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