Iron in PDB 1m56: Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
Enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type):
1.9.3.1;
Protein crystallography data
The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56
was solved by
M.Svensson-Ek,
J.Abramson,
G.Larsson,
S.Tornroth,
P.Brezezinski,
S.Iwata,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
2.30
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
340.360,
340.360,
89.668,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.6 /
27.5
|
Other elements in 1m56:
The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
(pdb code 1m56). 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 Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1m56
Go back to
Iron Binding Sites List in 1m56
Iron binding site 1 out
of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:28.6
occ:1.00
|
FE
|
A:HEA1001
|
0.0
|
28.6
|
1.0
|
ND
|
A:HEA1001
|
1.9
|
26.7
|
1.0
|
NA
|
A:HEA1001
|
1.9
|
27.3
|
1.0
|
NC
|
A:HEA1001
|
2.0
|
27.1
|
1.0
|
NB
|
A:HEA1001
|
2.0
|
27.1
|
1.0
|
NE2
|
A:HIS102
|
2.1
|
13.7
|
1.0
|
NE2
|
A:HIS421
|
2.1
|
16.0
|
1.0
|
CD2
|
A:HIS102
|
2.7
|
14.4
|
1.0
|
C4D
|
A:HEA1001
|
2.9
|
26.7
|
1.0
|
C1A
|
A:HEA1001
|
2.9
|
28.6
|
1.0
|
C1D
|
A:HEA1001
|
2.9
|
26.4
|
1.0
|
C4A
|
A:HEA1001
|
3.0
|
28.1
|
1.0
|
C4C
|
A:HEA1001
|
3.0
|
26.4
|
1.0
|
CE1
|
A:HIS421
|
3.0
|
17.6
|
1.0
|
CD2
|
A:HIS421
|
3.1
|
19.0
|
1.0
|
C1B
|
A:HEA1001
|
3.1
|
27.4
|
1.0
|
C4B
|
A:HEA1001
|
3.1
|
27.4
|
1.0
|
C1C
|
A:HEA1001
|
3.1
|
27.0
|
1.0
|
CE1
|
A:HIS102
|
3.2
|
14.8
|
1.0
|
CHA
|
A:HEA1001
|
3.2
|
27.4
|
1.0
|
CHD
|
A:HEA1001
|
3.3
|
26.0
|
1.0
|
CHB
|
A:HEA1001
|
3.4
|
27.8
|
1.0
|
CHC
|
A:HEA1001
|
3.5
|
27.6
|
1.0
|
CG
|
A:HIS102
|
4.0
|
16.4
|
1.0
|
C3D
|
A:HEA1001
|
4.1
|
25.4
|
1.0
|
C2D
|
A:HEA1001
|
4.1
|
24.7
|
1.0
|
C2A
|
A:HEA1001
|
4.1
|
28.7
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
15.4
|
1.0
|
ND1
|
A:HIS421
|
4.2
|
19.6
|
1.0
|
C3A
|
A:HEA1001
|
4.2
|
28.7
|
1.0
|
CG
|
A:HIS421
|
4.3
|
17.4
|
1.0
|
C3C
|
A:HEA1001
|
4.3
|
25.7
|
1.0
|
C2C
|
A:HEA1001
|
4.3
|
26.0
|
1.0
|
C2B
|
A:HEA1001
|
4.4
|
26.8
|
1.0
|
C3B
|
A:HEA1001
|
4.4
|
27.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 1m56
Go back to
Iron Binding Sites List in 1m56
Iron binding site 2 out
of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1002
b:20.6
occ:1.00
|
FE
|
A:HEA1002
|
0.0
|
20.6
|
1.0
|
ND
|
A:HEA1002
|
1.9
|
14.7
|
1.0
|
NA
|
A:HEA1002
|
1.9
|
14.9
|
1.0
|
NC
|
A:HEA1002
|
2.0
|
14.9
|
1.0
|
NB
|
A:HEA1002
|
2.0
|
14.7
|
1.0
|
NE2
|
A:HIS419
|
2.2
|
19.9
|
1.0
|
C4D
|
A:HEA1002
|
2.9
|
14.9
|
1.0
|
C1A
|
A:HEA1002
|
2.9
|
14.9
|
1.0
|
C1D
|
A:HEA1002
|
2.9
|
14.9
|
1.0
|
C4C
|
A:HEA1002
|
3.0
|
15.5
|
1.0
|
C4A
|
A:HEA1002
|
3.0
|
15.8
|
1.0
|
CE1
|
A:HIS419
|
3.0
|
23.5
|
1.0
|
C1B
|
A:HEA1002
|
3.1
|
14.4
|
1.0
|
C1C
|
A:HEA1002
|
3.1
|
14.2
|
1.0
|
C4B
|
A:HEA1002
|
3.1
|
16.0
|
1.0
|
CHA
|
A:HEA1002
|
3.2
|
14.7
|
1.0
|
CD2
|
A:HIS419
|
3.3
|
21.3
|
1.0
|
CHD
|
A:HEA1002
|
3.3
|
14.7
|
1.0
|
CHB
|
A:HEA1002
|
3.4
|
15.2
|
1.0
|
CHC
|
A:HEA1002
|
3.5
|
14.4
|
1.0
|
C3D
|
A:HEA1002
|
4.1
|
14.7
|
1.0
|
C2D
|
A:HEA1002
|
4.2
|
13.7
|
1.0
|
C2A
|
A:HEA1002
|
4.2
|
12.9
|
1.0
|
ND1
|
A:HIS419
|
4.2
|
24.1
|
1.0
|
C3A
|
A:HEA1002
|
4.2
|
14.4
|
1.0
|
C3C
|
A:HEA1002
|
4.3
|
14.9
|
1.0
|
C2C
|
A:HEA1002
|
4.3
|
13.5
|
1.0
|
C2B
|
A:HEA1002
|
4.3
|
15.0
|
1.0
|
C3B
|
A:HEA1002
|
4.3
|
15.1
|
1.0
|
CG
|
A:HIS419
|
4.4
|
20.6
|
1.0
|
CU
|
A:CU1005
|
4.8
|
26.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 1m56
Go back to
Iron Binding Sites List in 1m56
Iron binding site 3 out
of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe1001
b:30.0
occ:1.00
|
FE
|
G:HEA1001
|
0.0
|
30.0
|
1.0
|
ND
|
G:HEA1001
|
1.9
|
26.1
|
1.0
|
NA
|
G:HEA1001
|
1.9
|
27.4
|
1.0
|
NC
|
G:HEA1001
|
2.0
|
27.1
|
1.0
|
NB
|
G:HEA1001
|
2.0
|
27.5
|
1.0
|
NE2
|
G:HIS102
|
2.1
|
13.9
|
1.0
|
NE2
|
G:HIS421
|
2.2
|
16.9
|
1.0
|
CD2
|
G:HIS102
|
2.7
|
14.5
|
1.0
|
C4D
|
G:HEA1001
|
2.9
|
26.6
|
1.0
|
C1D
|
G:HEA1001
|
2.9
|
26.4
|
1.0
|
C1A
|
G:HEA1001
|
2.9
|
28.7
|
1.0
|
C4A
|
G:HEA1001
|
3.0
|
28.4
|
1.0
|
C4C
|
G:HEA1001
|
3.0
|
27.0
|
1.0
|
C1C
|
G:HEA1001
|
3.1
|
27.4
|
1.0
|
C4B
|
G:HEA1001
|
3.1
|
27.5
|
1.0
|
C1B
|
G:HEA1001
|
3.1
|
27.6
|
1.0
|
CE1
|
G:HIS421
|
3.1
|
17.1
|
1.0
|
CD2
|
G:HIS421
|
3.1
|
18.1
|
1.0
|
CE1
|
G:HIS102
|
3.2
|
14.5
|
1.0
|
CHA
|
G:HEA1001
|
3.2
|
27.4
|
1.0
|
CHD
|
G:HEA1001
|
3.3
|
25.8
|
1.0
|
CHC
|
G:HEA1001
|
3.4
|
27.8
|
1.0
|
CHB
|
G:HEA1001
|
3.4
|
27.9
|
1.0
|
CG
|
G:HIS102
|
4.0
|
16.4
|
1.0
|
C3D
|
G:HEA1001
|
4.1
|
25.2
|
1.0
|
C2D
|
G:HEA1001
|
4.2
|
25.0
|
1.0
|
ND1
|
G:HIS102
|
4.2
|
16.0
|
1.0
|
C2A
|
G:HEA1001
|
4.2
|
28.4
|
1.0
|
C3A
|
G:HEA1001
|
4.2
|
29.0
|
1.0
|
ND1
|
G:HIS421
|
4.2
|
18.6
|
1.0
|
CG
|
G:HIS421
|
4.3
|
17.4
|
1.0
|
C2C
|
G:HEA1001
|
4.3
|
26.0
|
1.0
|
C3C
|
G:HEA1001
|
4.3
|
25.8
|
1.0
|
C2B
|
G:HEA1001
|
4.4
|
26.8
|
1.0
|
C3B
|
G:HEA1001
|
4.4
|
26.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1m56
Go back to
Iron Binding Sites List in 1m56
Iron binding site 4 out
of 4 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe1002
b:20.2
occ:1.00
|
FE
|
G:HEA1002
|
0.0
|
20.2
|
1.0
|
ND
|
G:HEA1002
|
1.9
|
14.2
|
1.0
|
NA
|
G:HEA1002
|
1.9
|
15.3
|
1.0
|
NC
|
G:HEA1002
|
2.0
|
14.8
|
1.0
|
NB
|
G:HEA1002
|
2.0
|
14.9
|
1.0
|
NE2
|
G:HIS419
|
2.1
|
21.3
|
1.0
|
C4D
|
G:HEA1002
|
2.9
|
14.7
|
1.0
|
C1D
|
G:HEA1002
|
2.9
|
14.1
|
1.0
|
C1A
|
G:HEA1002
|
3.0
|
14.6
|
1.0
|
C4C
|
G:HEA1002
|
3.0
|
14.8
|
1.0
|
C4A
|
G:HEA1002
|
3.0
|
15.6
|
1.0
|
CE1
|
G:HIS419
|
3.0
|
24.3
|
1.0
|
C1B
|
G:HEA1002
|
3.1
|
14.4
|
1.0
|
C4B
|
G:HEA1002
|
3.1
|
16.4
|
1.0
|
C1C
|
G:HEA1002
|
3.1
|
14.2
|
1.0
|
CD2
|
G:HIS419
|
3.2
|
21.7
|
1.0
|
CHB
|
G:HEA1002
|
3.3
|
14.6
|
1.0
|
CHD
|
G:HEA1002
|
3.3
|
14.5
|
1.0
|
CHA
|
G:HEA1002
|
3.3
|
14.1
|
1.0
|
CHC
|
G:HEA1002
|
3.6
|
13.8
|
1.0
|
C3D
|
G:HEA1002
|
4.1
|
14.6
|
1.0
|
C2D
|
G:HEA1002
|
4.1
|
13.8
|
1.0
|
ND1
|
G:HIS419
|
4.2
|
23.4
|
1.0
|
C3A
|
G:HEA1002
|
4.2
|
13.6
|
1.0
|
C2A
|
G:HEA1002
|
4.2
|
13.0
|
1.0
|
C3C
|
G:HEA1002
|
4.3
|
14.4
|
1.0
|
CG
|
G:HIS419
|
4.3
|
20.6
|
1.0
|
C2C
|
G:HEA1002
|
4.3
|
13.3
|
1.0
|
C2B
|
G:HEA1002
|
4.3
|
15.6
|
1.0
|
C3B
|
G:HEA1002
|
4.3
|
15.1
|
1.0
|
CU
|
G:CU1005
|
4.6
|
28.5
|
1.0
|
|
Reference:
M.Svensson-Ek,
J.Abramson,
G.Larsson,
S.Tornroth,
P.Brzezinski,
S.Iwata.
The X-Ray Crystal Structures of Wild-Type and Eq(I-286) Mutant Cytochrome C Oxidases From Rhodobacter Sphaeroides. J.Mol.Biol. V. 321 329 2002.
ISSN: ISSN 0022-2836
PubMed: 12144789
DOI: 10.1016/S0022-2836(02)00619-8
Page generated: Sat Aug 3 10:02:07 2024
|