Iron in PDB 5b3i: Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus
Protein crystallography data
The structure of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus, PDB code: 5b3i
was solved by
S.Fujii,
H.Oki,
K.Kawahara,
D.Yamane,
M.Yamanaka,
T.Maruno,
Y.Kobayashi,
M.Masanari,
S.Wakai,
H.Nishihara,
T.Ohkubo,
Y.Sambongi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.95 /
1.89
|
Space group
|
P 21 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.243,
72.923,
132.365,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
24.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus
(pdb code 5b3i). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus, PDB code: 5b3i:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5b3i
Go back to
Iron Binding Sites List in 5b3i
Iron binding site 1 out
of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:15.0
occ:1.00
|
FE
|
A:HEC201
|
0.0
|
15.0
|
1.0
|
ND
|
A:HEC201
|
1.9
|
14.8
|
1.0
|
NA
|
A:HEC201
|
2.0
|
15.1
|
1.0
|
NC
|
A:HEC201
|
2.1
|
15.3
|
1.0
|
NB
|
A:HEC201
|
2.1
|
14.9
|
1.0
|
NE2
|
A:HIS128
|
2.2
|
15.5
|
1.0
|
C1D
|
A:HEC201
|
2.9
|
14.8
|
1.0
|
CD1
|
A:TYR16
|
2.9
|
15.3
|
1.0
|
C4D
|
A:HEC201
|
3.0
|
15.2
|
1.0
|
C1A
|
A:HEC201
|
3.0
|
14.9
|
1.0
|
C4C
|
A:HEC201
|
3.0
|
15.2
|
1.0
|
C4B
|
A:HEC201
|
3.1
|
15.5
|
1.0
|
C4A
|
A:HEC201
|
3.1
|
14.8
|
1.0
|
C1C
|
A:HEC201
|
3.1
|
14.9
|
1.0
|
CD2
|
A:HIS128
|
3.1
|
15.2
|
1.0
|
C1B
|
A:HEC201
|
3.1
|
15.1
|
1.0
|
CE1
|
A:HIS128
|
3.2
|
15.5
|
1.0
|
CE1
|
A:TYR16
|
3.3
|
15.5
|
1.0
|
CHD
|
A:HEC201
|
3.3
|
14.9
|
1.0
|
CG
|
A:TYR16
|
3.4
|
14.6
|
1.0
|
CHA
|
A:HEC201
|
3.4
|
15.1
|
1.0
|
CHC
|
A:HEC201
|
3.5
|
14.9
|
1.0
|
CHB
|
A:HEC201
|
3.6
|
14.8
|
1.0
|
CB
|
A:TYR16
|
3.9
|
14.2
|
1.0
|
CZ
|
A:TYR16
|
4.1
|
15.3
|
1.0
|
C2D
|
A:HEC201
|
4.2
|
15.1
|
1.0
|
CD2
|
A:TYR16
|
4.2
|
14.7
|
1.0
|
C3D
|
A:HEC201
|
4.2
|
15.2
|
1.0
|
C2A
|
A:HEC201
|
4.2
|
14.8
|
1.0
|
C3A
|
A:HEC201
|
4.2
|
14.8
|
1.0
|
C3C
|
A:HEC201
|
4.3
|
15.2
|
1.0
|
C2C
|
A:HEC201
|
4.3
|
15.7
|
1.0
|
CG
|
A:HIS128
|
4.3
|
16.5
|
1.0
|
ND1
|
A:HIS128
|
4.3
|
16.7
|
1.0
|
C3B
|
A:HEC201
|
4.3
|
15.2
|
1.0
|
C2B
|
A:HEC201
|
4.4
|
14.8
|
1.0
|
CE2
|
A:TYR16
|
4.5
|
15.3
|
1.0
|
NH1
|
A:ARG132
|
4.6
|
17.2
|
1.0
|
CD
|
A:ARG132
|
4.9
|
16.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 5b3i
Go back to
Iron Binding Sites List in 5b3i
Iron binding site 2 out
of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:16.1
occ:1.00
|
FE
|
B:HEC201
|
0.0
|
16.1
|
1.0
|
ND
|
B:HEC201
|
1.9
|
15.9
|
1.0
|
NA
|
B:HEC201
|
2.0
|
16.0
|
1.0
|
NC
|
B:HEC201
|
2.1
|
15.8
|
1.0
|
NB
|
B:HEC201
|
2.1
|
15.8
|
1.0
|
NE2
|
B:HIS128
|
2.2
|
16.7
|
1.0
|
CD1
|
B:TYR16
|
2.8
|
16.3
|
1.0
|
C1D
|
B:HEC201
|
2.9
|
15.9
|
1.0
|
C4D
|
B:HEC201
|
3.0
|
16.3
|
1.0
|
C1A
|
B:HEC201
|
3.0
|
16.1
|
1.0
|
C4B
|
B:HEC201
|
3.0
|
15.6
|
1.0
|
C4C
|
B:HEC201
|
3.0
|
15.6
|
1.0
|
C4A
|
B:HEC201
|
3.1
|
15.7
|
1.0
|
CE1
|
B:HIS128
|
3.1
|
16.5
|
1.0
|
C1B
|
B:HEC201
|
3.1
|
15.8
|
1.0
|
C1C
|
B:HEC201
|
3.1
|
15.8
|
1.0
|
CE1
|
B:TYR16
|
3.2
|
16.0
|
1.0
|
CD2
|
B:HIS128
|
3.2
|
16.6
|
1.0
|
CHD
|
B:HEC201
|
3.4
|
15.3
|
1.0
|
CHA
|
B:HEC201
|
3.4
|
15.8
|
1.0
|
CHC
|
B:HEC201
|
3.4
|
15.5
|
1.0
|
CG
|
B:TYR16
|
3.5
|
15.9
|
1.0
|
CHB
|
B:HEC201
|
3.5
|
15.9
|
1.0
|
CZ
|
B:TYR16
|
4.0
|
15.4
|
1.0
|
CB
|
B:TYR16
|
4.1
|
14.9
|
1.0
|
C2D
|
B:HEC201
|
4.2
|
15.7
|
1.0
|
C3D
|
B:HEC201
|
4.2
|
16.2
|
1.0
|
CD2
|
B:TYR16
|
4.2
|
15.5
|
1.0
|
ND1
|
B:HIS128
|
4.2
|
17.6
|
1.0
|
C2A
|
B:HEC201
|
4.2
|
16.0
|
1.0
|
C3A
|
B:HEC201
|
4.3
|
16.1
|
1.0
|
C3C
|
B:HEC201
|
4.3
|
15.2
|
1.0
|
C2C
|
B:HEC201
|
4.3
|
15.6
|
1.0
|
C2B
|
B:HEC201
|
4.3
|
15.9
|
1.0
|
CG
|
B:HIS128
|
4.3
|
17.7
|
1.0
|
C3B
|
B:HEC201
|
4.3
|
15.7
|
1.0
|
CE2
|
B:TYR16
|
4.5
|
15.2
|
1.0
|
NH1
|
B:ARG132
|
4.5
|
16.6
|
1.0
|
OH
|
B:TYR16
|
4.8
|
15.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 5b3i
Go back to
Iron Binding Sites List in 5b3i
Iron binding site 3 out
of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:16.2
occ:1.00
|
FE
|
C:HEC201
|
0.0
|
16.2
|
1.0
|
ND
|
C:HEC201
|
1.9
|
15.7
|
1.0
|
NA
|
C:HEC201
|
2.0
|
16.5
|
1.0
|
NC
|
C:HEC201
|
2.1
|
16.1
|
1.0
|
NB
|
C:HEC201
|
2.1
|
16.0
|
1.0
|
NE2
|
C:HIS128
|
2.2
|
17.0
|
1.0
|
C1D
|
C:HEC201
|
2.9
|
16.0
|
1.0
|
CD1
|
C:TYR16
|
3.0
|
16.0
|
1.0
|
C4D
|
C:HEC201
|
3.0
|
16.2
|
1.0
|
C4B
|
C:HEC201
|
3.0
|
15.8
|
1.0
|
C1A
|
C:HEC201
|
3.0
|
16.0
|
1.0
|
C4C
|
C:HEC201
|
3.0
|
16.7
|
1.0
|
C1C
|
C:HEC201
|
3.1
|
15.9
|
1.0
|
C4A
|
C:HEC201
|
3.1
|
16.3
|
1.0
|
C1B
|
C:HEC201
|
3.1
|
15.7
|
1.0
|
CD2
|
C:HIS128
|
3.1
|
17.0
|
1.0
|
CE1
|
C:HIS128
|
3.2
|
17.7
|
1.0
|
CE1
|
C:TYR16
|
3.3
|
15.8
|
1.0
|
CG
|
C:TYR16
|
3.3
|
15.3
|
1.0
|
CHD
|
C:HEC201
|
3.4
|
16.0
|
1.0
|
CHC
|
C:HEC201
|
3.4
|
15.2
|
1.0
|
CHA
|
C:HEC201
|
3.5
|
15.9
|
1.0
|
CHB
|
C:HEC201
|
3.5
|
15.7
|
1.0
|
CB
|
C:TYR16
|
3.9
|
15.0
|
1.0
|
CD2
|
C:TYR16
|
4.0
|
15.0
|
1.0
|
CZ
|
C:TYR16
|
4.0
|
15.7
|
1.0
|
C2D
|
C:HEC201
|
4.2
|
15.9
|
1.0
|
C3D
|
C:HEC201
|
4.2
|
15.8
|
1.0
|
C2A
|
C:HEC201
|
4.3
|
16.0
|
1.0
|
C2C
|
C:HEC201
|
4.3
|
16.1
|
1.0
|
C3C
|
C:HEC201
|
4.3
|
16.6
|
1.0
|
ND1
|
C:HIS128
|
4.3
|
17.7
|
1.0
|
C3B
|
C:HEC201
|
4.3
|
15.7
|
1.0
|
C3A
|
C:HEC201
|
4.3
|
15.9
|
1.0
|
C2B
|
C:HEC201
|
4.3
|
15.2
|
1.0
|
CG
|
C:HIS128
|
4.3
|
18.4
|
1.0
|
CE2
|
C:TYR16
|
4.3
|
15.2
|
1.0
|
NH1
|
C:ARG132
|
4.5
|
18.3
|
1.0
|
OH
|
C:TYR16
|
4.9
|
16.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 5b3i
Go back to
Iron Binding Sites List in 5b3i
Iron binding site 4 out
of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:15.4
occ:1.00
|
FE
|
D:HEC201
|
0.0
|
15.4
|
1.0
|
ND
|
D:HEC201
|
1.9
|
15.5
|
1.0
|
NA
|
D:HEC201
|
2.0
|
15.3
|
1.0
|
NC
|
D:HEC201
|
2.1
|
15.6
|
1.0
|
NB
|
D:HEC201
|
2.1
|
15.2
|
1.0
|
NE2
|
D:HIS128
|
2.2
|
16.5
|
1.0
|
CD1
|
D:TYR16
|
2.8
|
15.5
|
1.0
|
C1D
|
D:HEC201
|
2.9
|
14.9
|
1.0
|
C4D
|
D:HEC201
|
3.0
|
15.1
|
1.0
|
C1A
|
D:HEC201
|
3.0
|
15.4
|
1.0
|
C4B
|
D:HEC201
|
3.0
|
15.4
|
1.0
|
C4C
|
D:HEC201
|
3.0
|
16.2
|
1.0
|
C4A
|
D:HEC201
|
3.1
|
15.6
|
1.0
|
C1C
|
D:HEC201
|
3.1
|
15.7
|
1.0
|
C1B
|
D:HEC201
|
3.1
|
15.1
|
1.0
|
CD2
|
D:HIS128
|
3.1
|
16.6
|
1.0
|
CE1
|
D:HIS128
|
3.2
|
16.9
|
1.0
|
CE1
|
D:TYR16
|
3.2
|
16.1
|
1.0
|
CG
|
D:TYR16
|
3.3
|
14.9
|
1.0
|
CHD
|
D:HEC201
|
3.3
|
15.4
|
1.0
|
CHA
|
D:HEC201
|
3.4
|
15.8
|
1.0
|
CHC
|
D:HEC201
|
3.4
|
15.6
|
1.0
|
CHB
|
D:HEC201
|
3.5
|
15.2
|
1.0
|
CB
|
D:TYR16
|
3.8
|
14.7
|
1.0
|
CZ
|
D:TYR16
|
4.0
|
15.4
|
1.0
|
CD2
|
D:TYR16
|
4.0
|
15.4
|
1.0
|
C2D
|
D:HEC201
|
4.2
|
15.8
|
1.0
|
C3D
|
D:HEC201
|
4.2
|
15.7
|
1.0
|
C2A
|
D:HEC201
|
4.2
|
15.9
|
1.0
|
C3A
|
D:HEC201
|
4.3
|
15.5
|
1.0
|
ND1
|
D:HIS128
|
4.3
|
17.2
|
1.0
|
C2C
|
D:HEC201
|
4.3
|
15.8
|
1.0
|
C3C
|
D:HEC201
|
4.3
|
15.4
|
1.0
|
CG
|
D:HIS128
|
4.3
|
17.5
|
1.0
|
C2B
|
D:HEC201
|
4.3
|
15.2
|
1.0
|
C3B
|
D:HEC201
|
4.3
|
15.6
|
1.0
|
CE2
|
D:TYR16
|
4.3
|
15.1
|
1.0
|
NH1
|
D:ARG132
|
4.5
|
18.7
|
1.0
|
OH
|
D:TYR16
|
4.9
|
15.1
|
1.0
|
|
Reference:
S.Fujii,
H.Oki,
K.Kawahara,
D.Yamane,
M.Yamanaka,
T.Maruno,
Y.Kobayashi,
M.Masanari,
S.Wakai,
H.Nishihara,
T.Ohkubo,
Y.Sambongi.
Structural and Functional Insights Into Thermally Stable Cytochrome C' From A Thermophile Protein Sci. V. 26 737 2017.
ISSN: ESSN 1469-896X
PubMed: 28097774
DOI: 10.1002/PRO.3120
Page generated: Mon Aug 5 19:59:55 2024
|