0.027382 0.000000 0.000000 0.000000 0.027382 0.000000 0.000000 0.000000 0.007188 0.00000 0.00000 0.00000 THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS TO THE SG ATOMS OF CYS 14 AND CYS 17. Berghuis, A.M. Brayer, G.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 36.520 36.520 139.120 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 H32 Fe N4 O4 616.487 PROTOPORPHYRIN IX CONTAINING FE HEME 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 236 786 799 8114094 The role of a conserved internal water molecule and its associated hydrogen bond network in cytochrome c. 1994 To be Published 0353 Mutation of Tyrosine-67 in Cytochrome C Significantly Alters the Local Heme Environment UK J.Mol.Biol. JMOBAK 0070 0022-2836 224 589 Effect of the Asn 52-> Ile Mutation on the Redox Potential of Yeast Cytochrome C: Theory and Experiment 1992 UK J.Mol.Biol. JMOBAK 0070 0022-2836 223 959 Oxidation State-Dependent Conformational Changes in Cytochrome C 1992 US J.Biol.Chem. JBCHA3 0071 0021-9258 266 11686 Enhanced Thermodynamic Stabilities of Yeast Iso-1-Cytochrome C with Amino Acid Replacements at Position 52 and 102 1991 US Adv.Chem.Ser. ADCSAJ 0031 0065-2393 228 179 Effects of Reaction Free Energy in Biological Electron Transfer in Vitro and in Vivo (in: Electron Transfer in Inorganic, Organic, and Biological Systems) 1991 UK J.Mol.Biol. JMOBAK 0070 0022-2836 214 527 High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochrome C 1990 UK J.Mol.Biol. JMOBAK 0070 0022-2836 206 783 Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique 1989 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 12096.931 CYTOCHROME C 1 man polymer 96.063 SULFATE ION 1 syn non-polymer 616.487 PROTOPORPHYRIN IX CONTAINING FE 1 syn non-polymer 18.015 water 39 nat water no yes TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDAIIKKNVLWDENNMSEFLTNP (M3L)KYIPGTKMAFGGLKKEKDRNDLITYLKKATE TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDAIIKKNVLWDENNMSEFLTNPKKYI 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 sample POTENTIAL 4932 Saccharomyces cerevisiae 1.92 35.85 pdbx_database_status struct_conf struct_conf_type repository Initial release Version format compliance Version format compliance Derived calculations Other 1 0 1994-01-31 1 1 2009-01-06 1 2 2011-07-13 1 3 2017-11-29 _pdbx_database_status.process_site 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 1993-08-06 REL REL SO4 SULFATE ION HEM PROTOPORPHYRIN IX CONTAINING FE 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 HEM HEM 104 A HOH 109 4 HOH HOH 109 A HOH 110 4 HOH HOH 110 A HOH 113 4 HOH HOH 113 A HOH 121 4 HOH HOH 121 A HOH 122 4 HOH HOH 122 A HOH 128 4 HOH HOH 128 A HOH 129 4 HOH HOH 129 A HOH 133 4 HOH HOH 133 A HOH 136 4 HOH HOH 136 A HOH 142 4 HOH HOH 142 A HOH 149 4 HOH HOH 149 A HOH 150 4 HOH HOH 150 A HOH 153 4 HOH HOH 153 A HOH 154 4 HOH HOH 154 A HOH 156 4 HOH HOH 156 A HOH 158 4 HOH HOH 158 A HOH 160 4 HOH HOH 160 A HOH 167 4 HOH HOH 167 A HOH 168 4 HOH HOH 168 A HOH 169 4 HOH HOH 169 A HOH 174 4 HOH HOH 174 A HOH 195 4 HOH HOH 195 A HOH 196 4 HOH HOH 196 A HOH 197 4 HOH HOH 197 A HOH 204 4 HOH HOH 204 A HOH 205 4 HOH HOH 205 A HOH 208 4 HOH HOH 208 A HOH 209 4 HOH HOH 209 A HOH 214 4 HOH HOH 214 A HOH 215 4 HOH HOH 215 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 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 ILE 52 n 57 ILE 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 M3L 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 HEM 104 C FE HEM 1_555 A HEM 104 C NA HEM 1_555 93.2 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NB HEM 1_555 96.6 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NB HEM 1_555 91.0 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NC HEM 1_555 91.1 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NC HEM 1_555 174.7 A HEM 104 C NB HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C NC HEM 1_555 91.5 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 87.2 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 88.0 A HEM 104 C NB HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 176.1 A HEM 104 C NC HEM 1_555 A HEM 104 C FE HEM 1_555 A HEM 104 C ND HEM 1_555 89.3 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 171.5 A HEM 104 C NA HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 83.9 A HEM 104 C NB HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 91.5 A HEM 104 C NC HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 91.3 A HEM 104 C ND HEM 1_555 A HEM 104 C FE HEM 1_555 A MET 80 A SD MET 85 1_555 84.7 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 A A SG CAB CYS HEM 14 104 1.81 1 A A SG CAC CYS HEM 17 104 1.85 1 6.97 1.10 114.20 121.17 A A A CA CB SG CYS CYS CYS 14 14 14 N 1 4.76 0.50 120.30 125.06 A A A NE CZ NH1 ARG ARG ARG 38 38 38 N 1 18.21 2.20 113.40 131.61 A A A CA CB CG GLU GLU GLU 44 44 44 N 1 -4.19 0.60 121.00 116.81 A A A CB CG CD2 TYR TYR TYR 48 48 48 N 1 7.21 0.90 118.30 125.51 A A A CB CG OD1 ASP ASP ASP 60 60 60 N 1 -5.64 0.90 118.30 112.66 A A A CB CG OD2 ASP ASP ASP 60 60 60 N 1 -4.23 0.70 120.80 116.57 A A A CB CG CD1 PHE PHE PHE 67 67 67 N 1 11.78 1.60 100.20 111.98 A A A CG SD CE MET MET MET 80 80 80 N 1 7.69 0.90 118.30 125.99 A A A CB CG OD1 ASP ASP ASP 93 93 93 N 1 A A NZ NZ LYS LYS 5 5 1.98 1_555 7_465 1 A A OD2 OD2 ASP ASP 60 60 2.05 1_555 7_555 1 A GLU -4 -146.42 16.87 1 A LYS 27 -129.80 -131.64 1 A ASN 70 -164.12 102.53 0.1810000 2.0 1 2.0 39 937 48 0 850 0.022 refinement PROLSQ CYTOCHROME C (ISOZYME 1) (OXIDIZED) MUTANT WITH ASN 52 REPLACED BY ILE, TYR 67 REPLACED BY PHE, AND CYS 102 REPLACED BY THR (N52I,Y67F,C102T) THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C 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 1.362 A PRO 71 A C PRO 76 1_555 A M3L 72 A N M3L 77 1_555 covale 1.306 A M3L 72 A C M3L 77 1_555 A LYS 73 A N LYS 78 1_555 metalc 2.043 A HIS 18 A NE2 HIS 23 1_555 A HEM 104 C FE HEM 1_555 metalc 2.549 A MET 80 A SD MET 85 1_555 A HEM 104 C FE HEM 1_555 ELECTRON TRANSPORT(CYTOCHROME) ELECTRON TRANSPORT(CYTOCHROME) CYC1_YEAST UNP 1 1 P00044 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLITYLKKACE 1 108 1CRI -5 103 P00044 A 1 1 108 1 ASN CONFLICT ILE 52 1CRI A P00044 UNP 57 57 1 TYR CONFLICT PHE 67 1CRI A P00044 UNP 72 72 1 CYS CONFLICT THR 102 1CRI 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 Software 6 BINDING SITE FOR RESIDUE HEM A 104 Software 20 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 SER 47 A SER 52 6 3_554 A LYS 73 A LYS 78 6 7_565 A HOH 304 D HOH 6 7_565 A ARG 13 A ARG 18 20 1_555 A CYS 14 A CYS 19 20 1_555 A CYS 17 A CYS 22 20 1_555 A HIS 18 A HIS 23 20 1_555 A GLY 23 A GLY 28 20 6_465 A ILE 35 A ILE 40 20 1_555 A SER 40 A SER 45 20 1_555 A GLY 41 A GLY 46 20 1_555 A TYR 46 A TYR 51 20 1_555 A TYR 48 A TYR 53 20 1_555 A THR 49 A THR 54 20 1_555 A ILE 52 A ILE 57 20 1_555 A TRP 59 A TRP 64 20 1_555 A THR 78 A THR 83 20 1_555 A LYS 79 A LYS 84 20 1_555 A MET 80 A MET 85 20 1_555 A PHE 82 A PHE 87 20 1_555 A LEU 98 A LEU 103 20 1_555 A HOH 121 D HOH 20 1_555 A HOH 168 D HOH 20 1_555 96 P 43 21 2