1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schmitz, M. Tinoco Jr., I. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA 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 Co H18 N6 3 161.116 COBALT HEXAMMINE(III) non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK RNA RNARFU 2122 1355-8382 6 1212 1225 10.1017/S1355838200000881 10999599 Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA. 2000 10.2210/pdb1f79/pdb pdb_00001f79 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8634.127 RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT P4 STEM C70U 1 syn polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer no no GGAAGUUCGGUCUUCGGACCGGCUUCC GGAAGUUCGGUCUUCGGACCGGCUUCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n 46.861 1 19 A 1 A 27 -1.213 A_G1:C27_A 1 8.994 0.009 -0.373 -0.332 5.008 1 19 A 2 A 26 -8.054 A_G2:C26_A 2 -17.504 -0.133 0.530 -0.207 1.431 1 20 A 3 A 25 -4.414 A_A3:U25_A 3 -23.513 0.226 -0.390 -0.191 3.150 1 20 A 4 A 24 -1.916 A_A4:U24_A 4 -11.641 -0.012 -0.769 -0.162 -12.815 1 19 A 5 A 23 -2.275 A_G5:C23_A 5 -30.554 -0.172 -0.226 -0.207 -8.103 28 A 6 A 22 1.317 A_U6:G22_A 6 -1.484 2.409 0.393 -0.415 -16.290 1 19 A 8 A 21 -4.331 A_C8:G21_A 7 8.535 0.015 -1.236 -0.741 16.847 1 19 A 9 A 20 -2.581 A_G9:C20_A 8 5.673 -0.224 1.044 -0.305 -1.307 1 19 A 10 A 19 9.873 A_G10:C19_A 9 -24.101 -0.421 -0.944 -0.524 0.741 1 20 A 11 A 18 -0.041 A_U11:A18_A 10 -17.846 -0.081 -1.269 -0.499 -9.134 1 19 A 12 A 17 -1.763 A_C12:G17_A 11 -10.447 0.473 0.097 -0.238 38.120 2 A 13 A 16 -91.139 A_U13:G16_A 12 -12.862 1.139 -1.432 -5.278 3.899 35.002 A A 1 2 37.244 A A 27 26 5.523 20.909 -1.029 -1.117 AA_G1G2:C26C27_AA 1 -4.437 7.903 27.881 -6.950 0.630 3.082 35.548 A A 2 3 19.204 A A 26 25 3.600 11.493 0.271 -1.083 AA_G2A3:U25C26_AA 2 4.632 -7.739 33.384 -3.545 0.270 3.945 33.721 A A 3 4 -7.579 A A 25 24 3.842 -4.384 0.663 -0.889 AA_A3A4:U24U25_AA 3 1.242 -2.146 33.421 -0.682 -0.902 4.293 31.077 A A 4 5 7.880 A A 24 23 4.446 4.209 0.301 -0.874 AA_A4G5:C23U24_AA 4 0.138 -0.258 30.797 -2.714 -0.526 2.324 43.014 A A 5 6 27.179 A A 23 22 3.085 19.268 0.585 -0.974 AA_G5U6:G22C23_AA 5 -2.666 3.761 38.552 -3.000 -1.030 1.572 44.959 A A 6 8 59.983 A A 22 21 4.422 37.574 0.457 -0.740 AA_U6C8:G21G22_AA 6 14.685 -23.442 20.274 -5.405 1.137 1.859 30.070 A A 8 9 20.342 A A 21 20 2.574 10.147 0.178 -1.085 AA_C8G9:C20G21_AA 7 -10.045 20.138 26.533 -3.593 -1.830 3.365 42.345 A A 9 10 38.500 A A 20 19 4.236 25.479 1.245 -0.325 AA_G9G10:C19C20_AA 8 13.447 -20.320 31.370 -3.979 0.139 3.001 34.403 A A 10 11 16.963 A A 19 18 3.391 9.899 -0.592 -0.944 AA_G10U11:A18C19_AA 9 -0.622 1.066 32.984 -3.139 0.903 2.622 40.737 A A 11 12 35.576 A A 18 17 3.657 23.264 -0.663 -0.846 AA_U11C12:G17A18_AA 10 -6.267 9.584 33.095 -3.969 0.210 2.875 104.617 A A 12 13 -0.392 A A 17 16 3.000 -0.620 1.573 -0.999 AA_C12U13:G16G17_AA 11 -11.246 7.113 104.187 -0.623 -1.135 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-10-09 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1F6Z shows the structure of the free C70U mutant P4 stem oligoribonucleotide 1F6X shows the structure of the free wildtype P4 stem oligoribonucleotide RCSB Y RCSB 2000-06-23 REL REL NCO COBALT HEXAMMINE(III) synthesized from DNA ologonucleotide template by T7 RNA polymerase sample This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and derived intermolecular distance constraints were used to determine the site of cobalt (III) hexammine binding in the complex structure 1 2D NOESY 2D NOESY 2D NOESY 2D NOESY DQF-COSY 31P-1H-COSY 13C-1H-HMQC 100 mM Na 6.5 ambient 288 K 100 mM Na 6.5 ambient 288 K 100 mM Na, 10 mM Mg 6.5 ambient 288 K 100 mM Na, 3 mM Co(NH3)6 6.5 ambient 288 K The average structure is based on superposition of 12 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.5 Angstrom. A total of 268 NOE-derived intramolecular distance constraints, 171 dihedral restraint and 49 distance restraints from hydrogen bonds were used in the refinement. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt (III) hexammine restrained molecular dynamics and simulated annealing minimized average structure 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O 99.96% D2O 2 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4m RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O Bruker collection XwinNMR 3.1 MSI processing Felix 95 Brunger structure solution X-PLOR 3.841 Brunger refinement X-PLOR 3.841 600 Bruker AMX 500 Bruker DRX NCO 28 2 NCO NCO 28 A G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A A 4 n 4 A 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A U 7 n 7 U 7 A C 8 n 8 C 8 A G 9 n 9 G 9 A G 10 n 10 G 10 A U 11 n 11 U 11 A C 12 n 12 C 12 A U 13 n 13 U 13 A U 14 n 14 U 14 A C 15 n 15 C 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A C 19 n 19 C 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A G 22 n 22 G 22 A C 23 n 23 C 23 A U 24 n 24 U 24 A U 25 n 25 U 25 A C 26 n 26 C 26 A C 27 n 27 C 27 A author_defined_assembly 1 monomeric 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 A A O6 H41 G C 1 27 1.59 minimized average SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT(III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 26 A N3 C 26 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 26 A O2 C 26 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 26 A N4 C 26 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 25 A N3 U 25 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 25 A O4 U 25 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 24 A N3 U 24 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 24 A O4 U 24 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 23 A N3 C 23 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 23 A N4 C 23 1_555 hydrog TYPE_28_PAIR A U 6 A N3 U 6 1_555 A G 22 A O6 G 22 1_555 hydrog TYPE_28_PAIR A U 6 A O2 U 6 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 21 A N1 G 21 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 21 A O6 G 21 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 21 A N2 G 21 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 20 A N4 C 20 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 A C 19 A N4 C 19 1_555 hydrog WATSON-CRICK A U 11 A N3 U 11 1_555 A A 18 A N1 A 18 1_555 hydrog WATSON-CRICK A U 11 A O4 U 11 1_555 A A 18 A N6 A 18 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 A G 17 A N2 G 17 1_555 hydrog U-G MISPAIR A U 13 A O2 U 13 1_555 A G 16 A N1 G 16 1_555 RNA RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, C70U MUTANT, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE COMPLEX, RNA 1F79 PDB 1 1F79 1 27 1F79 1 27 1F79 A 1 1 27 BINDING SITE FOR RESIDUE NCO A 28 A NCO 28 Software 5 A G 5 A G 5 5 1_555 A U 6 A U 6 5 1_555 A C 20 A C 20 5 1_555 A G 21 A G 21 5 1_555 A C 23 A C 23 5 1_555 1 P 1