Iron in PDB 4o1w: Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Protein crystallography data
The structure of Crystal Structure of Colwellia Psychrerythraea Cytochrome C, PDB code: 4o1w
was solved by
P.B.Harvilla,
H.N.Wolcott,
J.S.Magyar,
L.S.Shapiro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.95 /
2.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.280,
45.043,
87.574,
90.00,
90.85,
90.00
|
R / Rfree (%)
|
17 /
21.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
(pdb code 4o1w). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Colwellia Psychrerythraea Cytochrome C, PDB code: 4o1w:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4o1w
Go back to
Iron Binding Sites List in 4o1w
Iron binding site 1 out
of 6 in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Colwellia Psychrerythraea Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:12.8
occ:1.00
|
FE
|
A:HEM101
|
0.0
|
12.8
|
1.0
|
NE2
|
A:HIS18
|
1.9
|
15.6
|
1.0
|
NB
|
A:HEM101
|
1.9
|
13.2
|
1.0
|
NC
|
A:HEM101
|
2.0
|
16.1
|
1.0
|
NA
|
A:HEM101
|
2.0
|
14.8
|
1.0
|
ND
|
A:HEM101
|
2.1
|
16.5
|
1.0
|
SD
|
A:MET57
|
2.3
|
16.0
|
1.0
|
CE1
|
A:HIS18
|
2.8
|
18.4
|
1.0
|
C4B
|
A:HEM101
|
2.9
|
16.6
|
1.0
|
C1B
|
A:HEM101
|
3.0
|
14.8
|
1.0
|
C4C
|
A:HEM101
|
3.0
|
13.2
|
1.0
|
C4A
|
A:HEM101
|
3.0
|
15.0
|
1.0
|
C1C
|
A:HEM101
|
3.0
|
16.4
|
1.0
|
C1A
|
A:HEM101
|
3.1
|
15.2
|
1.0
|
CD2
|
A:HIS18
|
3.1
|
15.0
|
1.0
|
C1D
|
A:HEM101
|
3.1
|
17.3
|
1.0
|
C4D
|
A:HEM101
|
3.1
|
16.4
|
1.0
|
CHC
|
A:HEM101
|
3.4
|
14.5
|
1.0
|
CHB
|
A:HEM101
|
3.4
|
12.2
|
1.0
|
CHD
|
A:HEM101
|
3.4
|
16.4
|
1.0
|
CG
|
A:MET57
|
3.4
|
12.0
|
1.0
|
CE
|
A:MET57
|
3.4
|
15.6
|
1.0
|
CHA
|
A:HEM101
|
3.5
|
15.9
|
1.0
|
ND1
|
A:HIS18
|
3.9
|
16.9
|
1.0
|
CG
|
A:HIS18
|
4.1
|
16.3
|
1.0
|
C3B
|
A:HEM101
|
4.2
|
14.9
|
1.0
|
C2B
|
A:HEM101
|
4.2
|
15.0
|
1.0
|
C3C
|
A:HEM101
|
4.2
|
14.8
|
1.0
|
C2C
|
A:HEM101
|
4.2
|
18.6
|
1.0
|
C3A
|
A:HEM101
|
4.2
|
14.6
|
1.0
|
C2A
|
A:HEM101
|
4.3
|
13.7
|
1.0
|
C2D
|
A:HEM101
|
4.3
|
12.1
|
1.0
|
C3D
|
A:HEM101
|
4.3
|
15.5
|
1.0
|
CB
|
A:MET57
|
4.9
|
16.2
|
1.0
|
|
Iron binding site 2 out
of 6 in 4o1w
Go back to
Iron Binding Sites List in 4o1w
Iron binding site 2 out
of 6 in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Colwellia Psychrerythraea Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe101
b:14.1
occ:1.00
|
FE
|
B:HEM101
|
0.0
|
14.1
|
1.0
|
NB
|
B:HEM101
|
2.0
|
14.7
|
1.0
|
NE2
|
B:HIS18
|
2.0
|
13.5
|
1.0
|
ND
|
B:HEM101
|
2.0
|
17.8
|
1.0
|
NA
|
B:HEM101
|
2.0
|
15.4
|
1.0
|
NC
|
B:HEM101
|
2.0
|
17.3
|
1.0
|
SD
|
B:MET57
|
2.3
|
17.2
|
1.0
|
CE1
|
B:HIS18
|
2.9
|
12.9
|
1.0
|
C4C
|
B:HEM101
|
3.0
|
16.1
|
1.0
|
C1D
|
B:HEM101
|
3.0
|
15.3
|
1.0
|
C4B
|
B:HEM101
|
3.0
|
18.5
|
1.0
|
C1B
|
B:HEM101
|
3.0
|
16.4
|
1.0
|
C4A
|
B:HEM101
|
3.0
|
14.4
|
1.0
|
C1A
|
B:HEM101
|
3.0
|
16.6
|
1.0
|
C4D
|
B:HEM101
|
3.1
|
16.8
|
1.0
|
CD2
|
B:HIS18
|
3.1
|
15.1
|
1.0
|
C1C
|
B:HEM101
|
3.1
|
13.7
|
1.0
|
CHD
|
B:HEM101
|
3.3
|
17.8
|
1.0
|
CHB
|
B:HEM101
|
3.4
|
14.3
|
1.0
|
CE
|
B:MET57
|
3.4
|
18.5
|
1.0
|
CHA
|
B:HEM101
|
3.4
|
14.1
|
1.0
|
CG
|
B:MET57
|
3.4
|
16.7
|
1.0
|
CHC
|
B:HEM101
|
3.4
|
17.2
|
1.0
|
ND1
|
B:HIS18
|
4.0
|
13.8
|
1.0
|
CG
|
B:HIS18
|
4.2
|
13.8
|
1.0
|
C3B
|
B:HEM101
|
4.2
|
21.5
|
1.0
|
C3C
|
B:HEM101
|
4.2
|
18.4
|
1.0
|
C2B
|
B:HEM101
|
4.2
|
19.5
|
1.0
|
C3A
|
B:HEM101
|
4.2
|
16.4
|
1.0
|
C2A
|
B:HEM101
|
4.3
|
13.7
|
1.0
|
C2D
|
B:HEM101
|
4.3
|
15.5
|
1.0
|
C2C
|
B:HEM101
|
4.3
|
20.7
|
1.0
|
C3D
|
B:HEM101
|
4.3
|
12.4
|
1.0
|
CB
|
B:MET57
|
4.9
|
17.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 4o1w
Go back to
Iron Binding Sites List in 4o1w
Iron binding site 3 out
of 6 in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Colwellia Psychrerythraea Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:18.2
occ:1.00
|
FE
|
C:HEM101
|
0.0
|
18.2
|
1.0
|
NE2
|
C:HIS18
|
1.8
|
13.2
|
1.0
|
NB
|
C:HEM101
|
2.0
|
19.2
|
1.0
|
ND
|
C:HEM101
|
2.1
|
21.0
|
1.0
|
NC
|
C:HEM101
|
2.1
|
18.6
|
1.0
|
NA
|
C:HEM101
|
2.1
|
21.4
|
1.0
|
SD
|
C:MET57
|
2.2
|
19.3
|
1.0
|
CE1
|
C:HIS18
|
2.6
|
20.0
|
1.0
|
C1B
|
C:HEM101
|
3.0
|
19.8
|
1.0
|
C4B
|
C:HEM101
|
3.0
|
22.5
|
1.0
|
CD2
|
C:HIS18
|
3.0
|
20.3
|
1.0
|
C4C
|
C:HEM101
|
3.0
|
20.2
|
1.0
|
C1D
|
C:HEM101
|
3.1
|
19.7
|
1.0
|
C4A
|
C:HEM101
|
3.1
|
15.9
|
1.0
|
C4D
|
C:HEM101
|
3.1
|
18.1
|
1.0
|
C1A
|
C:HEM101
|
3.1
|
20.1
|
1.0
|
C1C
|
C:HEM101
|
3.1
|
25.2
|
1.0
|
CG
|
C:MET57
|
3.3
|
20.6
|
1.0
|
CE
|
C:MET57
|
3.4
|
19.2
|
1.0
|
CHB
|
C:HEM101
|
3.4
|
17.4
|
1.0
|
CHD
|
C:HEM101
|
3.4
|
15.4
|
1.0
|
CHC
|
C:HEM101
|
3.4
|
21.6
|
1.0
|
CHA
|
C:HEM101
|
3.5
|
16.1
|
1.0
|
ND1
|
C:HIS18
|
3.8
|
15.1
|
1.0
|
CG
|
C:HIS18
|
4.0
|
18.8
|
1.0
|
C2B
|
C:HEM101
|
4.2
|
22.9
|
1.0
|
C3B
|
C:HEM101
|
4.2
|
24.7
|
1.0
|
C3C
|
C:HEM101
|
4.3
|
20.2
|
1.0
|
C3A
|
C:HEM101
|
4.3
|
18.6
|
1.0
|
C2D
|
C:HEM101
|
4.3
|
23.4
|
1.0
|
C3D
|
C:HEM101
|
4.3
|
18.8
|
1.0
|
C2A
|
C:HEM101
|
4.3
|
18.4
|
1.0
|
C2C
|
C:HEM101
|
4.4
|
22.1
|
1.0
|
CB
|
C:MET57
|
4.7
|
23.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 4o1w
Go back to
Iron Binding Sites List in 4o1w
Iron binding site 4 out
of 6 in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Colwellia Psychrerythraea Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe101
b:15.4
occ:1.00
|
FE
|
D:HEM101
|
0.0
|
15.4
|
1.0
|
NE2
|
D:HIS18
|
1.9
|
15.1
|
1.0
|
NB
|
D:HEM101
|
2.0
|
15.0
|
1.0
|
NC
|
D:HEM101
|
2.0
|
16.6
|
1.0
|
NA
|
D:HEM101
|
2.0
|
14.6
|
1.0
|
ND
|
D:HEM101
|
2.1
|
17.0
|
1.0
|
SD
|
D:MET57
|
2.3
|
18.1
|
1.0
|
CE1
|
D:HIS18
|
2.9
|
15.0
|
1.0
|
C4B
|
D:HEM101
|
2.9
|
16.8
|
1.0
|
CD2
|
D:HIS18
|
3.0
|
14.7
|
1.0
|
C1A
|
D:HEM101
|
3.0
|
11.4
|
1.0
|
C4C
|
D:HEM101
|
3.0
|
17.3
|
1.0
|
C1C
|
D:HEM101
|
3.0
|
19.0
|
1.0
|
C1D
|
D:HEM101
|
3.0
|
16.0
|
1.0
|
C4A
|
D:HEM101
|
3.1
|
12.3
|
1.0
|
C4D
|
D:HEM101
|
3.1
|
18.5
|
1.0
|
C1B
|
D:HEM101
|
3.1
|
18.1
|
1.0
|
CHC
|
D:HEM101
|
3.3
|
16.2
|
1.0
|
CHD
|
D:HEM101
|
3.4
|
19.3
|
1.0
|
CHA
|
D:HEM101
|
3.4
|
15.4
|
1.0
|
CE
|
D:MET57
|
3.4
|
16.0
|
1.0
|
CG
|
D:MET57
|
3.4
|
16.3
|
1.0
|
CHB
|
D:HEM101
|
3.5
|
15.3
|
1.0
|
ND1
|
D:HIS18
|
4.0
|
14.4
|
1.0
|
CG
|
D:HIS18
|
4.1
|
16.4
|
1.0
|
C3B
|
D:HEM101
|
4.2
|
19.9
|
1.0
|
C2B
|
D:HEM101
|
4.2
|
17.1
|
1.0
|
C3C
|
D:HEM101
|
4.2
|
19.5
|
1.0
|
C2A
|
D:HEM101
|
4.3
|
14.2
|
1.0
|
C2C
|
D:HEM101
|
4.3
|
19.0
|
1.0
|
C3A
|
D:HEM101
|
4.3
|
18.1
|
1.0
|
C2D
|
D:HEM101
|
4.3
|
16.2
|
1.0
|
C3D
|
D:HEM101
|
4.3
|
15.9
|
1.0
|
CB
|
D:MET57
|
4.8
|
19.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 4o1w
Go back to
Iron Binding Sites List in 4o1w
Iron binding site 5 out
of 6 in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Colwellia Psychrerythraea Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe101
b:14.9
occ:1.00
|
FE
|
E:HEM101
|
0.0
|
14.9
|
1.0
|
NB
|
E:HEM101
|
1.9
|
15.2
|
1.0
|
ND
|
E:HEM101
|
1.9
|
12.1
|
1.0
|
NE2
|
E:HIS18
|
2.0
|
14.7
|
1.0
|
NC
|
E:HEM101
|
2.0
|
16.8
|
1.0
|
NA
|
E:HEM101
|
2.1
|
16.1
|
1.0
|
SD
|
E:MET57
|
2.3
|
16.9
|
1.0
|
C4B
|
E:HEM101
|
2.8
|
16.3
|
1.0
|
CE1
|
E:HIS18
|
2.9
|
16.2
|
1.0
|
C4D
|
E:HEM101
|
2.9
|
15.2
|
1.0
|
C1C
|
E:HEM101
|
3.0
|
14.5
|
1.0
|
C1D
|
E:HEM101
|
3.0
|
18.9
|
1.0
|
C1B
|
E:HEM101
|
3.0
|
15.9
|
1.0
|
CD2
|
E:HIS18
|
3.0
|
20.7
|
1.0
|
C1A
|
E:HEM101
|
3.0
|
12.4
|
1.0
|
C4C
|
E:HEM101
|
3.0
|
16.3
|
1.0
|
C4A
|
E:HEM101
|
3.1
|
12.5
|
1.0
|
CHC
|
E:HEM101
|
3.2
|
18.9
|
1.0
|
CE
|
E:MET57
|
3.3
|
15.7
|
1.0
|
CHA
|
E:HEM101
|
3.3
|
12.6
|
1.0
|
CHD
|
E:HEM101
|
3.4
|
14.7
|
1.0
|
CG
|
E:MET57
|
3.5
|
18.3
|
1.0
|
CHB
|
E:HEM101
|
3.5
|
15.0
|
1.0
|
C3B
|
E:HEM101
|
4.0
|
14.8
|
1.0
|
ND1
|
E:HIS18
|
4.1
|
17.0
|
1.0
|
CG
|
E:HIS18
|
4.1
|
18.5
|
1.0
|
C2B
|
E:HEM101
|
4.2
|
13.2
|
1.0
|
C3D
|
E:HEM101
|
4.2
|
14.8
|
1.0
|
C2D
|
E:HEM101
|
4.2
|
14.7
|
1.0
|
C2C
|
E:HEM101
|
4.2
|
20.0
|
1.0
|
C3C
|
E:HEM101
|
4.2
|
15.9
|
1.0
|
C2A
|
E:HEM101
|
4.3
|
13.0
|
1.0
|
C3A
|
E:HEM101
|
4.3
|
15.0
|
1.0
|
CB
|
E:MET57
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 4o1w
Go back to
Iron Binding Sites List in 4o1w
Iron binding site 6 out
of 6 in the Crystal Structure of Colwellia Psychrerythraea Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Colwellia Psychrerythraea Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe101
b:14.5
occ:1.00
|
FE
|
F:HEM101
|
0.0
|
14.5
|
1.0
|
NE2
|
F:HIS18
|
2.0
|
18.3
|
1.0
|
NB
|
F:HEM101
|
2.0
|
15.9
|
1.0
|
NC
|
F:HEM101
|
2.0
|
16.6
|
1.0
|
NA
|
F:HEM101
|
2.1
|
14.1
|
1.0
|
ND
|
F:HEM101
|
2.1
|
16.4
|
1.0
|
SD
|
F:MET57
|
2.3
|
15.3
|
1.0
|
C4B
|
F:HEM101
|
2.9
|
19.5
|
1.0
|
CE1
|
F:HIS18
|
2.9
|
15.4
|
1.0
|
C1C
|
F:HEM101
|
3.0
|
15.4
|
1.0
|
CD2
|
F:HIS18
|
3.0
|
18.8
|
1.0
|
C1A
|
F:HEM101
|
3.0
|
13.9
|
1.0
|
C4D
|
F:HEM101
|
3.0
|
15.4
|
1.0
|
C1B
|
F:HEM101
|
3.1
|
16.0
|
1.0
|
C4C
|
F:HEM101
|
3.1
|
16.0
|
1.0
|
C1D
|
F:HEM101
|
3.1
|
19.4
|
1.0
|
C4A
|
F:HEM101
|
3.1
|
14.4
|
1.0
|
CHC
|
F:HEM101
|
3.3
|
16.4
|
1.0
|
CE
|
F:MET57
|
3.3
|
11.9
|
1.0
|
CHA
|
F:HEM101
|
3.4
|
13.2
|
1.0
|
CG
|
F:MET57
|
3.4
|
15.1
|
1.0
|
CHB
|
F:HEM101
|
3.5
|
13.3
|
1.0
|
CHD
|
F:HEM101
|
3.5
|
15.4
|
1.0
|
ND1
|
F:HIS18
|
4.0
|
17.0
|
1.0
|
CG
|
F:HIS18
|
4.1
|
20.3
|
1.0
|
C3B
|
F:HEM101
|
4.1
|
18.9
|
1.0
|
C2B
|
F:HEM101
|
4.2
|
18.6
|
1.0
|
C2C
|
F:HEM101
|
4.2
|
20.0
|
1.0
|
C3C
|
F:HEM101
|
4.3
|
15.8
|
1.0
|
C2A
|
F:HEM101
|
4.3
|
15.7
|
1.0
|
C3A
|
F:HEM101
|
4.3
|
13.0
|
1.0
|
C3D
|
F:HEM101
|
4.3
|
15.7
|
1.0
|
C2D
|
F:HEM101
|
4.3
|
17.1
|
1.0
|
CB
|
F:MET57
|
4.8
|
17.7
|
1.0
|
|
Reference:
P.B.Harvilla,
H.N.Wolcott,
J.S.Magyar.
The Structure of Ferricytochrome C552 From the Psychrophilic Marine Bacterium Colwellia Psychrerythraea 34H. Metallomics V. 6 1126 2014.
ISSN: ISSN 1756-5901
PubMed: 24727932
DOI: 10.1039/C4MT00045E
Page generated: Mon Aug 5 08:06:56 2024
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