1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Colmenarejo, G. 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 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 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 O N 37 N P N 38 N O N 39 N O N 40 N O N 41 N C N 42 R C N 43 N O N 44 S C N 45 N O N 46 R C N 47 N O N 48 R C Y 49 N N Y 50 N C Y 51 N N Y 52 N C N 53 N C N 54 N O N 55 N N N 56 N C N 57 N N N 58 N N Y 59 N C 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 H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N CO N 75 N N N 76 N N N 77 N N N 78 N N N 79 N N N 80 N N N 81 N H N 82 N H N 83 N H N 84 N H 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 O N 100 N P N 101 N O N 102 N O N 103 N O N 104 N C N 105 R C N 106 N O N 107 S C N 108 N O N 109 R C N 110 N O N 111 R C N 112 N N N 113 N C N 114 N O N 115 N N N 116 N C N 117 N O N 118 N C N 119 N C 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 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 doub N 104 N sing N 105 N sing 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 doub N 128 N sing N 129 N sing N 130 N sing N 131 N doub N 132 N sing N 133 N doub N 134 N sing N 135 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 290 119 135 10.1006/jmbi.1999.2867 10388561 Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme. 1999 10.2210/pdb1c0o/pdb pdb_00001c0o 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 CLOSED BY A UUCG TETRALOOP; COBALT (III) HEXAMMINE BINDS AT THE MAJOR GROOVE OF TWO TANDEM G-U WOBBLE PAIRS IN 5'-GU-3' ORIENTATION 4471.667 RNA (5'-R(*GP*GP*GP*UP*CP*UP*UP*CP*GP*GP*GP*UP*CP*C)-3') 1 man polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer no no GGGUCUUCGGGUCC GGGUCUUCGGGUCC A polyribonucleotide n n n n n n n n n n n n n n Tetrahymena sample SYNTHESIZED ENZYMATICALLY IN-VITRO USING T7 RNA POLYMERASE 5911 Tetrahymena thermophila -25.118 1 19 A 1 A 14 -4.366 A_G1:C14_A 1 -12.116 -0.744 -0.240 -0.369 -3.997 1 19 A 2 A 13 -2.522 A_G2:C13_A 2 -14.346 -0.750 -0.133 -0.476 -7.851 28 A 3 A 12 -0.617 A_G3:U12_A 3 -23.421 -2.780 -0.161 -0.944 -7.877 28 A 4 A 11 -2.014 A_U4:G11_A 4 -14.773 2.754 -0.092 -0.881 -2.624 1 19 A 5 A 10 -1.515 A_C5:G10_A 5 -4.836 1.032 -0.839 -0.721 -3.956 2 A 6 A 9 -95.639 A_U6:G9_A 6 -15.485 1.017 -0.272 -5.120 2.874 32.320 A A 1 2 20.155 A A 14 13 2.910 10.992 -0.361 0.329 AA_G1G2:C13C14_AA 1 -2.835 5.199 30.311 -1.188 0.189 1.608 34.456 A A 2 3 35.953 A A 13 12 3.062 19.854 0.626 -1.243 AA_G2G3:U12C13_AA 2 -7.385 13.374 27.332 -4.578 -1.979 3.142 59.683 A A 3 4 6.735 A A 12 11 3.206 6.691 -0.072 -0.472 AA_G3U4:G11U12_AA 3 -1.054 1.061 59.332 -0.801 0.021 1.648 28.560 A A 4 5 31.017 A A 11 10 3.060 14.305 -0.547 -1.295 AA_U4C5:G10G11_AA 4 9.422 -20.430 22.939 -5.237 2.829 2.779 90.045 A A 5 6 9.520 A A 10 9 2.879 13.392 -0.415 0.067 AA_C5U6:G9G10_AA 5 16.110 -11.452 88.088 -0.191 0.580 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection 1 0 1999-08-31 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-02-16 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 1999-03-16 REL NCO COBALT HEXAMMINE(III) THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. ALL 13C EXPERIMENTS WERE DONE USING NATURAL ABUNDANCE. COBALT (III) HEXAMMINE WAS LOCATED USING DOCKING WITH 7 INTERMOLECULAR NOES OBSERVED IN 2D WATER NOESY EXPERIMENTS. NOE ENERGY (LEAST RESTRAINT VIOLATIONS), DIHEDRAL ENERGY (LEAST RESTRAINT VIOLATIONS), TOTAL ENERGY 40 19 DQF-COSY D2O NOESY H2O NOESY TOCSY 13C-1H HMQC 31P-1H HETCOR 31P-1H TOCSY 31P-1H TOCSY-NOESY 100 mM NACL 6.4 1 atm 298 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE RESTRAINED MOLECULAR DYNAMICS PHOSPHATE BUFFER, EDTA BRUNGER refinement X-PLOR 3.1 structure solution FELIX95 structure solution X-PLOR 3.1 500 Bruker AMX600 600 Bruker DRX500 NCO 15 2 NCO NCO 15 A G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A C 5 n 5 C 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 G 11 n 11 G 11 A U 12 n 12 U 12 A C 13 n 13 C 13 A C 14 n 14 C 14 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 HO2' O6 U G 6 9 1.57 3 A A HO2' O6 U G 6 9 1.59 5 A A HO2' O6 U G 6 9 1.59 6 A A O2 H1 U G 6 9 1.59 6 A A HO2' O6 U G 6 9 1.60 6 A A O6 H41 G C 1 14 1.60 7 A A HO2' O6 U G 6 9 1.53 7 A A O2 H1 U G 6 9 1.59 8 A A HO2' O6 U G 6 9 1.55 8 A A O2 H1 U G 6 9 1.57 9 A A HO2' O6 U G 6 9 1.53 10 A A HO2' O6 U G 6 9 1.55 13 A A HO2' O6 U G 6 9 1.57 13 A A O2 H1 U G 6 9 1.58 14 A A HO2' O6 U G 6 9 1.56 15 A A HO2' O6 U G 6 9 1.59 17 A A HO2' O6 U G 6 9 1.60 17 A A O6 H41 G C 2 13 1.60 19 A A HO2' O6 U G 6 9 1.57 19 A A O2 H1 U G 6 9 1.60 SOLUTION STRUCTURE OF THE P5 HAIRPIN FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, 19 CONVERGED STRUCTURES 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 14 A N4 C 14 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 13 A N3 C 13 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 13 A O2 C 13 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 13 A N4 C 13 1_555 hydrog TYPE_28_PAIR A G 3 A N1 G 3 1_555 A U 12 A O2 U 12 1_555 hydrog TYPE_28_PAIR A G 3 A O6 G 3 1_555 A U 12 A N3 U 12 1_555 hydrog TYPE_28_PAIR A U 4 A N3 U 4 1_555 A G 11 A O6 G 11 1_555 hydrog TYPE_28_PAIR A U 4 A O2 U 4 1_555 A G 11 A N1 G 11 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 10 A N1 G 10 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 10 A O6 G 10 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 10 A N2 G 10 1_555 hydrog U-G MISPAIR A U 6 A O2 U 6 1_555 A G 9 A N1 G 9 1_555 hydrog TYPE_28_PAIR A U 6 A N3 U 6 1_555 A G 10 A O6 G 10 1_555 hydrog TYPE_28_PAIR A U 6 A O2 U 6 1_555 A G 10 A N1 G 10 1_555 RNA RIBONUCLEIC ACID, COBALT (III) HEXAMMINE, METAL BINDING, RNA STRUCTURE, RNA 1C0O PDB 1 1C0O 1 14 1C0O 1 14 1C0O A 1 1 14 BINDING SITE FOR RESIDUE NCO A 15 A NCO 15 Software 5 A G 2 A G 2 5 1_555 A G 3 A G 3 5 1_555 A U 4 A U 4 5 1_555 A G 11 A G 11 5 1_555 A U 12 A U 12 5 1_555 1 P 1