH 156 B HOH 157 4 HOH HOH 157 B HOH 159 4 HOH HOH 159 B HOH 160 4 HOH HOH 160 B HOH 161 4 HOH HOH 161 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 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 BRU 9 B author_defined_assembly 2 dimeric A BRU 9 A BRU 9 DU B BRU 9 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 -3.48 0.40 121.90 118.42 A A A N3 C4 C5 C C C 2 2 2 N 1 -4.76 0.60 127.00 122.24 A A A C2 N3 C4 U U U 3 3 3 N 1 4.33 0.60 114.60 118.93 A A A N3 C4 C5 U U U 3 3 3 N 1 -3.85 0.60 121.00 117.15 A A A C6 N1 C2 U U U 4 4 4 N 1 5.06 0.60 114.90 119.96 A A A N1 C2 N3 U U U 4 4 4 N 1 -5.08 0.70 122.80 117.72 A A A N1 C2 O2 U U U 4 4 4 N 1 -5.45 0.60 125.90 120.45 A A A C5 C4 O4 U U U 4 4 4 N 1 4.26 0.50 111.50 115.76 A A A C5 C6 N1 G G G 6 6 6 N 1 -4.28 0.60 128.60 124.32 A A A C5 C6 O6 G G G 6 6 6 N 1 -3.21 0.50 104.30 101.09 A A A C5 N7 C8 G G G 7 7 7 N 1 3.82 0.50 119.90 123.72 A A A C2 N3 C4 C C C 8 8 8 N 1 -2.71 0.40 121.90 119.19 A A A N3 C4 C5 C C C 8 8 8 N 1 9.26 1.20 119.70 128.96 A A A C3' O3' P C C BRU 8 8 9 Y 1 -3.71 0.60 125.10 121.39 B B B C6 N1 C2 G G G 1 1 1 N 1 4.00 0.60 114.90 118.90 B B B N1 C2 N3 U U U 3 3 3 N 1 -6.10 0.70 122.80 116.70 B B B N1 C2 O2 U U U 3 3 3 N 1 4.64 0.70 108.50 113.14 B B B O4' C1' N1 U U U 4 4 4 N 1 -4.69 0.60 125.90 121.21 B B B C5 C4 O4 U U U 4 4 4 N 1 3.03 0.50 119.90 122.93 B B B C2 N3 C4 C C C 5 5 5 N 1 -4.27 0.40 121.90 117.63 B B B N3 C4 C5 C C C 5 5 5 N 1 -4.88 0.80 109.40 104.52 B B B O5' C5' C4' G G G 6 6 6 N 1 6.16 1.00 102.60 108.76 B B B C4' C3' C2' C C C 8 8 8 N 1 -8.68 1.10 112.00 103.32 B B B N1 C1' C2' C C C 8 8 8 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 BRU 8 8 9 A Y 1 -8.59 1.20 119.70 111.11 B B B C3' O3' P C C BRU 8 8 9 B Y 1 12.24 1.90 104.00 116.24 B B B O3' P O5' C BRU BRU 8 9 9 A A Y 1 13.73 1.90 104.00 117.73 B B B O3' P O5' C BRU BRU 8 9 9 B B Y 1 6.62 1.10 110.50 117.12 B B B O3' P OP1 C BRU BRU 8 9 9 A A Y 1 B B C4' C3' C C 8 8 -0.074 0.010 1.521 1.447 N 1 B B C2' O2' C C 8 8 -0.084 0.013 1.412 1.328 N 16.3 chain B (iso <B>=11.8) is more agitated than chain A (iso <B>=18.9) 0.196 0.162 0.167 0.161 1.60 1.75 529 6346 6312 98 random 1 isotropic THROUGHOUT 2 4 MOLECULAR REPLACEMENT 165D from pdb personal dictionary from small molecules 1.60 1.75 61 469 19 389 0 0.011 0.035 0.093 0.05 0.191 0.02 0.147 1.75 125 90 0.19 0.02 0.153 1.95 101 90 0.193 0.02 0.162 2.35 135 97 0.197 0.02 0.169 3.05 95 100 0.22 0.02 0.181 9.5 73 100 17.0 1.6 9.5 1IHA 6400 6312 3 4 0.045 0.043 1 21.0 9.0 98 0.141 1.60 1.70 3.8 997 0.138 3 89 data reduction MOSFLM data reduction ROTAVATA phasing AMoRE refinement SHELXL-97 data scaling CCP4 (AGROVATA data scaling ROTAVATA Structure of the Hybrid RNA/DNA R-GCUUCGGC-D[BR]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 1.596 both A C 8 A O3' C 8 1_555 A BRU 9 A P BRU 9 1_555 covale 1.559 both B B C 8 B O3' C 8 1_555 B BRU 9 B P BRU 9 1_555 covale 1.591 both A B C 8 B O3' C 8 1_555 B BRU 9 B P BRU 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, BROMO URACIL, RHODIUM(III) HEXAMMINE, C-U G-U MISMATCH, DNA-RNA COMPLEX 1IHA PDB 1 1IHA 1 9 1IHA 1 9 1IHA A 1 1 9 1 9 1IHA 1 9 1IHA 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 4 BINDING SITE FOR RESIDUE CL B 31 B CL 31 Software 2 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 104 G HOH 4 1_555 A C 5 A C 5 4 1_555 A G 7 A G 7 4 4_546 A C 8 A C 8 4 4_546 B C 5 B C 5 4 1_555 A HOH 103 G HOH 2 1_555 B HOH 154 H HOH 2 1_555 5 C 1 2 1