0.027427 0.000000 0.000000 0.000000 0.027427 0.000000 0.000000 0.000000 0.007315 0.00000 0.00000 0.00000 RESIDUE LYS 72 AND TML 72 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 9 ABOVE. THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS TO THE SG ATOMS OF CYS 14 AND CYS 17. IN ORDER TO CORRECTLY INDICATE IDENTICAL ATOMS BETWEEN THE COORDINATE ENTRIES OF THE MUTANT AND WILD-TYPE FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1CTY AND 1YCC, RESPECTIVELY), THE SIDE-CHAIN ATOM NAMES OF SEVERAL RESIDUES CANNOT FOLLOW IUPAC/IUB SPECIFICATIONS WITH RESPECT TO THE DESIGNATION OF 1 AND 2 FOR BRANCHED SIDE CHAINS. THE AFFECTED RESIDUES ARE GLU -4, PHE 36, ARG 38, ASP 50, GLU 61, PHE 67, PHE 82, ASP 90, AND GLU 103. Berghuis, A.M. Brayer, G.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 36.460 36.460 136.710 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C34 H34 Fe N4 O4 618.503 HEME C non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H21 N2 O2 1 189.275 n N-TRIMETHYLLYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking O4 S -2 96.063 SULFATE ION non-polymer C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK J.Mol.Biol. JMOBAK 0070 0022-2836 235 1326 1341 10.1006/jmbi.1994.1086 8308895 Mutation of tyrosine-67 to phenylalanine in cytochrome c significantly alters the local heme environment. 1994 UK J.Mol.Biol. JMOBAK 0070 0022-2836 223 959 Oxidation State-Dependent Conformational Changes in Cytochrome C 1992 UK J.Mol.Biol. JMOBAK 0070 0022-2836 214 527 High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C 1990 UK J.Mol.Biol. JMOBAK 0070 0022-2836 210 313 A Polypeptide Chain-Refolding Event Occurs in the Gly82 Variant of Yeast Iso-1-Cytochrome C 1989 UK J.Mol.Biol. JMOBAK 0070 0022-2836 206 783 Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique 1989 UK J.Mol.Biol. JMOBAK 0070 0022-2836 199 295 Yeast Iso-1-Cytochrome C. A 2.8 Angstrom Resolution Three-Dimensional Structure Determination 1988 US Biochemistry BICHAW 0033 0006-2960 27 7870 Role of Phenylalanine-82 in Yeast Iso-1-Cytochrome C and Remote Conformational Changes Induced by a Serine Residue at This Position 1988 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 12097.876 CYTOCHROME C 1 man polymer 96.063 SULFATE ION 1 syn non-polymer 618.503 HEME C 1 syn non-polymer 18.015 water 48 nat water no yes TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEFLTNP (M3L)KYIPGTKMAFGGLKKEKDRNDLITYLKKATE TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEFLTNPKKYI PGTKMAFGGLKKEKDRNDLITYLKKATE A polypeptide(L) 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 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 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 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 baker's yeast Saccharomyces sample 4932 Saccharomyces cerevisiae 1.88 34.70 pdbx_database_status struct_conf struct_conf_type atom_site chem_comp entity pdbx_distant_solvent_atoms pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Derived calculations Other Advisory Atomic model Data collection Database references Derived calculations Non-polymer description Structure summary 1 0 1993-07-15 1 1 2008-03-21 1 2 2011-07-13 1 3 2017-11-29 2 0 2021-03-03 _pdbx_database_status.process_site _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.name _chem_comp.pdbx_synonyms _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _struct_site.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id REDUCED - WILD-TYPE OXIDIZED - C102T MUTANT OXIDIZED - Y67F, C102T MTUANT HELIX THE END OF THE 50 HELIX (RESIDUE 55) IS DISTORTED. SHEET RESIDUES IN SHEET S1 FORM A HIGHLY DISTORTED BETA TYPE CONFORMATION. Y BNL 1993-02-15 REL REL 1 A O HOH 157 8.27 1 A O HOH 306 6.19 SO4 SULFATE ION HEC HEME C HOH water THIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO A THREONINE RESIDUE. IN TURN T5 THE H-BOND IS MEDIATED THROUGH A WATER MOLECULE. SO4 117 2 SO4 SO4 117 A HEM 104 3 HEC HEC 104 A HOH 107 4 HOH HOH 107 A HOH 109 4 HOH HOH 109 A HOH 110 4 HOH HOH 110 A HOH 112 4 HOH HOH 112 A HOH 119 4 HOH HOH 119 A HOH 121 4 HOH HOH 121 A HOH 127 4 HOH HOH 127 A HOH 129 4 HOH HOH 129 A HOH 130 4 HOH HOH 130 A HOH 132 4 HOH HOH 132 A HOH 135 4 HOH HOH 135 A HOH 138 4 HOH HOH 138 A HOH 140 4 HOH HOH 140 A HOH 141 4 HOH HOH 141 A HOH 144 4 HOH HOH 144 A HOH 145 4 HOH HOH 145 A HOH 149 4 HOH HOH 149 A HOH 157 4 HOH HOH 157 A HOH 158 4 HOH HOH 158 A HOH 160 4 HOH HOH 160 A HOH 164 4 HOH HOH 164 A HOH 165 4 HOH HOH 165 A HOH 166 4 HOH HOH 166 A HOH 167 4 HOH HOH 167 A HOH 168 4 HOH HOH 168 A HOH 171 4 HOH HOH 171 A HOH 174 4 HOH HOH 174 A HOH 176 4 HOH HOH 176 A HOH 177 4 HOH HOH 177 A HOH 180 4 HOH HOH 180 A HOH 181 4 HOH HOH 181 A HOH 184 4 HOH HOH 184 A HOH 185 4 HOH HOH 185 A HOH 192 4 HOH HOH 192 A HOH 195 4 HOH HOH 195 A HOH 197 4 HOH HOH 197 A HOH 200 4 HOH HOH 200 A HOH 206 4 HOH HOH 206 A HOH 300 4 HOH HOH 300 A HOH 301 4 HOH HOH 301 A HOH 302 4 HOH HOH 302 A HOH 303 4 HOH HOH 303 A HOH 304 4 HOH HOH 304 A HOH 305 4 HOH HOH 305 A HOH 306 4 HOH HOH 306 A HOH 307 4 HOH HOH 307 A HOH 308 4 HOH HOH 308 A HOH 309 4 HOH HOH 309 A THR -5 n 1 THR -5 A GLU -4 n 2 GLU -4 A PHE -3 n 3 PHE -3 A LYS -2 n 4 LYS -2 A ALA -1 n 5 ALA -1 A GLY 1 n 6 GLY 1 A SER 2 n 7 SER 2 A ALA 3 n 8 ALA 3 A LYS 4 n 9 LYS 4 A LYS 5 n 10 LYS 5 A GLY 6 n 11 GLY 6 A ALA 7 n 12 ALA 7 A THR 8 n 13 THR 8 A LEU 9 n 14 LEU 9 A PHE 10 n 15 PHE 10 A LYS 11 n 16 LYS 11 A THR 12 n 17 THR 12 A ARG 13 n 18 ARG 13 A CYS 14 n 19 CYS 14 A LEU 15 n 20 LEU 15 A GLN 16 n 21 GLN 16 A CYS 17 n 22 CYS 17 A HIS 18 n 23 HIS 18 A THR 19 n 24 THR 19 A VAL 20 n 25 VAL 20 A GLU 21 n 26 GLU 21 A LYS 22 n 27 LYS 22 A GLY 23 n 28 GLY 23 A GLY 24 n 29 GLY 24 A PRO 25 n 30 PRO 25 A HIS 26 n 31 HIS 26 A LYS 27 n 32 LYS 27 A VAL 28 n 33 VAL 28 A GLY 29 n 34 GLY 29 A PRO 30 n 35 PRO 30 A ASN 31 n 36 ASN 31 A LEU 32 n 37 LEU 32 A HIS 33 n 38 HIS 33 A GLY 34 n 39 GLY 34 A ILE 35 n 40 ILE 35 A PHE 36 n 41 PHE 36 A GLY 37 n 42 GLY 37 A ARG 38 n 43 ARG 38 A HIS 39 n 44 HIS 39 A SER 40 n 45 SER 40 A GLY 41 n 46 GLY 41 A GLN 42 n 47 GLN 42 A ALA 43 n 48 ALA 43 A GLU 44 n 49 GLU 44 A GLY 45 n 50 GLY 45 A TYR 46 n 51 TYR 46 A SER 47 n 52 SER 47 A TYR 48 n 53 TYR 48 A THR 49 n 54 THR 49 A ASP 50 n 55 ASP 50 A ALA 51 n 56 ALA 51 A ASN 52 n 57 ASN 52 A ILE 53 n 58 ILE 53 A LYS 54 n 59 LYS 54 A LYS 55 n 60 LYS 55 A ASN 56 n 61 ASN 56 A VAL 57 n 62 VAL 57 A LEU 58 n 63 LEU 58 A TRP 59 n 64 TRP 59 A ASP 60 n 65 ASP 60 A GLU 61 n 66 GLU 61 A ASN 62 n 67 ASN 62 A ASN 63 n 68 ASN 63 A MET 64 n 69 MET 64 A SER 65 n 70 SER 65 A GLU 66 n 71 GLU 66 A PHE 67 n 72 PHE 67 A LEU 68 n 73 LEU 68 A THR 69 n 74 THR 69 A ASN 70 n 75 ASN 70 A PRO 71 n 76 PRO 71 A LYS 72 n 77 M3L 72 A LYS 73 n 78 LYS 73 A TYR 74 n 79 TYR 74 A ILE 75 n 80 ILE 75 A PRO 76 n 81 PRO 76 A GLY 77 n 82 GLY 77 A THR 78 n 83 THR 78 A LYS 79 n 84 LYS 79 A MET 80 n 85 MET 80 A ALA 81 n 86 ALA 81 A PHE 82 n 87 PHE 82 A GLY 83 n 88 GLY 83 A GLY 84 n 89 GLY 84 A LEU 85 n 90 LEU 85 A LYS 86 n 91 LYS 86 A LYS 87 n 92 LYS 87 A GLU 88 n 93 GLU 88 A LYS 89 n 94 LYS 89 A ASP 90 n 95 ASP 90 A ARG 91 n 96 ARG 91 A ASN 92 n 97 ASN 92 A ASP 93 n 98 ASP 93 A LEU 94 n 99 LEU 94 A ILE 95 n 100 ILE 95 A THR 96 n 101 THR 96 A TYR 97 n 102 TYR 97 A LEU 98 n 103 LEU 98 A LYS 99 n 104 LYS 99 A LYS 100 n 105 LYS 100 A ALA 101 n 106 ALA 101 A THR 102 n 107 THR 102 A GLU 103 n 108 GLU 103 A author_defined_assembly 1 monomeric A HIS 18 A NE2 HIS 23 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C NA HEC 1_555 84.7 A HIS 18 A NE2 HIS 23 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C NB HEC 1_555 84.9 A HEC 104 C NA HEC 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C NB HEC 1_555 91.1 A HIS 18 A NE2 HIS 23 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C NC HEC 1_555 90.4 A HEC 104 C NA HEC 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C NC HEC 1_555 174.5 A HEC 104 C NB HEC 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C NC HEC 1_555 90.9 A HIS 18 A NE2 HIS 23 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C ND HEC 1_555 90.0 A HEC 104 C NA HEC 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C ND HEC 1_555 86.2 A HEC 104 C NB HEC 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C ND HEC 1_555 174.4 A HEC 104 C NC HEC 1_555 A HEC 104 C FE HEC 1_555 A HEC 104 C ND HEC 1_555 91.4 A HIS 18 A NE2 HIS 23 1_555 A HEC 104 C FE HEC 1_555 A MET 80 A SD MET 85 1_555 177.7 A HEC 104 C NA HEC 1_555 A HEC 104 C FE HEC 1_555 A MET 80 A SD MET 85 1_555 93.4 A HEC 104 C NB HEC 1_555 A HEC 104 C FE HEC 1_555 A MET 80 A SD MET 85 1_555 96.3 A HEC 104 C NC HEC 1_555 A HEC 104 C FE HEC 1_555 A MET 80 A SD MET 85 1_555 91.5 A HEC 104 C ND HEC 1_555 A HEC 104 C FE HEC 1_555 A MET 80 A SD MET 85 1_555 88.8 A M3L 72 N-TRIMETHYLLYSINE A M3L 77 LYS 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 A N SER 40 A N SER 45 A O VAL 57 A O VAL 62 1 6.20 0.50 120.30 126.50 A A A NE CZ NH1 ARG ARG ARG 13 13 13 N 1 10.09 1.10 114.20 124.29 A A A CA CB SG CYS CYS CYS 14 14 14 N 1 11.12 1.70 113.60 124.72 A A A CA CB CG HIS HIS HIS 18 18 18 N 1 13.22 2.10 120.10 133.32 A A A CA C O HIS HIS HIS 18 18 18 N 1 9.19 1.50 110.90 120.09 A A A CA CB CG1 VAL VAL VAL 20 20 20 N 1 8.44 1.20 123.30 131.74 A A A OE1 CD OE2 GLU GLU GLU 21 21 21 N 1 16.62 2.00 110.40 127.02 A A A CB CA C ASN ASN ASN 31 31 31 N 1 14.62 2.30 115.30 129.92 A A A CA CB CG LEU LEU LEU 32 32 32 N 1 5.25 0.50 120.30 125.55 A A A NE CZ NH2 ARG ARG ARG 38 38 38 N 1 16.77 2.20 113.40 130.17 A A A CA CB CG GLN GLN GLN 42 42 42 N 1 17.31 2.20 113.40 130.71 A A A CA CB CG GLU GLU GLU 44 44 44 N 1 8.26 0.90 118.30 126.56 A A A CB CG OD1 ASP ASP ASP 50 50 50 N 1 -5.72 0.90 118.30 112.58 A A A CB CG OD2 ASP ASP ASP 50 50 50 N 1 13.50 2.20 113.40 126.90 A A A CA CB CG LYS LYS LYS 86 86 86 N 1 9.75 1.60 122.70 132.45 A A A O C N LYS LYS ASP 89 89 90 Y 1 4.19 0.50 120.30 124.49 A A A NE CZ NH1 ARG ARG ARG 91 91 91 N 1 A A CB SG CYS CYS 17 17 0.147 0.017 1.818 1.965 N 1 A A CG CD2 HIS HIS 18 18 0.064 0.009 1.354 1.418 N 1 A A N CA GLY GLY 23 23 0.099 0.015 1.456 1.555 N 1 A A OD2 NZ ASP LYS 50 73 1.66 1_555 6_555 1 A A OD2 CE ASP LYS 50 73 2.00 1_555 6_555 1 A A NZ O LYS THR 5 8 2.16 1_555 7_465 1 A GLU -4 -171.22 30.67 1 A LYS 4 -38.88 -72.86 1 A ALA 7 -59.66 -2.11 1 A PHE 10 -48.42 -71.09 1 A LYS 22 -51.39 103.58 1 A LYS 27 -123.94 -120.53 1 A ASN 56 48.33 71.68 0.2010000 1.9 1 1.9 48 946 51 0 847 0.024 0.046 refinement PROLSQ CYTOCHROME C (ISOZYME 1) (REDUCED) MUTANT WITH TYR 67 REPLACED BY PHE AND CYS 102 REPLACED BY THR (Y67F, C102T) MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT 1 N N 2 N N 3 N N 4 N N A SER 2 A SER 7 HELX_P A CYS 14 A CYS 19 1 NT 13 A THR 49 A THR 54 HELX_P RESIDUE 55 DISTORTED A LYS 55 A LYS 60 1 50 7 A ASP 60 A ASP 65 HELX_P A ASN 70 A ASN 75 1 60 11 A ASN 70 A ASN 75 HELX_P A ILE 75 A ILE 80 1 70 6 A LYS 87 A LYS 92 HELX_P A THR 102 A THR 107 1 CT 16 covale 1.830 none A CYS 14 A SG CYS 19 1_555 A HEC 104 C CAB HEC 1_555 covale 1.815 none A CYS 17 A SG CYS 22 1_555 A HEC 104 C CAC HEC 1_555 covale 1.327 both A PRO 71 A C PRO 76 1_555 A M3L 72 A N M3L 77 1_555 covale 1.293 both A M3L 72 A C M3L 77 1_555 A LYS 73 A N LYS 78 1_555 metalc 1.963 A HIS 18 A NE2 HIS 23 1_555 A HEC 104 C FE HEC 1_555 metalc 2.354 A MET 80 A SD MET 85 1_555 A HEC 104 C FE HEC 1_555 ELECTRON TRANSPORT (HEME PROTEIN) ELECTRON TRANSPORT (HEME PROTEIN) CYC1_YEAST UNP 1 1 P00044 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLITYLKKACE 1 108 1CTZ -5 103 P00044 A 1 1 108 1 TYR conflict PHE 67 1CTZ A P00044 UNP 72 72 1 CYS conflict THR 102 1CTZ A P00044 UNP 107 107 2 anti-parallel A GLY 37 A GLY 42 A SER 40 A SER 45 A VAL 57 A VAL 62 A TRP 59 A TRP 64 BINDING SITE FOR RESIDUE SO4 A 117 A SO4 117 Software 6 BINDING SITE FOR RESIDUE HEC A 104 A HEC 104 Software 22 A SER 2 A SER 7 6 1_555 A ALA 3 A ALA 8 6 1_555 A LYS 4 A LYS 9 6 1_555 A LYS 11 A LYS 16 6 7_465 A SER 47 A SER 52 6 3_554 A HOH 164 D HOH 6 1_555 A ARG 13 A ARG 18 22 1_555 A CYS 14 A CYS 19 22 1_555 A CYS 17 A CYS 22 22 1_555 A HIS 18 A HIS 23 22 1_555 A GLY 23 A GLY 28 22 6_465 A LEU 32 A LEU 37 22 1_555 A SER 40 A SER 45 22 1_555 A GLY 41 A GLY 46 22 1_555 A TYR 46 A TYR 51 22 1_555 A TYR 48 A TYR 53 22 1_555 A THR 49 A THR 54 22 1_555 A ASN 52 A ASN 57 22 1_555 A TRP 59 A TRP 64 22 1_555 A MET 64 A MET 69 22 1_555 A LEU 68 A LEU 73 22 1_555 A THR 78 A THR 83 22 1_555 A LYS 79 A LYS 84 22 1_555 A MET 80 A MET 85 22 1_555 A LEU 94 A LEU 99 22 1_555 A LEU 98 A LEU 103 22 1_555 A HOH 121 D HOH 22 1_555 A HOH 300 D HOH 22 1_555 96 P 43 21 2