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 53.750 19.400 45.840 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 Ir N6 3 294.400 IRIDIUM HEXAMMINE 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 IR 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/pdb1icg/pdb pdb_00001icg 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(III) curvated crystal IMAGE PLATE 1998-10-10 MARRESEARCH Si(III) 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 35.453 CHLORIDE ION 2 syn non-polymer 294.400 IRIDIUM HEXAMMINE ION 2 syn non-polymer 18.015 water 49 nat water no yes GCUUCGGC(UFP) GCUUCGGCN A,B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n 1 2.03 39.55 VAPOR DIFFUSION, SITTING DROP 6.5 cacodylate, iridium hexammine, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 cacodylate 1 Iridium hexammine 1 MPD 1 MPD 2 -7.457 1 19 A 1 B 8 -0.226 A_G1:C8_B 1 -10.242 -0.116 -0.145 -0.141 0.591 1 19 A 2 B 7 -0.964 A_C2:G7_B 2 -11.051 0.060 0.122 -0.191 3.345 28 A 3 B 6 -3.220 A_U3:G6_B 3 -7.995 2.554 0.136 -0.598 0.798 A 4 B 5 -41.887 A_U4:C5_B 4 0.630 -0.636 -0.044 0.087 10.606 A 5 B 4 -43.201 A_C5:U4_B 5 -3.793 0.526 -0.251 0.171 0.851 28 A 6 B 3 -2.077 A_G6:U3_B 6 -10.233 -2.358 -0.305 -0.664 -6.867 1 19 A 7 B 2 -0.885 A_G7:C2_B 7 -13.082 -0.230 -0.045 -0.204 -5.184 1 19 A 8 B 1 -2.370 A_C8:G1_B 8 -2.530 0.250 0.125 -0.197 2.811 33.146 A A 1 2 11.595 B B 8 7 3.104 6.555 -0.597 -1.480 AA_G1C2:G7C8_BB 1 -4.287 7.582 32.233 -3.605 0.385 3.022 42.431 A A 2 3 8.255 B B 7 6 3.233 5.955 0.035 -1.348 AA_C2U3:G6G7_BB 2 1.709 -2.369 41.997 -2.445 0.118 2.881 19.501 A A 3 4 18.567 B B 6 5 3.377 6.176 -3.840 -1.914 AA_U3U4:C5G6_BB 3 -1.461 4.391 18.448 -8.631 10.634 2.890 39.079 A A 4 5 11.438 B B 5 4 3.312 7.605 -0.120 -1.952 AA_U4C5:U4C5_BB 4 -0.977 1.470 38.348 -3.794 0.067 2.711 28.157 A A 5 6 24.812 B B 4 3 3.578 11.714 3.214 -1.661 AA_C5G6:U3U4_BB 5 1.152 -2.441 25.624 -6.180 -6.335 3.307 39.924 A A 6 7 7.977 B B 3 2 3.580 5.426 0.222 -1.646 AA_G6G7:C2U3_BB 6 -3.178 4.673 39.446 -3.073 -0.713 3.183 34.107 A A 7 8 3.445 B B 2 1 3.303 2.019 0.091 -1.985 AA_G7C8:G1C2_BB 7 0.102 -0.175 34.049 -3.702 -0.138 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 2001-04-09 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 A bromo-U replaces the fluoro-U and Rh(III) hexammine cations replace the Ir(III) hexammine cations. RCSB Y RCSB 2001-03-31 REL REL CL CHLORIDE ION IRI IRIDIUM HEXAMMINE ION HOH water phosphoramidite method sample 165D PDB ENTRY 165D PDB experimental model CL 32 2 CL CL 32 A IRI 19 3 IRI IRI 19 A IRI 20 3 IRI IRI 20 A CL 31 2 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 105 4 HOH HOH 105 A HOH 107 4 HOH HOH 107 A HOH 112 4 HOH HOH 112 A HOH 113 4 HOH HOH 113 A HOH 114 4 HOH HOH 114 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 126 4 HOH HOH 126 A HOH 127 4 HOH HOH 127 A HOH 128 4 HOH HOH 128 A HOH 131 4 HOH HOH 131 A HOH 135 4 HOH HOH 135 A HOH 137 4 HOH HOH 137 A HOH 140 4 HOH HOH 140 A HOH 141 4 HOH HOH 141 A HOH 142 4 HOH HOH 142 A HOH 149 4 HOH HOH 149 A HOH 104 4 HOH HOH 104 B HOH 106 4 HOH HOH 106 B HOH 108 4 HOH HOH 108 B HOH 109 4 HOH HOH 109 B HOH 110 4 HOH HOH 110 B HOH 111 4 HOH HOH 111 B HOH 115 4 HOH HOH 115 B HOH 120 4 HOH HOH 120 B HOH 122 4 HOH HOH 122 B HOH 123 4 HOH HOH 123 B HOH 125 4 HOH HOH 125 B HOH 129 4 HOH HOH 129 B HOH 130 4 HOH HOH 130 B HOH 132 4 HOH HOH 132 B HOH 133 4 HOH HOH 133 B HOH 134 4 HOH HOH 134 B HOH 136 4 HOH HOH 136 B HOH 138 4 HOH HOH 138 B HOH 139 4 HOH HOH 139 B HOH 143 4 HOH HOH 143 B HOH 144 4 HOH HOH 144 B HOH 145 4 HOH HOH 145 B HOH 146 4 HOH HOH 146 B HOH 147 4 HOH HOH 147 B HOH 148 4 HOH HOH 148 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 3.43 0.50 119.90 123.33 A A A C2 N3 C4 C C C 2 2 2 N 1 -3.22 0.40 121.90 118.68 A A A N3 C4 C5 C C C 2 2 2 N 1 3.59 0.50 121.00 124.59 A A A C5 C6 N1 C C C 2 2 2 N 1 5.10 0.70 108.50 113.60 A A A O4' C1' N1 U U U 3 3 3 N 1 -5.30 0.60 127.00 121.70 A A A C2 N3 C4 U U U 3 3 3 N 1 4.39 0.60 114.60 118.99 A A A N3 C4 C5 U U U 3 3 3 N 1 -4.28 0.70 122.20 117.92 A A A N3 C2 O2 U U U 3 3 3 N 1 -4.49 0.60 125.90 121.41 A A A C5 C4 O4 U U U 3 3 3 N 1 4.37 0.60 114.90 119.27 A A A N1 C2 N3 U U U 4 4 4 N 1 -4.45 0.60 127.00 122.55 A A A C2 N3 C4 U U U 4 4 4 N 1 -4.07 0.60 125.90 121.83 A A A C5 C4 O4 U U U 4 4 4 N 1 -5.28 0.60 128.60 123.32 A A A C5 C6 O6 G G G 6 6 6 N 1 -3.49 0.40 121.90 118.41 A A A N3 C4 C5 C C C 8 8 8 N 1 -5.03 0.60 128.60 123.57 B B B C5 C6 O6 G G G 1 1 1 N 1 -5.33 0.80 109.40 104.07 B B B O5' C5' C4' C C C 2 2 2 N 1 3.23 0.50 119.90 123.13 B B B C2 N3 C4 C C C 2 2 2 N 1 -2.71 0.40 121.90 119.19 B B B N3 C4 C5 C C C 2 2 2 N 1 4.67 0.70 119.40 124.07 B B B N3 C4 O4 U U U 3 3 3 N 1 -6.10 0.60 125.90 119.80 B B B C5 C4 O4 U U U 3 3 3 N 1 3.61 0.60 114.90 118.51 B B B N1 C2 N3 U U U 4 4 4 N 1 -4.42 0.60 127.00 122.58 B B B C2 N3 C4 U U U 4 4 4 N 1 -6.04 0.60 125.90 119.86 B B B C5 C4 O4 U U U 4 4 4 N 1 5.32 0.70 108.50 113.82 B B B O4' C1' N9 G G G 6 6 6 N 1 4.25 0.70 108.50 112.75 B B B O4' C1' N1 C C C 8 8 8 N 1 -2.62 0.40 121.90 119.28 B B B N3 C4 C5 C C C 8 8 8 N 18.5 the two iridium and the two chlorine atoms were refined anisotropically 0.205 0.177 0.18 0.177 1.53 8 562 6772 6518 96.2 RANDOM 1 ISOTROPIC THROUGHOUT 2 4 MOLECULAR REPLACEMENT PDB ENTRY 165D LOCAL DICTIONARY FROM SMALL MOLECULE STRUCTURES 1.53 8 49 437 18 370 0 0.012 0.026 0.075 0.027 0.291 0.02 0.235 1.6 51 75.3 0.291 0.02 0.235 1.8 152 88.2 0.291 0.02 0.235 2.0 89 95.1 0.291 0.02 0.235 4.0 233 97.5 0.291 0.02 0.235 10.0 37 96.4 13.5 1.53 10. 1ICG 6772 6518 2.0 4.0 0.044 0.046 1 25. 6.5 91.5 0.156 1.53 1.6 4.4 729 0.167 3. 75. 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 IR(NH3)6+++ 1 N N 1 N N 2 N N 3 N N 3 N N 2 N N 4 N N 4 N N covale 1.589 both A C 8 A O3' C 8 1_555 A UFP 9 A P UFP 9 1_555 covale 1.611 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, C-U MISMATCH, G-U MISMATCH, RHODIUM HEXAMMINE, IRIDIUM HEXAMMINE, DNA-RNA COMPLEX 1ICG PDB 1 1ICG 1 9 1ICG 1 9 1ICG A 1 1 9 1 9 1ICG 1 9 1ICG B 1 1 9 BINDING SITE FOR RESIDUE CL B 31 B CL 31 Software 1 BINDING SITE FOR RESIDUE IRI A 19 A IRI 19 Software 5 BINDING SITE FOR RESIDUE IRI A 20 A IRI 20 Software 7 B HOH 111 H HOH 1 1_555 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 142 G HOH 5 1_555 A C 5 A C 5 7 4_545 A G 7 A G 7 7 1_545 A C 8 A C 8 7 1_545 A HOH 116 G HOH 7 1_545 A HOH 137 G HOH 7 1_545 B C 5 B C 5 7 4_545 B HOH 109 H HOH 7 4_545 5 C 1 2 1