Iron in PDB 1gm4: Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6
Protein crystallography data
The structure of Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6, PDB code: 1gm4
was solved by
I.Bento,
R.Louro,
P.M.Matias,
T.Catarino,
A.M.Baptista,
C.M.Soares,
M.A.Carrondo,
D.L.Turner,
A.V.Xavier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.00 /
2.05
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.490,
61.490,
105.660,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.9 /
24
|
Iron Binding Sites:
The binding sites of Iron atom in the Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6
(pdb code 1gm4). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6, PDB code: 1gm4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1gm4
Go back to
Iron Binding Sites List in 1gm4
Iron binding site 1 out
of 4 in the Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:21.5
occ:1.00
|
FE
|
A:HEC201
|
0.0
|
21.5
|
1.0
|
NB
|
A:HEC201
|
1.9
|
21.9
|
1.0
|
NA
|
A:HEC201
|
2.0
|
22.2
|
1.0
|
ND
|
A:HEC201
|
2.0
|
19.0
|
1.0
|
NE2
|
A:HIS34
|
2.0
|
21.2
|
1.0
|
NE2
|
A:HIS22
|
2.0
|
18.2
|
1.0
|
NC
|
A:HEC201
|
2.0
|
21.1
|
1.0
|
CE1
|
A:HIS22
|
2.9
|
19.1
|
1.0
|
CE1
|
A:HIS34
|
2.9
|
21.9
|
1.0
|
C1B
|
A:HEC201
|
3.0
|
23.2
|
1.0
|
C4A
|
A:HEC201
|
3.0
|
22.2
|
1.0
|
C4B
|
A:HEC201
|
3.0
|
20.6
|
1.0
|
C4D
|
A:HEC201
|
3.0
|
18.9
|
1.0
|
C1A
|
A:HEC201
|
3.0
|
20.8
|
1.0
|
C1D
|
A:HEC201
|
3.0
|
18.3
|
1.0
|
C1C
|
A:HEC201
|
3.1
|
20.1
|
1.0
|
C4C
|
A:HEC201
|
3.1
|
18.8
|
1.0
|
CD2
|
A:HIS34
|
3.1
|
22.9
|
1.0
|
CD2
|
A:HIS22
|
3.1
|
19.7
|
1.0
|
CHB
|
A:HEC201
|
3.4
|
22.1
|
1.0
|
CHA
|
A:HEC201
|
3.4
|
19.9
|
1.0
|
CHC
|
A:HEC201
|
3.4
|
19.6
|
1.0
|
CHD
|
A:HEC201
|
3.4
|
17.3
|
1.0
|
ND1
|
A:HIS22
|
4.1
|
17.9
|
1.0
|
ND1
|
A:HIS34
|
4.1
|
23.3
|
1.0
|
CG
|
A:HIS34
|
4.2
|
20.9
|
1.0
|
C2B
|
A:HEC201
|
4.2
|
22.2
|
1.0
|
C3A
|
A:HEC201
|
4.2
|
21.8
|
1.0
|
CG
|
A:HIS22
|
4.2
|
19.5
|
1.0
|
C3B
|
A:HEC201
|
4.3
|
21.2
|
1.0
|
C2D
|
A:HEC201
|
4.3
|
18.8
|
1.0
|
C3D
|
A:HEC201
|
4.3
|
18.5
|
1.0
|
C2A
|
A:HEC201
|
4.3
|
21.0
|
1.0
|
C2C
|
A:HEC201
|
4.4
|
22.4
|
1.0
|
C3C
|
A:HEC201
|
4.4
|
20.7
|
1.0
|
CE2
|
A:PHE20
|
4.7
|
20.5
|
1.0
|
CD
|
A:PRO5
|
4.8
|
26.1
|
1.0
|
CG2
|
A:VAL4
|
5.0
|
27.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 1gm4
Go back to
Iron Binding Sites List in 1gm4
Iron binding site 2 out
of 4 in the Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:27.0
occ:1.00
|
FE
|
A:HEC202
|
0.0
|
27.0
|
1.0
|
NA
|
A:HEC202
|
1.9
|
26.2
|
1.0
|
NE2
|
A:HIS35
|
1.9
|
23.5
|
1.0
|
NE2
|
A:HIS52
|
1.9
|
25.7
|
1.0
|
ND
|
A:HEC202
|
2.0
|
25.9
|
1.0
|
NC
|
A:HEC202
|
2.0
|
27.4
|
1.0
|
NB
|
A:HEC202
|
2.1
|
26.3
|
1.0
|
CE1
|
A:HIS35
|
2.8
|
21.3
|
1.0
|
CE1
|
A:HIS52
|
2.8
|
24.8
|
1.0
|
C4A
|
A:HEC202
|
3.0
|
27.1
|
1.0
|
C1A
|
A:HEC202
|
3.0
|
25.5
|
1.0
|
C4D
|
A:HEC202
|
3.0
|
26.0
|
1.0
|
C1D
|
A:HEC202
|
3.0
|
25.4
|
1.0
|
C1B
|
A:HEC202
|
3.0
|
25.8
|
1.0
|
C4C
|
A:HEC202
|
3.1
|
25.6
|
1.0
|
CD2
|
A:HIS35
|
3.1
|
21.2
|
1.0
|
C1C
|
A:HEC202
|
3.1
|
26.1
|
1.0
|
CD2
|
A:HIS52
|
3.1
|
23.9
|
1.0
|
C4B
|
A:HEC202
|
3.2
|
24.2
|
1.0
|
CHA
|
A:HEC202
|
3.3
|
24.5
|
1.0
|
CHB
|
A:HEC202
|
3.4
|
26.8
|
1.0
|
CHD
|
A:HEC202
|
3.4
|
24.3
|
1.0
|
CHC
|
A:HEC202
|
3.5
|
25.0
|
1.0
|
ND1
|
A:HIS35
|
4.0
|
20.4
|
1.0
|
ND1
|
A:HIS52
|
4.0
|
25.9
|
1.0
|
CG
|
A:HIS35
|
4.1
|
21.7
|
1.0
|
CG
|
A:HIS52
|
4.2
|
25.8
|
1.0
|
C2A
|
A:HEC202
|
4.2
|
25.0
|
1.0
|
C3A
|
A:HEC202
|
4.2
|
26.1
|
1.0
|
C3D
|
A:HEC202
|
4.3
|
25.0
|
1.0
|
C2D
|
A:HEC202
|
4.3
|
25.6
|
1.0
|
C2B
|
A:HEC202
|
4.3
|
24.3
|
1.0
|
C3C
|
A:HEC202
|
4.3
|
26.6
|
1.0
|
C2C
|
A:HEC202
|
4.3
|
24.8
|
1.0
|
C3B
|
A:HEC202
|
4.4
|
21.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 1gm4
Go back to
Iron Binding Sites List in 1gm4
Iron binding site 3 out
of 4 in the Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:17.8
occ:1.00
|
FE
|
A:HEC203
|
0.0
|
17.8
|
1.0
|
ND
|
A:HEC203
|
1.9
|
17.7
|
1.0
|
NE2
|
A:HIS83
|
2.0
|
17.3
|
1.0
|
NA
|
A:HEC203
|
2.0
|
18.4
|
1.0
|
NE2
|
A:HIS25
|
2.0
|
17.9
|
1.0
|
NC
|
A:HEC203
|
2.0
|
18.4
|
1.0
|
NB
|
A:HEC203
|
2.0
|
16.8
|
1.0
|
CE1
|
A:HIS83
|
2.9
|
14.5
|
1.0
|
CE1
|
A:HIS25
|
3.0
|
18.0
|
1.0
|
C4D
|
A:HEC203
|
3.0
|
17.6
|
1.0
|
C1D
|
A:HEC203
|
3.0
|
17.5
|
1.0
|
C1A
|
A:HEC203
|
3.0
|
16.7
|
1.0
|
CD2
|
A:HIS83
|
3.0
|
16.1
|
1.0
|
C4A
|
A:HEC203
|
3.1
|
17.8
|
1.0
|
CD2
|
A:HIS25
|
3.1
|
15.9
|
1.0
|
C1C
|
A:HEC203
|
3.1
|
18.6
|
1.0
|
C4B
|
A:HEC203
|
3.1
|
16.8
|
1.0
|
C4C
|
A:HEC203
|
3.1
|
16.7
|
1.0
|
C1B
|
A:HEC203
|
3.1
|
17.1
|
1.0
|
CHA
|
A:HEC203
|
3.4
|
16.9
|
1.0
|
CHC
|
A:HEC203
|
3.4
|
19.6
|
1.0
|
CHD
|
A:HEC203
|
3.4
|
16.1
|
1.0
|
CHB
|
A:HEC203
|
3.5
|
15.7
|
1.0
|
ND1
|
A:HIS83
|
4.1
|
16.2
|
1.0
|
ND1
|
A:HIS25
|
4.1
|
16.7
|
1.0
|
CG
|
A:HIS83
|
4.2
|
18.8
|
1.0
|
CG
|
A:HIS25
|
4.2
|
17.1
|
1.0
|
C3D
|
A:HEC203
|
4.2
|
18.1
|
1.0
|
C2D
|
A:HEC203
|
4.2
|
18.3
|
1.0
|
C2A
|
A:HEC203
|
4.2
|
17.7
|
1.0
|
C3A
|
A:HEC203
|
4.3
|
17.1
|
1.0
|
C2C
|
A:HEC203
|
4.3
|
18.0
|
1.0
|
C3B
|
A:HEC203
|
4.3
|
17.6
|
1.0
|
C2B
|
A:HEC203
|
4.3
|
14.8
|
1.0
|
C3C
|
A:HEC203
|
4.3
|
16.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1gm4
Go back to
Iron Binding Sites List in 1gm4
Iron binding site 4 out
of 4 in the Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Oxidised Structure of Cytochrome C3 From Desulfovibrio Desulfuricans Atcc 27774 at pH 7.6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe204
b:22.0
occ:1.00
|
FE
|
A:HEC204
|
0.0
|
22.0
|
1.0
|
NA
|
A:HEC204
|
1.9
|
22.9
|
1.0
|
ND
|
A:HEC204
|
2.0
|
18.9
|
1.0
|
NE2
|
A:HIS69
|
2.0
|
18.7
|
1.0
|
NB
|
A:HEC204
|
2.0
|
21.9
|
1.0
|
NE2
|
A:HIS106
|
2.0
|
18.7
|
1.0
|
NC
|
A:HEC204
|
2.0
|
19.4
|
1.0
|
CE1
|
A:HIS106
|
2.9
|
18.8
|
1.0
|
C1A
|
A:HEC204
|
3.0
|
24.9
|
1.0
|
CE1
|
A:HIS69
|
3.0
|
17.4
|
1.0
|
C4D
|
A:HEC204
|
3.0
|
22.2
|
1.0
|
C4A
|
A:HEC204
|
3.0
|
23.7
|
1.0
|
C1B
|
A:HEC204
|
3.0
|
23.8
|
1.0
|
CD2
|
A:HIS69
|
3.0
|
17.9
|
1.0
|
C1D
|
A:HEC204
|
3.0
|
21.2
|
1.0
|
C1C
|
A:HEC204
|
3.1
|
22.5
|
1.0
|
C4C
|
A:HEC204
|
3.1
|
20.0
|
1.0
|
C4B
|
A:HEC204
|
3.1
|
22.8
|
1.0
|
CD2
|
A:HIS106
|
3.1
|
19.1
|
1.0
|
CHA
|
A:HEC204
|
3.3
|
22.8
|
1.0
|
CHB
|
A:HEC204
|
3.4
|
25.1
|
1.0
|
CHD
|
A:HEC204
|
3.4
|
19.0
|
1.0
|
CHC
|
A:HEC204
|
3.5
|
22.2
|
1.0
|
ND1
|
A:HIS106
|
4.1
|
18.9
|
1.0
|
ND1
|
A:HIS69
|
4.1
|
17.2
|
1.0
|
CG
|
A:HIS69
|
4.2
|
18.2
|
1.0
|
C2A
|
A:HEC204
|
4.2
|
25.1
|
1.0
|
CG
|
A:HIS106
|
4.2
|
18.1
|
1.0
|
C2D
|
A:HEC204
|
4.2
|
19.8
|
1.0
|
C3A
|
A:HEC204
|
4.2
|
25.3
|
1.0
|
C3D
|
A:HEC204
|
4.2
|
21.7
|
1.0
|
C2B
|
A:HEC204
|
4.3
|
22.6
|
1.0
|
C2C
|
A:HEC204
|
4.3
|
22.5
|
1.0
|
C3B
|
A:HEC204
|
4.3
|
23.4
|
1.0
|
C3C
|
A:HEC204
|
4.3
|
21.0
|
1.0
|
|
Reference:
R.O.Louro,
I.Bento,
P.M.Matias,
T.Catarino,
A.M.Baptista,
C.M.Soares,
M.A.Carrondo,
D.L.Turner,
A.V.Xavier.
Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in A Monomeric Tetraheme Cytochrome. J.Biol.Chem. V. 276 44044 2001.
ISSN: ISSN 0021-9258
PubMed: 11551953
DOI: 10.1074/JBC.M107136200
Page generated: Sat Aug 3 06:12:16 2024
|