Iron in PDB 1qjd: Flavocytochrome C3 From Shewanella Frigidimarina
Protein crystallography data
The structure of Flavocytochrome C3 From Shewanella Frigidimarina, PDB code: 1qjd
was solved by
P.Taylor,
S.L.Pealing,
G.A.Reid,
S.K.Chapman,
M.D.Walkinshaw,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.00 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.393,
91.946,
78.288,
90.00,
91.09,
90.00
|
R / Rfree (%)
|
19.2 /
26.7
|
Other elements in 1qjd:
The structure of Flavocytochrome C3 From Shewanella Frigidimarina also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Flavocytochrome C3 From Shewanella Frigidimarina
(pdb code 1qjd). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Flavocytochrome C3 From Shewanella Frigidimarina, PDB code: 1qjd:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1qjd
Go back to
Iron Binding Sites List in 1qjd
Iron binding site 1 out
of 4 in the Flavocytochrome C3 From Shewanella Frigidimarina
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Flavocytochrome C3 From Shewanella Frigidimarina within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1569
b:15.0
occ:1.00
|
FE
|
A:HEC1569
|
0.0
|
15.0
|
1.0
|
ND
|
A:HEC1569
|
1.9
|
9.7
|
1.0
|
NA
|
A:HEC1569
|
1.9
|
17.2
|
1.0
|
NC
|
A:HEC1569
|
2.0
|
18.8
|
1.0
|
NE2
|
A:HIS18
|
2.0
|
17.9
|
1.0
|
NE2
|
A:HIS75
|
2.0
|
18.6
|
1.0
|
NB
|
A:HEC1569
|
2.1
|
17.3
|
1.0
|
CE1
|
A:HIS18
|
2.8
|
16.2
|
1.0
|
C1A
|
A:HEC1569
|
2.9
|
19.8
|
1.0
|
C1D
|
A:HEC1569
|
2.9
|
19.9
|
1.0
|
C4D
|
A:HEC1569
|
3.0
|
10.2
|
1.0
|
CD2
|
A:HIS75
|
3.0
|
13.5
|
1.0
|
C4C
|
A:HEC1569
|
3.0
|
16.4
|
1.0
|
C4A
|
A:HEC1569
|
3.0
|
19.8
|
1.0
|
C1B
|
A:HEC1569
|
3.1
|
18.3
|
1.0
|
C1C
|
A:HEC1569
|
3.1
|
23.1
|
1.0
|
CE1
|
A:HIS75
|
3.1
|
16.1
|
1.0
|
C4B
|
A:HEC1569
|
3.1
|
17.3
|
1.0
|
CD2
|
A:HIS18
|
3.2
|
15.5
|
1.0
|
CHD
|
A:HEC1569
|
3.3
|
15.7
|
1.0
|
CHA
|
A:HEC1569
|
3.3
|
22.6
|
1.0
|
CHB
|
A:HEC1569
|
3.4
|
19.3
|
1.0
|
CHC
|
A:HEC1569
|
3.5
|
17.5
|
1.0
|
ND1
|
A:HIS18
|
4.0
|
12.7
|
1.0
|
CG
|
A:HIS75
|
4.1
|
15.6
|
1.0
|
ND1
|
A:HIS75
|
4.2
|
13.3
|
1.0
|
C2D
|
A:HEC1569
|
4.2
|
23.3
|
1.0
|
C2A
|
A:HEC1569
|
4.2
|
13.8
|
1.0
|
C3D
|
A:HEC1569
|
4.2
|
18.9
|
1.0
|
CG
|
A:HIS18
|
4.2
|
13.0
|
1.0
|
C3A
|
A:HEC1569
|
4.2
|
21.0
|
1.0
|
C3C
|
A:HEC1569
|
4.3
|
21.0
|
1.0
|
C2C
|
A:HEC1569
|
4.3
|
16.9
|
1.0
|
C2B
|
A:HEC1569
|
4.3
|
16.3
|
1.0
|
C3B
|
A:HEC1569
|
4.4
|
21.1
|
1.0
|
O
|
A:HOH2025
|
4.8
|
24.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 1qjd
Go back to
Iron Binding Sites List in 1qjd
Iron binding site 2 out
of 4 in the Flavocytochrome C3 From Shewanella Frigidimarina
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Flavocytochrome C3 From Shewanella Frigidimarina within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1570
b:18.1
occ:1.00
|
FE
|
A:HEC1570
|
0.0
|
18.1
|
1.0
|
NC
|
A:HEC1570
|
1.9
|
11.8
|
1.0
|
ND
|
A:HEC1570
|
1.9
|
13.0
|
1.0
|
NA
|
A:HEC1570
|
2.0
|
12.2
|
1.0
|
NE2
|
A:HIS40
|
2.0
|
20.3
|
1.0
|
NB
|
A:HEC1570
|
2.0
|
12.5
|
1.0
|
NE2
|
A:HIS8
|
2.0
|
16.9
|
1.0
|
CE1
|
A:HIS40
|
2.8
|
10.2
|
1.0
|
C4C
|
A:HEC1570
|
2.9
|
23.2
|
1.0
|
C1C
|
A:HEC1570
|
2.9
|
18.9
|
1.0
|
C1D
|
A:HEC1570
|
2.9
|
14.5
|
1.0
|
CE1
|
A:HIS8
|
3.0
|
18.2
|
1.0
|
C4D
|
A:HEC1570
|
3.0
|
17.5
|
1.0
|
C4B
|
A:HEC1570
|
3.0
|
18.5
|
1.0
|
C1A
|
A:HEC1570
|
3.0
|
15.4
|
1.0
|
C4A
|
A:HEC1570
|
3.0
|
19.3
|
1.0
|
CD2
|
A:HIS8
|
3.1
|
20.9
|
1.0
|
C1B
|
A:HEC1570
|
3.1
|
13.5
|
1.0
|
CD2
|
A:HIS40
|
3.1
|
15.0
|
1.0
|
CHD
|
A:HEC1570
|
3.3
|
18.5
|
1.0
|
CHC
|
A:HEC1570
|
3.3
|
19.6
|
1.0
|
CHA
|
A:HEC1570
|
3.4
|
13.4
|
1.0
|
CHB
|
A:HEC1570
|
3.5
|
15.3
|
1.0
|
ND1
|
A:HIS40
|
4.0
|
18.7
|
1.0
|
ND1
|
A:HIS8
|
4.1
|
18.4
|
1.0
|
C2C
|
A:HEC1570
|
4.2
|
27.5
|
1.0
|
C3C
|
A:HEC1570
|
4.2
|
26.8
|
1.0
|
CG
|
A:HIS40
|
4.2
|
14.5
|
1.0
|
CG
|
A:HIS8
|
4.2
|
18.4
|
1.0
|
C2D
|
A:HEC1570
|
4.2
|
23.7
|
1.0
|
C3D
|
A:HEC1570
|
4.2
|
26.6
|
1.0
|
C2A
|
A:HEC1570
|
4.3
|
16.8
|
1.0
|
C3A
|
A:HEC1570
|
4.3
|
19.3
|
1.0
|
C3B
|
A:HEC1570
|
4.3
|
11.9
|
1.0
|
C2B
|
A:HEC1570
|
4.3
|
10.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 1qjd
Go back to
Iron Binding Sites List in 1qjd
Iron binding site 3 out
of 4 in the Flavocytochrome C3 From Shewanella Frigidimarina
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Flavocytochrome C3 From Shewanella Frigidimarina within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1571
b:15.4
occ:1.00
|
FE
|
A:HEC1571
|
0.0
|
15.4
|
1.0
|
ND
|
A:HEC1571
|
1.9
|
13.6
|
1.0
|
NC
|
A:HEC1571
|
2.0
|
11.3
|
1.0
|
NA
|
A:HEC1571
|
2.0
|
18.3
|
1.0
|
NB
|
A:HEC1571
|
2.0
|
12.3
|
1.0
|
NE2
|
A:HIS72
|
2.1
|
11.2
|
1.0
|
NE2
|
A:HIS58
|
2.1
|
13.5
|
1.0
|
CD2
|
A:HIS72
|
3.0
|
11.1
|
1.0
|
C4D
|
A:HEC1571
|
3.0
|
16.5
|
1.0
|
C1D
|
A:HEC1571
|
3.0
|
19.2
|
1.0
|
C4C
|
A:HEC1571
|
3.0
|
11.1
|
1.0
|
CD2
|
A:HIS58
|
3.0
|
14.9
|
1.0
|
C1B
|
A:HEC1571
|
3.0
|
15.3
|
1.0
|
C1C
|
A:HEC1571
|
3.0
|
8.3
|
1.0
|
C4B
|
A:HEC1571
|
3.0
|
16.3
|
1.0
|
C1A
|
A:HEC1571
|
3.0
|
19.8
|
1.0
|
C4A
|
A:HEC1571
|
3.0
|
15.7
|
1.0
|
CE1
|
A:HIS58
|
3.1
|
20.1
|
1.0
|
CE1
|
A:HIS72
|
3.1
|
14.2
|
1.0
|
CHD
|
A:HEC1571
|
3.4
|
12.8
|
1.0
|
CHB
|
A:HEC1571
|
3.4
|
10.1
|
1.0
|
CHA
|
A:HEC1571
|
3.4
|
15.0
|
1.0
|
CHC
|
A:HEC1571
|
3.4
|
11.2
|
1.0
|
CG
|
A:HIS72
|
4.1
|
10.9
|
1.0
|
ND1
|
A:HIS72
|
4.2
|
14.1
|
1.0
|
ND1
|
A:HIS58
|
4.2
|
10.9
|
1.0
|
CG
|
A:HIS58
|
4.2
|
9.8
|
1.0
|
C2D
|
A:HEC1571
|
4.2
|
12.3
|
1.0
|
C3D
|
A:HEC1571
|
4.2
|
15.3
|
1.0
|
C2C
|
A:HEC1571
|
4.2
|
9.4
|
1.0
|
C3C
|
A:HEC1571
|
4.3
|
8.4
|
1.0
|
C2B
|
A:HEC1571
|
4.3
|
12.0
|
1.0
|
C3B
|
A:HEC1571
|
4.3
|
13.2
|
1.0
|
C3A
|
A:HEC1571
|
4.3
|
19.0
|
1.0
|
C2A
|
A:HEC1571
|
4.3
|
19.4
|
1.0
|
CG1
|
A:VAL46
|
4.9
|
15.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1qjd
Go back to
Iron Binding Sites List in 1qjd
Iron binding site 4 out
of 4 in the Flavocytochrome C3 From Shewanella Frigidimarina
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Flavocytochrome C3 From Shewanella Frigidimarina within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1572
b:12.0
occ:1.00
|
FE
|
A:HEC1572
|
0.0
|
12.0
|
1.0
|
ND
|
A:HEC1572
|
1.9
|
9.6
|
1.0
|
NC
|
A:HEC1572
|
2.0
|
10.6
|
1.0
|
NE2
|
A:HIS61
|
2.0
|
16.4
|
1.0
|
NB
|
A:HEC1572
|
2.0
|
11.0
|
1.0
|
NA
|
A:HEC1572
|
2.0
|
9.6
|
1.0
|
NE2
|
A:HIS86
|
2.1
|
16.8
|
1.0
|
C4D
|
A:HEC1572
|
2.9
|
12.4
|
1.0
|
C1D
|
A:HEC1572
|
3.0
|
8.8
|
1.0
|
CE1
|
A:HIS61
|
3.0
|
8.7
|
1.0
|
C4C
|
A:HEC1572
|
3.0
|
13.9
|
1.0
|
C1A
|
A:HEC1572
|
3.0
|
16.8
|
1.0
|
C1C
|
A:HEC1572
|
3.0
|
14.7
|
1.0
|
CD2
|
A:HIS61
|
3.0
|
9.9
|
1.0
|
C4B
|
A:HEC1572
|
3.0
|
10.6
|
1.0
|
CE1
|
A:HIS86
|
3.0
|
17.0
|
1.0
|
C1B
|
A:HEC1572
|
3.1
|
10.7
|
1.0
|
C4A
|
A:HEC1572
|
3.1
|
14.6
|
1.0
|
CD2
|
A:HIS86
|
3.1
|
12.7
|
1.0
|
CHA
|
A:HEC1572
|
3.3
|
17.0
|
1.0
|
CHD
|
A:HEC1572
|
3.4
|
12.0
|
1.0
|
CHC
|
A:HEC1572
|
3.4
|
19.9
|
1.0
|
CHB
|
A:HEC1572
|
3.5
|
12.7
|
1.0
|
ND1
|
A:HIS61
|
4.1
|
13.4
|
1.0
|
CG
|
A:HIS61
|
4.2
|
14.6
|
1.0
|
ND1
|
A:HIS86
|
4.2
|
16.7
|
1.0
|
C3D
|
A:HEC1572
|
4.2
|
10.5
|
1.0
|
C2D
|
A:HEC1572
|
4.2
|
9.2
|
1.0
|
CG
|
A:HIS86
|
4.2
|
12.7
|
1.0
|
C2C
|
A:HEC1572
|
4.2
|
12.6
|
1.0
|
C3C
|
A:HEC1572
|
4.2
|
11.9
|
1.0
|
C2A
|
A:HEC1572
|
4.3
|
11.9
|
1.0
|
C3B
|
A:HEC1572
|
4.3
|
8.3
|
1.0
|
C3A
|
A:HEC1572
|
4.3
|
15.1
|
1.0
|
C2B
|
A:HEC1572
|
4.3
|
13.7
|
1.0
|
|
Reference:
P.Taylor,
S.L.Pealing,
G.A.Reid,
S.K.Chapman,
M.D.Walkinshaw.
Structural and Mechanistic Mapping of A Unique Fumarate Reductase Nat.Struct.Biol. V. 6 1108 1999.
ISSN: ISSN 1072-8368
PubMed: 10581550
DOI: 10.1038/70045
Page generated: Sat Aug 3 13:29:02 2024
|