Iron in PDB 1ql3: Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State
Protein crystallography data
The structure of Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State, PDB code: 1ql3
was solved by
A.Harrenga,
B.Reincke,
H.Rueterjans,
B.Ludwig,
H.Michel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.690,
54.320,
140.740,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
24.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State
(pdb code 1ql3). 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 the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State, PDB code: 1ql3:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1ql3
Go back to
Iron Binding Sites List in 1ql3
Iron binding site 1 out
of 4 in the Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:9.2
occ:1.00
|
FE
|
A:HEC101
|
0.0
|
9.2
|
1.0
|
NE2
|
A:HIS18
|
2.0
|
9.1
|
1.0
|
NA
|
A:HEC101
|
2.0
|
7.8
|
1.0
|
ND
|
A:HEC101
|
2.0
|
9.3
|
1.0
|
NC
|
A:HEC101
|
2.0
|
8.2
|
1.0
|
NB
|
A:HEC101
|
2.1
|
9.4
|
1.0
|
SD
|
A:MET78
|
2.2
|
10.1
|
1.0
|
CE1
|
A:HIS18
|
2.9
|
9.1
|
1.0
|
C1A
|
A:HEC101
|
3.0
|
9.0
|
1.0
|
C4D
|
A:HEC101
|
3.0
|
8.3
|
1.0
|
C1D
|
A:HEC101
|
3.0
|
9.8
|
1.0
|
C4A
|
A:HEC101
|
3.0
|
9.2
|
1.0
|
C4C
|
A:HEC101
|
3.0
|
9.6
|
1.0
|
C1B
|
A:HEC101
|
3.1
|
9.3
|
1.0
|
CD2
|
A:HIS18
|
3.1
|
9.7
|
1.0
|
C1C
|
A:HEC101
|
3.1
|
10.1
|
1.0
|
C4B
|
A:HEC101
|
3.1
|
10.1
|
1.0
|
CHA
|
A:HEC101
|
3.4
|
9.4
|
1.0
|
CHD
|
A:HEC101
|
3.4
|
7.5
|
1.0
|
CE
|
A:MET78
|
3.4
|
10.5
|
1.0
|
CHB
|
A:HEC101
|
3.4
|
9.4
|
1.0
|
CG
|
A:MET78
|
3.5
|
9.8
|
1.0
|
CHC
|
A:HEC101
|
3.5
|
10.1
|
1.0
|
ND1
|
A:HIS18
|
4.1
|
8.2
|
1.0
|
CG
|
A:HIS18
|
4.2
|
9.2
|
1.0
|
CB
|
A:MET78
|
4.2
|
9.6
|
1.0
|
C3A
|
A:HEC101
|
4.3
|
8.8
|
1.0
|
C2A
|
A:HEC101
|
4.3
|
9.2
|
1.0
|
C2D
|
A:HEC101
|
4.3
|
9.6
|
1.0
|
C3D
|
A:HEC101
|
4.3
|
9.2
|
1.0
|
C3C
|
A:HEC101
|
4.3
|
10.4
|
1.0
|
C2C
|
A:HEC101
|
4.3
|
10.8
|
1.0
|
C2B
|
A:HEC101
|
4.3
|
9.4
|
1.0
|
C3B
|
A:HEC101
|
4.3
|
9.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 1ql3
Go back to
Iron Binding Sites List in 1ql3
Iron binding site 2 out
of 4 in the Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe101
b:9.1
occ:1.00
|
FE
|
B:HEC101
|
0.0
|
9.1
|
1.0
|
NC
|
B:HEC101
|
2.0
|
9.1
|
1.0
|
ND
|
B:HEC101
|
2.0
|
9.6
|
1.0
|
NA
|
B:HEC101
|
2.0
|
9.2
|
1.0
|
NE2
|
B:HIS18
|
2.0
|
7.3
|
1.0
|
NB
|
B:HEC101
|
2.1
|
8.8
|
1.0
|
SD
|
B:MET78
|
2.2
|
9.3
|
1.0
|
CE1
|
B:HIS18
|
3.0
|
7.1
|
1.0
|
C1D
|
B:HEC101
|
3.0
|
10.0
|
1.0
|
C4C
|
B:HEC101
|
3.0
|
9.3
|
1.0
|
C1A
|
B:HEC101
|
3.1
|
10.2
|
1.0
|
C1C
|
B:HEC101
|
3.1
|
10.0
|
1.0
|
C4A
|
B:HEC101
|
3.1
|
10.6
|
1.0
|
C4D
|
B:HEC101
|
3.1
|
8.8
|
1.0
|
C1B
|
B:HEC101
|
3.1
|
8.8
|
1.0
|
C4B
|
B:HEC101
|
3.1
|
9.5
|
1.0
|
CD2
|
B:HIS18
|
3.1
|
8.2
|
1.0
|
CHD
|
B:HEC101
|
3.4
|
9.5
|
1.0
|
CE
|
B:MET78
|
3.4
|
9.7
|
1.0
|
CHB
|
B:HEC101
|
3.4
|
8.9
|
1.0
|
CHA
|
B:HEC101
|
3.5
|
9.9
|
1.0
|
CHC
|
B:HEC101
|
3.5
|
9.8
|
1.0
|
CG
|
B:MET78
|
3.5
|
8.9
|
1.0
|
ND1
|
B:HIS18
|
4.1
|
7.3
|
1.0
|
CG
|
B:HIS18
|
4.2
|
8.4
|
1.0
|
CB
|
B:MET78
|
4.2
|
9.6
|
1.0
|
C2D
|
B:HEC101
|
4.3
|
9.7
|
1.0
|
C3C
|
B:HEC101
|
4.3
|
10.3
|
1.0
|
C2C
|
B:HEC101
|
4.3
|
9.6
|
1.0
|
C3D
|
B:HEC101
|
4.3
|
9.7
|
1.0
|
C3A
|
B:HEC101
|
4.3
|
10.6
|
1.0
|
C2A
|
B:HEC101
|
4.3
|
11.5
|
1.0
|
C2B
|
B:HEC101
|
4.3
|
9.2
|
1.0
|
C3B
|
B:HEC101
|
4.3
|
9.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 1ql3
Go back to
Iron Binding Sites List in 1ql3
Iron binding site 3 out
of 4 in the Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:16.2
occ:1.00
|
FE
|
C:HEC101
|
0.0
|
16.2
|
1.0
|
NC
|
C:HEC101
|
2.0
|
17.2
|
1.0
|
NE2
|
C:HIS18
|
2.0
|
16.4
|
1.0
|
NA
|
C:HEC101
|
2.0
|
17.3
|
1.0
|
NB
|
C:HEC101
|
2.0
|
16.0
|
1.0
|
ND
|
C:HEC101
|
2.1
|
17.8
|
1.0
|
SD
|
C:MET78
|
2.2
|
16.6
|
1.0
|
CE1
|
C:HIS18
|
3.0
|
15.1
|
1.0
|
C4C
|
C:HEC101
|
3.0
|
19.6
|
1.0
|
C1C
|
C:HEC101
|
3.1
|
17.5
|
1.0
|
C1B
|
C:HEC101
|
3.1
|
16.5
|
1.0
|
C4A
|
C:HEC101
|
3.1
|
17.9
|
1.0
|
C1D
|
C:HEC101
|
3.1
|
19.1
|
1.0
|
CD2
|
C:HIS18
|
3.1
|
15.1
|
1.0
|
C1A
|
C:HEC101
|
3.1
|
18.4
|
1.0
|
C4D
|
C:HEC101
|
3.1
|
18.1
|
1.0
|
C4B
|
C:HEC101
|
3.1
|
16.6
|
1.0
|
CHD
|
C:HEC101
|
3.4
|
19.0
|
1.0
|
CHB
|
C:HEC101
|
3.4
|
17.0
|
1.0
|
CHC
|
C:HEC101
|
3.4
|
15.9
|
1.0
|
CHA
|
C:HEC101
|
3.5
|
17.7
|
1.0
|
CG
|
C:MET78
|
3.5
|
15.8
|
1.0
|
CE
|
C:MET78
|
3.5
|
16.9
|
1.0
|
ND1
|
C:HIS18
|
4.1
|
15.4
|
1.0
|
CG
|
C:HIS18
|
4.2
|
15.4
|
1.0
|
C3C
|
C:HEC101
|
4.3
|
18.1
|
1.0
|
CB
|
C:MET78
|
4.3
|
17.1
|
1.0
|
C2C
|
C:HEC101
|
4.3
|
17.6
|
1.0
|
C3A
|
C:HEC101
|
4.3
|
18.1
|
1.0
|
C3D
|
C:HEC101
|
4.3
|
19.2
|
1.0
|
C2B
|
C:HEC101
|
4.3
|
15.9
|
1.0
|
C2D
|
C:HEC101
|
4.3
|
18.9
|
1.0
|
C2A
|
C:HEC101
|
4.3
|
18.7
|
1.0
|
C3B
|
C:HEC101
|
4.3
|
16.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 1ql3
Go back to
Iron Binding Sites List in 1ql3
Iron binding site 4 out
of 4 in the Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe101
b:17.5
occ:1.00
|
FE
|
D:HEC101
|
0.0
|
17.5
|
1.0
|
NA
|
D:HEC101
|
2.0
|
17.0
|
1.0
|
NE2
|
D:HIS18
|
2.0
|
14.9
|
1.0
|
ND
|
D:HEC101
|
2.0
|
16.5
|
1.0
|
NC
|
D:HEC101
|
2.0
|
15.6
|
1.0
|
NB
|
D:HEC101
|
2.1
|
14.5
|
1.0
|
SD
|
D:MET78
|
2.2
|
16.3
|
1.0
|
CE1
|
D:HIS18
|
3.0
|
15.3
|
1.0
|
C1A
|
D:HEC101
|
3.0
|
15.9
|
1.0
|
C4A
|
D:HEC101
|
3.0
|
16.7
|
1.0
|
C4C
|
D:HEC101
|
3.0
|
16.3
|
1.0
|
C4D
|
D:HEC101
|
3.0
|
17.7
|
1.0
|
C1D
|
D:HEC101
|
3.1
|
16.8
|
1.0
|
CD2
|
D:HIS18
|
3.1
|
15.9
|
1.0
|
C1B
|
D:HEC101
|
3.1
|
14.1
|
1.0
|
C1C
|
D:HEC101
|
3.1
|
14.9
|
1.0
|
C4B
|
D:HEC101
|
3.1
|
14.1
|
1.0
|
CHA
|
D:HEC101
|
3.4
|
17.0
|
1.0
|
CHD
|
D:HEC101
|
3.4
|
16.3
|
1.0
|
CHB
|
D:HEC101
|
3.4
|
15.8
|
1.0
|
CE
|
D:MET78
|
3.4
|
15.8
|
1.0
|
CG
|
D:MET78
|
3.5
|
17.8
|
1.0
|
CHC
|
D:HEC101
|
3.5
|
15.1
|
1.0
|
ND1
|
D:HIS18
|
4.1
|
14.9
|
1.0
|
CG
|
D:HIS18
|
4.2
|
15.6
|
1.0
|
C3A
|
D:HEC101
|
4.2
|
16.2
|
1.0
|
C2A
|
D:HEC101
|
4.3
|
17.1
|
1.0
|
CB
|
D:MET78
|
4.3
|
20.2
|
1.0
|
C3C
|
D:HEC101
|
4.3
|
16.7
|
1.0
|
C3D
|
D:HEC101
|
4.3
|
18.8
|
1.0
|
C2D
|
D:HEC101
|
4.3
|
18.4
|
1.0
|
C2C
|
D:HEC101
|
4.3
|
17.4
|
1.0
|
C2B
|
D:HEC101
|
4.3
|
14.8
|
1.0
|
C3B
|
D:HEC101
|
4.3
|
13.5
|
1.0
|
|
Reference:
A.Harrenga,
B.Reincke,
H.Rueterjans,
B.Ludwig,
H.Michel.
Structure of the Soluble Domain of Cytochrome C552 From Paracoccus Denitrificans in the Oxidized and Reduced States J.Mol.Biol. V. 295 667 2000.
ISSN: ISSN 0022-2836
PubMed: 10623555
DOI: 10.1006/JMBI.1999.3382
Page generated: Sat Aug 3 13:32:09 2024
|