Iron in PDB 1occ: Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
Enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
All present enzymatic activity of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;
Protein crystallography data
The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1occ
was solved by
T.Tsukihara,
H.Aoyama,
E.Yamashita,
T.Tomizaki,
H.Yamaguchi,
K.Shinzawa-Itoh,
R.Nakashima,
R.Yaono,
S.Yoshikawa,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
189.100,
210.500,
178.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.1 /
25.2
|
Other elements in 1occ:
The structure of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
(pdb code 1occ). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1occ:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1occ
Go back to
Iron Binding Sites List in 1occ
Iron binding site 1 out
of 4 in the Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe515
b:9.8
occ:1.00
|
FE
|
A:HEA515
|
0.0
|
9.8
|
1.0
|
NE2
|
A:HIS61
|
1.8
|
7.0
|
1.0
|
NE2
|
A:HIS378
|
1.9
|
7.0
|
1.0
|
NB
|
A:HEA515
|
1.9
|
13.1
|
1.0
|
NA
|
A:HEA515
|
1.9
|
20.1
|
1.0
|
ND
|
A:HEA515
|
2.0
|
9.7
|
1.0
|
NC
|
A:HEA515
|
2.0
|
22.6
|
1.0
|
CE1
|
A:HIS378
|
2.6
|
7.0
|
1.0
|
CE1
|
A:HIS61
|
2.7
|
13.2
|
1.0
|
C1B
|
A:HEA515
|
2.9
|
12.2
|
1.0
|
CD2
|
A:HIS61
|
2.9
|
9.3
|
1.0
|
C4A
|
A:HEA515
|
3.0
|
15.2
|
1.0
|
C1D
|
A:HEA515
|
3.0
|
14.3
|
1.0
|
C4B
|
A:HEA515
|
3.0
|
19.0
|
1.0
|
C4C
|
A:HEA515
|
3.0
|
17.6
|
1.0
|
C1A
|
A:HEA515
|
3.1
|
10.3
|
1.0
|
C4D
|
A:HEA515
|
3.1
|
15.1
|
1.0
|
C1C
|
A:HEA515
|
3.1
|
17.1
|
1.0
|
CD2
|
A:HIS378
|
3.1
|
8.6
|
1.0
|
CHB
|
A:HEA515
|
3.3
|
11.5
|
1.0
|
CHD
|
A:HEA515
|
3.4
|
16.3
|
1.0
|
CHA
|
A:HEA515
|
3.5
|
9.4
|
1.0
|
CHC
|
A:HEA515
|
3.5
|
13.9
|
1.0
|
ND1
|
A:HIS378
|
3.9
|
11.0
|
1.0
|
ND1
|
A:HIS61
|
4.0
|
13.6
|
1.0
|
CG
|
A:HIS61
|
4.1
|
8.7
|
1.0
|
C2B
|
A:HEA515
|
4.2
|
16.0
|
1.0
|
C3A
|
A:HEA515
|
4.2
|
13.5
|
1.0
|
CG
|
A:HIS378
|
4.2
|
7.0
|
1.0
|
C2A
|
A:HEA515
|
4.2
|
9.1
|
1.0
|
C2D
|
A:HEA515
|
4.3
|
18.3
|
1.0
|
C3B
|
A:HEA515
|
4.3
|
17.7
|
1.0
|
C3C
|
A:HEA515
|
4.3
|
18.0
|
1.0
|
C3D
|
A:HEA515
|
4.3
|
18.0
|
1.0
|
C2C
|
A:HEA515
|
4.3
|
18.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 1occ
Go back to
Iron Binding Sites List in 1occ
Iron binding site 2 out
of 4 in the Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe516
b:8.0
occ:1.00
|
FE
|
A:HEA516
|
0.0
|
8.0
|
1.0
|
ND
|
A:HEA516
|
1.9
|
7.6
|
1.0
|
NB
|
A:HEA516
|
2.0
|
10.9
|
1.0
|
NC
|
A:HEA516
|
2.0
|
16.3
|
1.0
|
NA
|
A:HEA516
|
2.0
|
14.8
|
1.0
|
NE2
|
A:HIS376
|
2.1
|
7.0
|
1.0
|
C1D
|
A:HEA516
|
3.0
|
11.3
|
1.0
|
C4D
|
A:HEA516
|
3.0
|
14.8
|
1.0
|
CE1
|
A:HIS376
|
3.0
|
10.5
|
1.0
|
C1B
|
A:HEA516
|
3.0
|
14.2
|
1.0
|
C4B
|
A:HEA516
|
3.0
|
14.2
|
1.0
|
C4C
|
A:HEA516
|
3.1
|
13.7
|
1.0
|
C4A
|
A:HEA516
|
3.1
|
14.3
|
1.0
|
C1C
|
A:HEA516
|
3.1
|
13.1
|
1.0
|
C1A
|
A:HEA516
|
3.1
|
7.0
|
1.0
|
CD2
|
A:HIS376
|
3.2
|
9.2
|
1.0
|
CHD
|
A:HEA516
|
3.4
|
12.9
|
1.0
|
CHB
|
A:HEA516
|
3.4
|
17.8
|
1.0
|
CHA
|
A:HEA516
|
3.4
|
8.6
|
1.0
|
CHC
|
A:HEA516
|
3.4
|
10.2
|
1.0
|
C3D
|
A:HEA516
|
4.2
|
13.9
|
1.0
|
C2D
|
A:HEA516
|
4.2
|
12.4
|
1.0
|
C2B
|
A:HEA516
|
4.3
|
11.5
|
1.0
|
ND1
|
A:HIS376
|
4.3
|
7.0
|
1.0
|
C3B
|
A:HEA516
|
4.3
|
16.1
|
1.0
|
C3A
|
A:HEA516
|
4.3
|
7.0
|
1.0
|
C3C
|
A:HEA516
|
4.3
|
14.3
|
1.0
|
CG
|
A:HIS376
|
4.3
|
7.0
|
1.0
|
C2C
|
A:HEA516
|
4.3
|
15.4
|
1.0
|
C2A
|
A:HEA516
|
4.4
|
7.0
|
1.0
|
CU
|
A:CU517
|
4.7
|
15.3
|
1.0
|
CE1
|
A:HIS240
|
4.9
|
27.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 1occ
Go back to
Iron Binding Sites List in 1occ
Iron binding site 3 out
of 4 in the Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe515
b:9.8
occ:1.00
|
FE
|
N:HEA515
|
0.0
|
9.8
|
1.0
|
NE2
|
N:HIS61
|
1.8
|
7.0
|
1.0
|
NE2
|
N:HIS378
|
1.9
|
7.0
|
1.0
|
NB
|
N:HEA515
|
1.9
|
13.1
|
1.0
|
NA
|
N:HEA515
|
1.9
|
20.1
|
1.0
|
ND
|
N:HEA515
|
2.0
|
9.7
|
1.0
|
NC
|
N:HEA515
|
2.0
|
22.6
|
1.0
|
CE1
|
N:HIS378
|
2.6
|
7.0
|
1.0
|
CE1
|
N:HIS61
|
2.7
|
13.2
|
1.0
|
C1B
|
N:HEA515
|
2.9
|
12.2
|
1.0
|
CD2
|
N:HIS61
|
2.9
|
9.3
|
1.0
|
C4A
|
N:HEA515
|
3.0
|
15.2
|
1.0
|
C1D
|
N:HEA515
|
3.0
|
14.3
|
1.0
|
C4C
|
N:HEA515
|
3.0
|
17.6
|
1.0
|
C4B
|
N:HEA515
|
3.0
|
19.0
|
1.0
|
C1A
|
N:HEA515
|
3.1
|
10.3
|
1.0
|
C4D
|
N:HEA515
|
3.1
|
15.1
|
1.0
|
C1C
|
N:HEA515
|
3.1
|
17.1
|
1.0
|
CD2
|
N:HIS378
|
3.1
|
8.6
|
1.0
|
CHB
|
N:HEA515
|
3.3
|
11.5
|
1.0
|
CHD
|
N:HEA515
|
3.4
|
16.3
|
1.0
|
CHA
|
N:HEA515
|
3.5
|
9.4
|
1.0
|
CHC
|
N:HEA515
|
3.5
|
13.9
|
1.0
|
ND1
|
N:HIS378
|
3.9
|
11.0
|
1.0
|
ND1
|
N:HIS61
|
4.0
|
13.6
|
1.0
|
CG
|
N:HIS61
|
4.1
|
8.7
|
1.0
|
C2B
|
N:HEA515
|
4.2
|
16.0
|
1.0
|
C3A
|
N:HEA515
|
4.2
|
13.5
|
1.0
|
CG
|
N:HIS378
|
4.2
|
7.0
|
1.0
|
C2A
|
N:HEA515
|
4.2
|
9.1
|
1.0
|
C2D
|
N:HEA515
|
4.3
|
18.3
|
1.0
|
C3B
|
N:HEA515
|
4.3
|
17.7
|
1.0
|
C3C
|
N:HEA515
|
4.3
|
18.0
|
1.0
|
C3D
|
N:HEA515
|
4.3
|
18.0
|
1.0
|
C2C
|
N:HEA515
|
4.3
|
18.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 1occ
Go back to
Iron Binding Sites List in 1occ
Iron binding site 4 out
of 4 in the Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe516
b:8.0
occ:1.00
|
FE
|
N:HEA516
|
0.0
|
8.0
|
1.0
|
ND
|
N:HEA516
|
1.9
|
7.6
|
1.0
|
NB
|
N:HEA516
|
2.0
|
10.9
|
1.0
|
NC
|
N:HEA516
|
2.0
|
16.3
|
1.0
|
NA
|
N:HEA516
|
2.0
|
14.8
|
1.0
|
NE2
|
N:HIS376
|
2.1
|
7.0
|
1.0
|
C1D
|
N:HEA516
|
3.0
|
11.3
|
1.0
|
C4D
|
N:HEA516
|
3.0
|
14.8
|
1.0
|
CE1
|
N:HIS376
|
3.0
|
10.5
|
1.0
|
C1B
|
N:HEA516
|
3.0
|
14.2
|
1.0
|
C4B
|
N:HEA516
|
3.0
|
14.2
|
1.0
|
C4C
|
N:HEA516
|
3.1
|
13.7
|
1.0
|
C4A
|
N:HEA516
|
3.1
|
14.3
|
1.0
|
C1C
|
N:HEA516
|
3.1
|
13.1
|
1.0
|
C1A
|
N:HEA516
|
3.1
|
7.0
|
1.0
|
CD2
|
N:HIS376
|
3.2
|
9.2
|
1.0
|
CHD
|
N:HEA516
|
3.4
|
12.9
|
1.0
|
CHB
|
N:HEA516
|
3.4
|
17.8
|
1.0
|
CHA
|
N:HEA516
|
3.4
|
8.6
|
1.0
|
CHC
|
N:HEA516
|
3.4
|
10.2
|
1.0
|
C3D
|
N:HEA516
|
4.2
|
13.9
|
1.0
|
C2D
|
N:HEA516
|
4.2
|
12.4
|
1.0
|
C2B
|
N:HEA516
|
4.3
|
11.5
|
1.0
|
ND1
|
N:HIS376
|
4.3
|
7.0
|
1.0
|
C3B
|
N:HEA516
|
4.3
|
16.1
|
1.0
|
C3A
|
N:HEA516
|
4.3
|
7.0
|
1.0
|
C3C
|
N:HEA516
|
4.3
|
14.3
|
1.0
|
CG
|
N:HIS376
|
4.3
|
7.0
|
1.0
|
C2C
|
N:HEA516
|
4.3
|
15.4
|
1.0
|
C2A
|
N:HEA516
|
4.4
|
7.0
|
1.0
|
CU
|
N:CU517
|
4.7
|
15.3
|
1.0
|
CE1
|
N:HIS240
|
4.9
|
27.2
|
1.0
|
|
Reference:
T.Tsukihara,
H.Aoyama,
E.Yamashita,
T.Tomizaki,
H.Yamaguchi,
K.Shinzawa-Itoh,
R.Nakashima,
R.Yaono,
S.Yoshikawa.
The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 A. Science V. 272 1136 1996.
ISSN: ISSN 0036-8075
PubMed: 8638158
Page generated: Sat Aug 3 12:16:11 2024
|