Iron in PDB 5gyr: Tetrameric Allochromatium Vinosum Cytochrome C'
Protein crystallography data
The structure of Tetrameric Allochromatium Vinosum Cytochrome C', PDB code: 5gyr
was solved by
M.Yamanaka,
M.Hoshizumi,
S.Nagao,
R.Nakayama,
N.Shibata,
Y.Higuchi,
S.Hirota,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
41.40 /
1.60
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.949,
48.620,
130.550,
90.00,
92.28,
90.00
|
|
R / Rfree (%)
|
20.4 /
23.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Tetrameric Allochromatium Vinosum Cytochrome C'
(pdb code 5gyr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Tetrameric Allochromatium Vinosum Cytochrome C', PDB code: 5gyr:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 1 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:19.9
occ:1.00
|
FE
|
A:HEC201
|
0.0
|
19.9
|
1.0
|
|
ND
|
A:HEC201
|
1.9
|
17.8
|
1.0
|
|
NA
|
A:HEC201
|
2.0
|
20.6
|
1.0
|
|
NB
|
A:HEC201
|
2.1
|
18.2
|
1.0
|
|
NC
|
A:HEC201
|
2.1
|
15.7
|
1.0
|
|
NE2
|
A:HIS125
|
2.3
|
21.6
|
1.0
|
|
C4D
|
A:HEC201
|
2.9
|
22.3
|
1.0
|
|
C1D
|
A:HEC201
|
2.9
|
21.0
|
1.0
|
|
C4B
|
A:HEC201
|
3.0
|
17.0
|
1.0
|
|
C1A
|
A:HEC201
|
3.0
|
19.0
|
1.0
|
|
C1C
|
A:HEC201
|
3.1
|
16.3
|
1.0
|
|
C4A
|
A:HEC201
|
3.1
|
20.4
|
1.0
|
|
C1B
|
A:HEC201
|
3.1
|
19.7
|
1.0
|
|
C4C
|
A:HEC201
|
3.1
|
19.3
|
1.0
|
|
CE1
|
A:HIS125
|
3.2
|
18.9
|
1.0
|
|
CD2
|
A:HIS125
|
3.2
|
21.7
|
1.0
|
|
CD1
|
N:TYR16
|
3.4
|
20.1
|
1.0
|
|
CHC
|
A:HEC201
|
3.4
|
12.6
|
1.0
|
|
CHA
|
A:HEC201
|
3.4
|
14.9
|
1.0
|
|
CHD
|
A:HEC201
|
3.4
|
19.5
|
1.0
|
|
CHB
|
A:HEC201
|
3.5
|
17.5
|
1.0
|
|
CG
|
N:TYR16
|
3.7
|
18.7
|
1.0
|
|
CE1
|
N:TYR16
|
3.7
|
17.7
|
1.0
|
|
C3D
|
A:HEC201
|
4.2
|
22.3
|
1.0
|
|
CB
|
N:TYR16
|
4.2
|
20.0
|
1.0
|
|
C2D
|
A:HEC201
|
4.2
|
21.6
|
1.0
|
|
CD2
|
N:TYR16
|
4.2
|
16.2
|
1.0
|
|
CZ
|
N:TYR16
|
4.2
|
18.7
|
1.0
|
|
C3A
|
A:HEC201
|
4.3
|
21.4
|
1.0
|
|
C2A
|
A:HEC201
|
4.3
|
21.8
|
1.0
|
|
C3B
|
A:HEC201
|
4.3
|
18.8
|
1.0
|
|
C2B
|
A:HEC201
|
4.3
|
19.4
|
1.0
|
|
C2C
|
A:HEC201
|
4.3
|
19.7
|
1.0
|
|
C3C
|
A:HEC201
|
4.3
|
18.1
|
1.0
|
|
ND1
|
A:HIS125
|
4.3
|
20.6
|
1.0
|
|
CG
|
A:HIS125
|
4.4
|
20.4
|
1.0
|
|
CE2
|
N:TYR16
|
4.5
|
20.8
|
1.0
|
|
NH1
|
A:ARG129
|
4.7
|
29.4
|
1.0
|
|
Iron binding site 2 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 2 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:12.3
occ:1.00
|
FE
|
B:HEC201
|
0.0
|
12.3
|
1.0
|
|
ND
|
B:HEC201
|
1.9
|
11.0
|
1.0
|
|
NA
|
B:HEC201
|
2.0
|
12.3
|
1.0
|
|
NB
|
B:HEC201
|
2.1
|
12.7
|
1.0
|
|
NC
|
B:HEC201
|
2.1
|
14.0
|
1.0
|
|
NE2
|
B:HIS125
|
2.2
|
14.0
|
1.0
|
|
C4D
|
B:HEC201
|
3.0
|
12.2
|
1.0
|
|
C1D
|
B:HEC201
|
3.0
|
11.7
|
1.0
|
|
C4B
|
B:HEC201
|
3.0
|
13.4
|
1.0
|
|
C1A
|
B:HEC201
|
3.0
|
11.4
|
1.0
|
|
C1B
|
B:HEC201
|
3.1
|
13.0
|
1.0
|
|
C4A
|
B:HEC201
|
3.1
|
11.3
|
1.0
|
|
C4C
|
B:HEC201
|
3.1
|
12.9
|
1.0
|
|
C1C
|
B:HEC201
|
3.1
|
13.9
|
1.0
|
|
CD2
|
B:HIS125
|
3.1
|
15.6
|
1.0
|
|
CE1
|
B:HIS125
|
3.2
|
17.2
|
1.0
|
|
CD1
|
B:TYR16
|
3.2
|
11.3
|
1.0
|
|
CHD
|
B:HEC201
|
3.4
|
13.0
|
1.0
|
|
CHA
|
B:HEC201
|
3.4
|
11.5
|
1.0
|
|
CHC
|
B:HEC201
|
3.4
|
13.4
|
1.0
|
|
CHB
|
B:HEC201
|
3.4
|
12.2
|
1.0
|
|
CE1
|
B:TYR16
|
3.5
|
12.8
|
1.0
|
|
CG
|
B:TYR16
|
3.6
|
11.6
|
1.0
|
|
CZ
|
B:TYR16
|
4.1
|
12.9
|
1.0
|
|
CB
|
B:TYR16
|
4.2
|
12.8
|
1.0
|
|
CD2
|
B:TYR16
|
4.2
|
11.0
|
1.0
|
|
C3D
|
B:HEC201
|
4.2
|
11.6
|
1.0
|
|
C2D
|
B:HEC201
|
4.2
|
11.7
|
1.0
|
|
C3A
|
B:HEC201
|
4.3
|
12.9
|
1.0
|
|
ND1
|
B:HIS125
|
4.3
|
19.0
|
1.0
|
|
C2A
|
B:HEC201
|
4.3
|
13.6
|
1.0
|
|
C2B
|
B:HEC201
|
4.3
|
12.8
|
1.0
|
|
CG
|
B:HIS125
|
4.3
|
17.3
|
1.0
|
|
C3C
|
B:HEC201
|
4.3
|
14.9
|
1.0
|
|
C2C
|
B:HEC201
|
4.3
|
15.4
|
1.0
|
|
C3B
|
B:HEC201
|
4.3
|
13.5
|
1.0
|
|
CE2
|
B:TYR16
|
4.4
|
12.6
|
1.0
|
|
NH1
|
B:ARG129
|
4.5
|
18.1
|
1.0
|
|
OH
|
B:TYR16
|
5.0
|
13.4
|
1.0
|
|
CD
|
B:ARG129
|
5.0
|
16.7
|
1.0
|
|
Iron binding site 3 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 3 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:19.9
occ:1.00
|
FE
|
E:HEC201
|
0.0
|
19.9
|
1.0
|
|
ND
|
E:HEC201
|
1.9
|
21.1
|
1.0
|
|
NA
|
E:HEC201
|
2.0
|
20.5
|
1.0
|
|
NB
|
E:HEC201
|
2.1
|
17.2
|
1.0
|
|
NC
|
E:HEC201
|
2.1
|
18.0
|
1.0
|
|
NE2
|
E:HIS125
|
2.3
|
21.9
|
1.0
|
|
C4D
|
E:HEC201
|
2.9
|
21.6
|
1.0
|
|
C1D
|
E:HEC201
|
2.9
|
19.5
|
1.0
|
|
C4B
|
E:HEC201
|
3.0
|
17.7
|
1.0
|
|
C1A
|
E:HEC201
|
3.0
|
20.5
|
1.0
|
|
C4A
|
E:HEC201
|
3.1
|
18.9
|
1.0
|
|
C1B
|
E:HEC201
|
3.1
|
18.5
|
1.0
|
|
C4C
|
E:HEC201
|
3.1
|
19.3
|
1.0
|
|
C1C
|
E:HEC201
|
3.1
|
17.9
|
1.0
|
|
CD2
|
E:HIS125
|
3.2
|
20.8
|
1.0
|
|
CE1
|
E:HIS125
|
3.2
|
18.6
|
1.0
|
|
CD1
|
J:TYR16
|
3.3
|
18.5
|
1.0
|
|
CHA
|
E:HEC201
|
3.4
|
17.5
|
1.0
|
|
CHD
|
E:HEC201
|
3.4
|
19.3
|
1.0
|
|
CHC
|
E:HEC201
|
3.4
|
16.1
|
1.0
|
|
CHB
|
E:HEC201
|
3.5
|
16.6
|
1.0
|
|
CE1
|
J:TYR16
|
3.7
|
17.6
|
1.0
|
|
CG
|
J:TYR16
|
3.7
|
17.8
|
1.0
|
|
CB
|
J:TYR16
|
4.2
|
20.2
|
1.0
|
|
C3D
|
E:HEC201
|
4.2
|
20.1
|
1.0
|
|
C2D
|
E:HEC201
|
4.2
|
19.2
|
1.0
|
|
CZ
|
J:TYR16
|
4.3
|
18.1
|
1.0
|
|
CD2
|
J:TYR16
|
4.3
|
16.6
|
1.0
|
|
C3A
|
E:HEC201
|
4.3
|
20.9
|
1.0
|
|
C2A
|
E:HEC201
|
4.3
|
24.2
|
1.0
|
|
C2C
|
E:HEC201
|
4.3
|
19.7
|
1.0
|
|
C2B
|
E:HEC201
|
4.3
|
19.0
|
1.0
|
|
C3B
|
E:HEC201
|
4.3
|
19.2
|
1.0
|
|
C3C
|
E:HEC201
|
4.3
|
19.8
|
1.0
|
|
ND1
|
E:HIS125
|
4.4
|
20.5
|
1.0
|
|
CG
|
E:HIS125
|
4.4
|
20.5
|
1.0
|
|
CE2
|
J:TYR16
|
4.5
|
16.2
|
1.0
|
|
NH1
|
E:ARG129
|
4.6
|
27.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 4 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:12.6
occ:1.00
|
FE
|
F:HEC201
|
0.0
|
12.6
|
1.0
|
|
ND
|
F:HEC201
|
1.9
|
12.0
|
1.0
|
|
NA
|
F:HEC201
|
2.0
|
12.9
|
1.0
|
|
NB
|
F:HEC201
|
2.1
|
12.3
|
1.0
|
|
NC
|
F:HEC201
|
2.1
|
13.7
|
1.0
|
|
NE2
|
F:HIS125
|
2.2
|
16.3
|
1.0
|
|
C4D
|
F:HEC201
|
3.0
|
14.2
|
1.0
|
|
C1D
|
F:HEC201
|
3.0
|
11.8
|
1.0
|
|
C4B
|
F:HEC201
|
3.0
|
12.2
|
1.0
|
|
C1B
|
F:HEC201
|
3.0
|
13.2
|
1.0
|
|
C4A
|
F:HEC201
|
3.0
|
11.4
|
1.0
|
|
C1A
|
F:HEC201
|
3.1
|
12.4
|
1.0
|
|
C4C
|
F:HEC201
|
3.1
|
12.0
|
1.0
|
|
C1C
|
F:HEC201
|
3.1
|
12.9
|
1.0
|
|
CD2
|
F:HIS125
|
3.1
|
16.1
|
1.0
|
|
CE1
|
F:HIS125
|
3.2
|
16.6
|
1.0
|
|
CD1
|
F:TYR16
|
3.2
|
13.1
|
1.0
|
|
CHA
|
F:HEC201
|
3.4
|
12.8
|
1.0
|
|
CHB
|
F:HEC201
|
3.4
|
12.0
|
1.0
|
|
CHD
|
F:HEC201
|
3.4
|
12.2
|
1.0
|
|
CHC
|
F:HEC201
|
3.4
|
12.5
|
1.0
|
|
CE1
|
F:TYR16
|
3.5
|
12.9
|
1.0
|
|
CG
|
F:TYR16
|
3.6
|
11.4
|
1.0
|
|
CZ
|
F:TYR16
|
4.1
|
13.2
|
1.0
|
|
CD2
|
F:TYR16
|
4.2
|
11.6
|
1.0
|
|
CB
|
F:TYR16
|
4.2
|
12.2
|
1.0
|
|
C3D
|
F:HEC201
|
4.2
|
13.0
|
1.0
|
|
C2D
|
F:HEC201
|
4.2
|
12.9
|
1.0
|
|
ND1
|
F:HIS125
|
4.3
|
15.4
|
1.0
|
|
C3A
|
F:HEC201
|
4.3
|
13.1
|
1.0
|
|
C2B
|
F:HEC201
|
4.3
|
12.7
|
1.0
|
|
CG
|
F:HIS125
|
4.3
|
16.8
|
1.0
|
|
C2C
|
F:HEC201
|
4.3
|
14.5
|
1.0
|
|
C3C
|
F:HEC201
|
4.3
|
13.5
|
1.0
|
|
C2A
|
F:HEC201
|
4.3
|
14.1
|
1.0
|
|
C3B
|
F:HEC201
|
4.3
|
13.4
|
1.0
|
|
CE2
|
F:TYR16
|
4.4
|
13.4
|
1.0
|
|
NH1
|
F:ARG129
|
4.5
|
17.2
|
1.0
|
|
CD
|
F:ARG129
|
4.9
|
16.5
|
1.0
|
|
OH
|
F:TYR16
|
4.9
|
14.7
|
1.0
|
|
Iron binding site 5 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 5 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe201
b:20.4
occ:1.00
|
FE
|
I:HEC201
|
0.0
|
20.4
|
1.0
|
|
ND
|
I:HEC201
|
1.9
|
20.3
|
1.0
|
|
NA
|
I:HEC201
|
2.0
|
20.1
|
1.0
|
|
NC
|
I:HEC201
|
2.1
|
22.9
|
1.0
|
|
NB
|
I:HEC201
|
2.1
|
23.2
|
1.0
|
|
NE2
|
I:HIS125
|
2.3
|
24.6
|
1.0
|
|
C1D
|
I:HEC201
|
2.9
|
21.2
|
1.0
|
|
C4D
|
I:HEC201
|
2.9
|
20.3
|
1.0
|
|
C1A
|
I:HEC201
|
3.0
|
20.0
|
1.0
|
|
C4A
|
I:HEC201
|
3.0
|
20.6
|
1.0
|
|
C4C
|
I:HEC201
|
3.1
|
23.0
|
1.0
|
|
C4B
|
I:HEC201
|
3.1
|
20.4
|
1.0
|
|
C1B
|
I:HEC201
|
3.1
|
20.5
|
1.0
|
|
C1C
|
I:HEC201
|
3.1
|
22.4
|
1.0
|
|
CD2
|
I:HIS125
|
3.2
|
22.8
|
1.0
|
|
CD1
|
I:TYR16
|
3.2
|
21.8
|
1.0
|
|
CE1
|
I:HIS125
|
3.3
|
22.9
|
1.0
|
|
CHD
|
I:HEC201
|
3.4
|
19.4
|
1.0
|
|
CHA
|
I:HEC201
|
3.4
|
19.8
|
1.0
|
|
CHB
|
I:HEC201
|
3.4
|
20.1
|
1.0
|
|
CHC
|
I:HEC201
|
3.5
|
20.4
|
1.0
|
|
CE1
|
I:TYR16
|
3.5
|
20.7
|
1.0
|
|
CG
|
I:TYR16
|
3.6
|
18.9
|
1.0
|
|
CZ
|
I:TYR16
|
4.1
|
20.2
|
1.0
|
|
CB
|
I:TYR16
|
4.1
|
19.2
|
1.0
|
|
CD2
|
I:TYR16
|
4.1
|
19.2
|
1.0
|
|
C2D
|
I:HEC201
|
4.2
|
21.4
|
1.0
|
|
C3D
|
I:HEC201
|
4.2
|
22.1
|
1.0
|
|
C2A
|
I:HEC201
|
4.2
|
21.5
|
1.0
|
|
C3A
|
I:HEC201
|
4.2
|
20.9
|
1.0
|
|
C3C
|
I:HEC201
|
4.3
|
22.6
|
1.0
|
|
C2C
|
I:HEC201
|
4.3
|
22.6
|
1.0
|
|
C2B
|
I:HEC201
|
4.3
|
22.2
|
1.0
|
|
C3B
|
I:HEC201
|
4.3
|
22.6
|
1.0
|
|
ND1
|
I:HIS125
|
4.4
|
25.0
|
1.0
|
|
CG
|
I:HIS125
|
4.4
|
21.0
|
1.0
|
|
CE2
|
I:TYR16
|
4.4
|
19.3
|
1.0
|
|
NH1
|
I:ARG129
|
4.6
|
25.4
|
1.0
|
|
OH
|
I:TYR16
|
4.9
|
24.5
|
1.0
|
|
Iron binding site 6 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 6 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe201
b:16.0
occ:1.00
|
FE
|
J:HEC201
|
0.0
|
16.0
|
1.0
|
|
ND
|
J:HEC201
|
1.9
|
15.7
|
1.0
|
|
NA
|
J:HEC201
|
2.0
|
16.2
|
1.0
|
|
NC
|
J:HEC201
|
2.1
|
14.4
|
1.0
|
|
NB
|
J:HEC201
|
2.1
|
16.3
|
1.0
|
|
NE2
|
J:HIS125
|
2.2
|
17.1
|
1.0
|
|
C1D
|
J:HEC201
|
2.9
|
15.6
|
1.0
|
|
C4D
|
J:HEC201
|
2.9
|
16.5
|
1.0
|
|
C1A
|
J:HEC201
|
3.0
|
16.7
|
1.0
|
|
C4A
|
J:HEC201
|
3.0
|
14.9
|
1.0
|
|
C4B
|
J:HEC201
|
3.1
|
13.7
|
1.0
|
|
C4C
|
J:HEC201
|
3.1
|
15.8
|
1.0
|
|
C1B
|
J:HEC201
|
3.1
|
14.6
|
1.0
|
|
C1C
|
J:HEC201
|
3.1
|
16.2
|
1.0
|
|
CD2
|
J:HIS125
|
3.2
|
17.9
|
1.0
|
|
CE1
|
J:HIS125
|
3.2
|
15.6
|
1.0
|
|
CD1
|
E:TYR16
|
3.3
|
14.0
|
1.0
|
|
CHD
|
J:HEC201
|
3.4
|
15.2
|
1.0
|
|
CHA
|
J:HEC201
|
3.4
|
16.4
|
1.0
|
|
CHB
|
J:HEC201
|
3.4
|
14.9
|
1.0
|
|
CHC
|
J:HEC201
|
3.5
|
14.5
|
1.0
|
|
CE1
|
E:TYR16
|
3.6
|
13.9
|
1.0
|
|
CG
|
E:TYR16
|
3.6
|
13.7
|
1.0
|
|
CB
|
E:TYR16
|
4.2
|
13.9
|
1.0
|
|
C2D
|
J:HEC201
|
4.2
|
16.6
|
1.0
|
|
CZ
|
E:TYR16
|
4.2
|
14.0
|
1.0
|
|
CD2
|
E:TYR16
|
4.2
|
15.0
|
1.0
|
|
C3D
|
J:HEC201
|
4.2
|
16.1
|
1.0
|
|
C3A
|
J:HEC201
|
4.2
|
15.3
|
1.0
|
|
C2A
|
J:HEC201
|
4.2
|
17.2
|
1.0
|
|
C2C
|
J:HEC201
|
4.3
|
15.7
|
1.0
|
|
C3C
|
J:HEC201
|
4.3
|
16.4
|
1.0
|
|
C2B
|
J:HEC201
|
4.3
|
16.1
|
1.0
|
|
ND1
|
J:HIS125
|
4.3
|
17.4
|
1.0
|
|
C3B
|
J:HEC201
|
4.3
|
14.7
|
1.0
|
|
CG
|
J:HIS125
|
4.4
|
19.9
|
1.0
|
|
CE2
|
E:TYR16
|
4.5
|
14.0
|
1.0
|
|
NH1
|
J:ARG129
|
4.6
|
21.5
|
1.0
|
|
Iron binding site 7 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 7 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe201
b:21.2
occ:1.00
|
FE
|
M:HEC201
|
0.0
|
21.2
|
1.0
|
|
ND
|
M:HEC201
|
1.9
|
23.1
|
1.0
|
|
NA
|
M:HEC201
|
2.0
|
19.6
|
1.0
|
|
NC
|
M:HEC201
|
2.1
|
24.6
|
1.0
|
|
NB
|
M:HEC201
|
2.1
|
22.4
|
1.0
|
|
NE2
|
M:HIS125
|
2.2
|
24.7
|
1.0
|
|
C4D
|
M:HEC201
|
2.9
|
21.0
|
1.0
|
|
C1D
|
M:HEC201
|
3.0
|
22.1
|
1.0
|
|
C1A
|
M:HEC201
|
3.0
|
21.2
|
1.0
|
|
C4A
|
M:HEC201
|
3.0
|
19.9
|
1.0
|
|
C4B
|
M:HEC201
|
3.1
|
22.7
|
1.0
|
|
C4C
|
M:HEC201
|
3.1
|
24.1
|
1.0
|
|
C1C
|
M:HEC201
|
3.1
|
24.3
|
1.0
|
|
C1B
|
M:HEC201
|
3.1
|
20.6
|
1.0
|
|
CD2
|
M:HIS125
|
3.2
|
22.5
|
1.0
|
|
CE1
|
M:HIS125
|
3.2
|
22.0
|
1.0
|
|
CD1
|
M:TYR16
|
3.2
|
22.9
|
1.0
|
|
CHA
|
M:HEC201
|
3.4
|
20.5
|
1.0
|
|
CHD
|
M:HEC201
|
3.4
|
21.5
|
1.0
|
|
CHC
|
M:HEC201
|
3.5
|
23.7
|
1.0
|
|
CHB
|
M:HEC201
|
3.5
|
19.0
|
1.0
|
|
CE1
|
M:TYR16
|
3.5
|
24.4
|
1.0
|
|
CG
|
M:TYR16
|
3.6
|
21.0
|
1.0
|
|
CZ
|
M:TYR16
|
4.1
|
21.7
|
1.0
|
|
CD2
|
M:TYR16
|
4.2
|
20.6
|
1.0
|
|
C2D
|
M:HEC201
|
4.2
|
23.1
|
1.0
|
|
C3D
|
M:HEC201
|
4.2
|
23.7
|
1.0
|
|
CB
|
M:TYR16
|
4.2
|
19.6
|
1.0
|
|
C3A
|
M:HEC201
|
4.2
|
20.8
|
1.0
|
|
C2A
|
M:HEC201
|
4.2
|
22.5
|
1.0
|
|
C2C
|
M:HEC201
|
4.3
|
25.1
|
1.0
|
|
C3C
|
M:HEC201
|
4.3
|
25.9
|
1.0
|
|
C2B
|
M:HEC201
|
4.3
|
22.0
|
1.0
|
|
ND1
|
M:HIS125
|
4.3
|
24.1
|
1.0
|
|
CG
|
M:HIS125
|
4.3
|
22.1
|
1.0
|
|
C3B
|
M:HEC201
|
4.3
|
23.7
|
1.0
|
|
CE2
|
M:TYR16
|
4.4
|
22.1
|
1.0
|
|
NH1
|
M:ARG129
|
4.6
|
27.5
|
1.0
|
|
OH
|
M:TYR16
|
4.9
|
26.9
|
1.0
|
|
Iron binding site 8 out
of 8 in 5gyr
Go back to
Iron Binding Sites List in 5gyr
Iron binding site 8 out
of 8 in the Tetrameric Allochromatium Vinosum Cytochrome C'
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Tetrameric Allochromatium Vinosum Cytochrome C' within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe201
b:14.4
occ:1.00
|
FE
|
N:HEC201
|
0.0
|
14.4
|
1.0
|
|
ND
|
N:HEC201
|
1.9
|
15.2
|
1.0
|
|
NA
|
N:HEC201
|
2.0
|
12.3
|
1.0
|
|
NB
|
N:HEC201
|
2.1
|
13.0
|
1.0
|
|
NC
|
N:HEC201
|
2.1
|
13.4
|
1.0
|
|
NE2
|
N:HIS125
|
2.2
|
14.4
|
1.0
|
|
C1D
|
N:HEC201
|
3.0
|
14.1
|
1.0
|
|
C4D
|
N:HEC201
|
3.0
|
15.0
|
1.0
|
|
C4A
|
N:HEC201
|
3.0
|
13.0
|
1.0
|
|
C1A
|
N:HEC201
|
3.0
|
13.4
|
1.0
|
|
C4B
|
N:HEC201
|
3.0
|
12.7
|
1.0
|
|
C1B
|
N:HEC201
|
3.1
|
11.9
|
1.0
|
|
C4C
|
N:HEC201
|
3.1
|
12.5
|
1.0
|
|
C1C
|
N:HEC201
|
3.1
|
13.4
|
1.0
|
|
CD2
|
N:HIS125
|
3.2
|
15.2
|
1.0
|
|
CE1
|
N:HIS125
|
3.2
|
12.8
|
1.0
|
|
CD1
|
A:TYR16
|
3.3
|
14.2
|
1.0
|
|
CHD
|
N:HEC201
|
3.4
|
14.1
|
1.0
|
|
CHA
|
N:HEC201
|
3.4
|
13.4
|
1.0
|
|
CHB
|
N:HEC201
|
3.4
|
11.7
|
1.0
|
|
CHC
|
N:HEC201
|
3.4
|
13.8
|
1.0
|
|
CE1
|
A:TYR16
|
3.6
|
12.2
|
1.0
|
|
CG
|
A:TYR16
|
3.7
|
13.3
|
1.0
|
|
CB
|
A:TYR16
|
4.2
|
13.6
|
1.0
|
|
CZ
|
A:TYR16
|
4.2
|
13.3
|
1.0
|
|
CD2
|
A:TYR16
|
4.2
|
14.9
|
1.0
|
|
C2D
|
N:HEC201
|
4.2
|
14.5
|
1.0
|
|
C3D
|
N:HEC201
|
4.2
|
13.7
|
1.0
|
|
C3A
|
N:HEC201
|
4.2
|
13.2
|
1.0
|
|
C2A
|
N:HEC201
|
4.2
|
14.8
|
1.0
|
|
C2C
|
N:HEC201
|
4.3
|
13.3
|
1.0
|
|
ND1
|
N:HIS125
|
4.3
|
16.3
|
1.0
|
|
C3C
|
N:HEC201
|
4.3
|
14.8
|
1.0
|
|
C2B
|
N:HEC201
|
4.3
|
14.5
|
1.0
|
|
C3B
|
N:HEC201
|
4.3
|
14.0
|
1.0
|
|
CG
|
N:HIS125
|
4.3
|
16.7
|
1.0
|
|
CE2
|
A:TYR16
|
4.5
|
11.9
|
1.0
|
|
NH1
|
N:ARG129
|
4.6
|
18.2
|
1.0
|
|
Reference:
M.Yamanaka,
M.Hoshizumi,
S.Nagao,
R.Nakayama,
N.Shibata,
Y.Higuchi,
S.Hirota.
Formation and Carbon Monoxide-Dependent Dissociation of Allochromatium Vinosum Cytochrome C' Oligomers Using Domain-Swapped Dimers Protein Sci. V. 26 464 2017.
ISSN: ESSN 1469-896X
PubMed: 27883268
DOI: 10.1002/PRO.3090
Page generated: Tue Aug 5 21:45:20 2025
|
