Iron in PDB 2zbo: Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
Protein crystallography data
The structure of Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution, PDB code: 2zbo
was solved by
H.Akazaki,
F.Kawai,
H.Chida,
Y.Matsumoto,
I.Sirasaki,
H.Nakade,
M.Hirayama,
K.Hosikawa,
K.Suruga,
T.Satoh,
S.Yamada,
S.Unzai,
W.Hakamata,
T.Nishio,
S.-Y.Park,
T.Oku,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.60
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.578,
84.578,
232.911,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
20.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
(pdb code 2zbo). 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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution, PDB code: 2zbo:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2zbo
Go back to
Iron Binding Sites List in 2zbo
Iron binding site 1 out
of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe111
b:12.8
occ:1.00
|
FE
|
A:HEM111
|
0.0
|
12.8
|
1.0
|
NE2
|
A:HIS42
|
1.9
|
10.3
|
1.0
|
NB
|
A:HEM111
|
2.0
|
10.5
|
1.0
|
NA
|
A:HEM111
|
2.0
|
12.3
|
1.0
|
NC
|
A:HEM111
|
2.0
|
12.4
|
1.0
|
ND
|
A:HEM111
|
2.0
|
12.4
|
1.0
|
SD
|
A:MET82
|
2.3
|
13.0
|
1.0
|
CD2
|
A:HIS42
|
2.9
|
11.4
|
1.0
|
CE1
|
A:HIS42
|
3.0
|
12.5
|
1.0
|
C1B
|
A:HEM111
|
3.0
|
11.7
|
1.0
|
C4A
|
A:HEM111
|
3.0
|
13.5
|
1.0
|
C1C
|
A:HEM111
|
3.0
|
11.8
|
1.0
|
C4D
|
A:HEM111
|
3.0
|
12.0
|
1.0
|
C1A
|
A:HEM111
|
3.1
|
11.0
|
1.0
|
C4B
|
A:HEM111
|
3.1
|
10.7
|
1.0
|
C4C
|
A:HEM111
|
3.1
|
12.9
|
1.0
|
C1D
|
A:HEM111
|
3.1
|
13.0
|
1.0
|
CHB
|
A:HEM111
|
3.4
|
13.2
|
1.0
|
CHA
|
A:HEM111
|
3.4
|
12.9
|
1.0
|
CHD
|
A:HEM111
|
3.4
|
12.7
|
1.0
|
CHC
|
A:HEM111
|
3.4
|
12.0
|
1.0
|
CG
|
A:MET82
|
3.4
|
12.2
|
1.0
|
CE
|
A:MET82
|
3.5
|
12.5
|
1.0
|
ND1
|
A:HIS42
|
4.1
|
11.8
|
1.0
|
CG
|
A:HIS42
|
4.1
|
11.5
|
1.0
|
CB
|
A:MET82
|
4.2
|
13.7
|
1.0
|
C2B
|
A:HEM111
|
4.3
|
11.2
|
1.0
|
C3A
|
A:HEM111
|
4.3
|
12.4
|
1.0
|
C2C
|
A:HEM111
|
4.3
|
13.9
|
1.0
|
C3C
|
A:HEM111
|
4.3
|
14.7
|
1.0
|
C3B
|
A:HEM111
|
4.3
|
11.4
|
1.0
|
C3D
|
A:HEM111
|
4.3
|
13.4
|
1.0
|
C2A
|
A:HEM111
|
4.3
|
12.9
|
1.0
|
C2D
|
A:HEM111
|
4.3
|
12.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 2zbo
Go back to
Iron Binding Sites List in 2zbo
Iron binding site 2 out
of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe111
b:12.1
occ:1.00
|
FE
|
C:HEM111
|
0.0
|
12.1
|
1.0
|
NE2
|
C:HIS42
|
2.0
|
12.4
|
1.0
|
NA
|
C:HEM111
|
2.0
|
11.3
|
1.0
|
NB
|
C:HEM111
|
2.0
|
12.8
|
1.0
|
NC
|
C:HEM111
|
2.0
|
11.5
|
1.0
|
ND
|
C:HEM111
|
2.1
|
12.3
|
1.0
|
SD
|
C:MET82
|
2.3
|
13.2
|
1.0
|
CD2
|
C:HIS42
|
3.0
|
12.0
|
1.0
|
CE1
|
C:HIS42
|
3.0
|
12.9
|
1.0
|
C4A
|
C:HEM111
|
3.0
|
12.4
|
1.0
|
C1C
|
C:HEM111
|
3.0
|
12.9
|
1.0
|
C1A
|
C:HEM111
|
3.0
|
11.5
|
1.0
|
C1B
|
C:HEM111
|
3.1
|
11.4
|
1.0
|
C4C
|
C:HEM111
|
3.1
|
12.9
|
1.0
|
C4B
|
C:HEM111
|
3.1
|
11.2
|
1.0
|
C4D
|
C:HEM111
|
3.1
|
11.8
|
1.0
|
C1D
|
C:HEM111
|
3.1
|
11.9
|
1.0
|
CG
|
C:MET82
|
3.4
|
14.3
|
1.0
|
CHA
|
C:HEM111
|
3.4
|
12.2
|
1.0
|
CHC
|
C:HEM111
|
3.4
|
12.6
|
1.0
|
CHB
|
C:HEM111
|
3.4
|
11.8
|
1.0
|
CE
|
C:MET82
|
3.4
|
13.3
|
1.0
|
CHD
|
C:HEM111
|
3.5
|
13.6
|
1.0
|
ND1
|
C:HIS42
|
4.1
|
13.4
|
1.0
|
CG
|
C:HIS42
|
4.1
|
12.9
|
1.0
|
CB
|
C:MET82
|
4.1
|
14.7
|
1.0
|
C2C
|
C:HEM111
|
4.3
|
13.8
|
1.0
|
C3A
|
C:HEM111
|
4.3
|
12.4
|
1.0
|
C2A
|
C:HEM111
|
4.3
|
13.4
|
1.0
|
C2B
|
C:HEM111
|
4.3
|
12.3
|
1.0
|
C3C
|
C:HEM111
|
4.3
|
14.4
|
1.0
|
C3B
|
C:HEM111
|
4.3
|
13.1
|
1.0
|
C3D
|
C:HEM111
|
4.3
|
12.5
|
1.0
|
C2D
|
C:HEM111
|
4.3
|
13.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 2zbo
Go back to
Iron Binding Sites List in 2zbo
Iron binding site 3 out
of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe111
b:15.6
occ:1.00
|
FE
|
E:HEM111
|
0.0
|
15.6
|
1.0
|
NE2
|
E:HIS42
|
1.9
|
15.7
|
1.0
|
NA
|
E:HEM111
|
2.0
|
16.1
|
1.0
|
ND
|
E:HEM111
|
2.0
|
14.8
|
1.0
|
NC
|
E:HEM111
|
2.0
|
15.6
|
1.0
|
NB
|
E:HEM111
|
2.1
|
14.7
|
1.0
|
SD
|
E:MET82
|
2.3
|
16.0
|
1.0
|
CE1
|
E:HIS42
|
2.9
|
13.9
|
1.0
|
CD2
|
E:HIS42
|
2.9
|
13.8
|
1.0
|
C1A
|
E:HEM111
|
3.0
|
16.9
|
1.0
|
C1D
|
E:HEM111
|
3.0
|
16.4
|
1.0
|
C4D
|
E:HEM111
|
3.1
|
16.6
|
1.0
|
C1C
|
E:HEM111
|
3.1
|
15.0
|
1.0
|
C4C
|
E:HEM111
|
3.1
|
16.2
|
1.0
|
C4A
|
E:HEM111
|
3.1
|
17.6
|
1.0
|
C1B
|
E:HEM111
|
3.1
|
16.8
|
1.0
|
C4B
|
E:HEM111
|
3.1
|
16.2
|
1.0
|
CG
|
E:MET82
|
3.4
|
14.8
|
1.0
|
CHA
|
E:HEM111
|
3.4
|
17.6
|
1.0
|
CHD
|
E:HEM111
|
3.4
|
16.3
|
1.0
|
CHB
|
E:HEM111
|
3.5
|
16.9
|
1.0
|
CHC
|
E:HEM111
|
3.5
|
16.1
|
1.0
|
CE
|
E:MET82
|
3.5
|
16.2
|
1.0
|
ND1
|
E:HIS42
|
4.0
|
15.4
|
1.0
|
CG
|
E:HIS42
|
4.1
|
14.7
|
1.0
|
CB
|
E:MET82
|
4.1
|
16.3
|
1.0
|
C2A
|
E:HEM111
|
4.3
|
17.9
|
1.0
|
C2D
|
E:HEM111
|
4.3
|
17.0
|
1.0
|
C2C
|
E:HEM111
|
4.3
|
16.6
|
1.0
|
C3A
|
E:HEM111
|
4.3
|
17.1
|
1.0
|
C3D
|
E:HEM111
|
4.3
|
17.9
|
1.0
|
C3C
|
E:HEM111
|
4.3
|
16.3
|
1.0
|
C2B
|
E:HEM111
|
4.3
|
16.8
|
1.0
|
C3B
|
E:HEM111
|
4.3
|
15.5
|
1.0
|
|
Iron binding site 4 out
of 6 in 2zbo
Go back to
Iron Binding Sites List in 2zbo
Iron binding site 4 out
of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe111
b:15.4
occ:1.00
|
FE
|
G:HEM111
|
0.0
|
15.4
|
1.0
|
NE2
|
G:HIS42
|
1.9
|
13.6
|
1.0
|
NA
|
G:HEM111
|
2.0
|
15.1
|
1.0
|
NB
|
G:HEM111
|
2.0
|
15.0
|
1.0
|
NC
|
G:HEM111
|
2.0
|
14.7
|
1.0
|
ND
|
G:HEM111
|
2.1
|
15.5
|
1.0
|
SD
|
G:MET82
|
2.3
|
16.7
|
1.0
|
CE1
|
G:HIS42
|
2.9
|
15.9
|
1.0
|
CD2
|
G:HIS42
|
2.9
|
14.3
|
1.0
|
C1A
|
G:HEM111
|
3.0
|
16.1
|
1.0
|
C4A
|
G:HEM111
|
3.0
|
15.4
|
1.0
|
C1C
|
G:HEM111
|
3.0
|
14.1
|
1.0
|
C1B
|
G:HEM111
|
3.0
|
14.2
|
1.0
|
C4C
|
G:HEM111
|
3.1
|
15.3
|
1.0
|
C4B
|
G:HEM111
|
3.1
|
14.0
|
1.0
|
C4D
|
G:HEM111
|
3.1
|
14.3
|
1.0
|
C1D
|
G:HEM111
|
3.1
|
14.1
|
1.0
|
CHA
|
G:HEM111
|
3.4
|
16.4
|
1.0
|
CHB
|
G:HEM111
|
3.4
|
15.8
|
1.0
|
CHC
|
G:HEM111
|
3.4
|
15.0
|
1.0
|
CHD
|
G:HEM111
|
3.4
|
15.0
|
1.0
|
CE
|
G:MET82
|
3.5
|
17.2
|
1.0
|
CG
|
G:MET82
|
3.5
|
16.4
|
1.0
|
ND1
|
G:HIS42
|
4.0
|
15.5
|
1.0
|
CG
|
G:HIS42
|
4.1
|
15.2
|
1.0
|
CB
|
G:MET82
|
4.2
|
16.5
|
1.0
|
C2A
|
G:HEM111
|
4.2
|
16.8
|
1.0
|
C3A
|
G:HEM111
|
4.3
|
16.9
|
1.0
|
C2C
|
G:HEM111
|
4.3
|
14.8
|
1.0
|
C2B
|
G:HEM111
|
4.3
|
15.1
|
1.0
|
C3B
|
G:HEM111
|
4.3
|
14.7
|
1.0
|
C3C
|
G:HEM111
|
4.3
|
15.2
|
1.0
|
C2D
|
G:HEM111
|
4.3
|
15.8
|
1.0
|
C3D
|
G:HEM111
|
4.3
|
15.0
|
1.0
|
|
Iron binding site 5 out
of 6 in 2zbo
Go back to
Iron Binding Sites List in 2zbo
Iron binding site 5 out
of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe111
b:14.7
occ:1.00
|
FE
|
I:HEM111
|
0.0
|
14.7
|
1.0
|
NE2
|
I:HIS42
|
1.9
|
13.1
|
1.0
|
NB
|
I:HEM111
|
2.0
|
14.4
|
1.0
|
NA
|
I:HEM111
|
2.0
|
13.3
|
1.0
|
NC
|
I:HEM111
|
2.0
|
13.7
|
1.0
|
ND
|
I:HEM111
|
2.1
|
14.6
|
1.0
|
SD
|
I:MET82
|
2.3
|
16.0
|
1.0
|
CD2
|
I:HIS42
|
2.9
|
13.6
|
1.0
|
CE1
|
I:HIS42
|
3.0
|
14.4
|
1.0
|
C1C
|
I:HEM111
|
3.0
|
13.9
|
1.0
|
C1A
|
I:HEM111
|
3.0
|
13.5
|
1.0
|
C4A
|
I:HEM111
|
3.0
|
14.0
|
1.0
|
C4D
|
I:HEM111
|
3.1
|
13.1
|
1.0
|
C1B
|
I:HEM111
|
3.1
|
13.4
|
1.0
|
C4B
|
I:HEM111
|
3.1
|
13.4
|
1.0
|
C4C
|
I:HEM111
|
3.1
|
12.9
|
1.0
|
C1D
|
I:HEM111
|
3.1
|
12.9
|
1.0
|
CHC
|
I:HEM111
|
3.4
|
13.6
|
1.0
|
CG
|
I:MET82
|
3.4
|
16.1
|
1.0
|
CHA
|
I:HEM111
|
3.4
|
13.8
|
1.0
|
CHB
|
I:HEM111
|
3.4
|
14.4
|
1.0
|
CE
|
I:MET82
|
3.4
|
16.6
|
1.0
|
CHD
|
I:HEM111
|
3.5
|
14.3
|
1.0
|
ND1
|
I:HIS42
|
4.1
|
14.9
|
1.0
|
CG
|
I:HIS42
|
4.1
|
15.0
|
1.0
|
CB
|
I:MET82
|
4.1
|
16.2
|
1.0
|
C2C
|
I:HEM111
|
4.2
|
14.9
|
1.0
|
C3A
|
I:HEM111
|
4.3
|
13.9
|
1.0
|
C2A
|
I:HEM111
|
4.3
|
13.9
|
1.0
|
C3C
|
I:HEM111
|
4.3
|
14.4
|
1.0
|
C2B
|
I:HEM111
|
4.3
|
15.2
|
1.0
|
C3B
|
I:HEM111
|
4.3
|
15.2
|
1.0
|
C3D
|
I:HEM111
|
4.3
|
13.7
|
1.0
|
C2D
|
I:HEM111
|
4.3
|
13.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 2zbo
Go back to
Iron Binding Sites List in 2zbo
Iron binding site 6 out
of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution
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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe111
b:12.1
occ:1.00
|
FE
|
K:HEM111
|
0.0
|
12.1
|
1.0
|
NE2
|
K:HIS42
|
1.9
|
11.8
|
1.0
|
NB
|
K:HEM111
|
2.0
|
12.3
|
1.0
|
NA
|
K:HEM111
|
2.0
|
11.9
|
1.0
|
ND
|
K:HEM111
|
2.0
|
12.0
|
1.0
|
NC
|
K:HEM111
|
2.0
|
12.1
|
1.0
|
SD
|
K:MET82
|
2.3
|
15.6
|
1.0
|
CE1
|
K:HIS42
|
2.9
|
11.3
|
1.0
|
CD2
|
K:HIS42
|
3.0
|
12.0
|
1.0
|
C4A
|
K:HEM111
|
3.0
|
12.7
|
1.0
|
C1B
|
K:HEM111
|
3.0
|
12.1
|
1.0
|
C1A
|
K:HEM111
|
3.0
|
12.3
|
1.0
|
C1C
|
K:HEM111
|
3.0
|
13.3
|
1.0
|
C1D
|
K:HEM111
|
3.0
|
12.0
|
1.0
|
C4D
|
K:HEM111
|
3.0
|
11.6
|
1.0
|
C4B
|
K:HEM111
|
3.1
|
13.0
|
1.0
|
C4C
|
K:HEM111
|
3.1
|
12.9
|
1.0
|
CHB
|
K:HEM111
|
3.4
|
12.6
|
1.0
|
CE
|
K:MET82
|
3.4
|
15.2
|
1.0
|
CHC
|
K:HEM111
|
3.4
|
13.9
|
1.0
|
CHA
|
K:HEM111
|
3.4
|
12.5
|
1.0
|
CHD
|
K:HEM111
|
3.4
|
12.4
|
1.0
|
CG
|
K:MET82
|
3.4
|
15.1
|
1.0
|
ND1
|
K:HIS42
|
4.0
|
12.8
|
1.0
|
CG
|
K:HIS42
|
4.1
|
12.7
|
1.0
|
CB
|
K:MET82
|
4.1
|
14.5
|
1.0
|
C3A
|
K:HEM111
|
4.2
|
13.1
|
1.0
|
C2A
|
K:HEM111
|
4.2
|
13.4
|
1.0
|
C2B
|
K:HEM111
|
4.3
|
12.2
|
1.0
|
C2D
|
K:HEM111
|
4.3
|
11.9
|
1.0
|
C2C
|
K:HEM111
|
4.3
|
13.4
|
1.0
|
C3D
|
K:HEM111
|
4.3
|
13.3
|
1.0
|
C3C
|
K:HEM111
|
4.3
|
13.1
|
1.0
|
C3B
|
K:HEM111
|
4.3
|
12.5
|
1.0
|
|
Reference:
H.Akazaki,
F.Kawai,
H.Chida,
Y.Matsumoto,
M.Hirayama,
K.Hoshikawa,
S.Unzai,
W.Hakamata,
T.Nishio,
S.-Y.Park,
T.Oku.
Cloning, Expression and Purification of Cytochrome C(6) From the Brown Alga Hizikia Fusiformis and Complete X-Ray Diffraction Analysis of the Structure Acta Crystallogr.,Sect.F V. 64 674 2008.
ISSN: ESSN 1744-3091
PubMed: 18678931
DOI: 10.1107/S1744309108017752
Page generated: Sun Aug 4 05:57:06 2024
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