Iron in PDB 3rde: Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
Enzymatic activity of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
All present enzymatic activity of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase:
1.13.11.31;
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase, PDB code: 3rde
was solved by
M.O.Funk,
S.Xu,
L.J.Marnett,
T.C.Mueser,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.97 /
1.89
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.450,
181.540,
91.610,
90.00,
92.86,
90.00
|
R / Rfree (%)
|
17.2 /
21.4
|
Other elements in 3rde:
The structure of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
(pdb code 3rde). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase, PDB code: 3rde:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3rde
Go back to
Iron Binding Sites List in 3rde
Iron binding site 1 out
of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
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 the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1
b:8.9
occ:1.00
|
NE2
|
A:HIS541
|
2.1
|
8.2
|
1.0
|
NE2
|
A:HIS366
|
2.2
|
9.0
|
1.0
|
O
|
A:HOH5
|
2.2
|
9.5
|
1.0
|
ND1
|
A:HIS545
|
2.3
|
9.7
|
1.0
|
NE2
|
A:HIS361
|
2.3
|
5.2
|
1.0
|
OXT
|
A:ILE663
|
2.3
|
8.6
|
1.0
|
CE1
|
A:HIS361
|
3.0
|
8.7
|
1.0
|
CE1
|
A:HIS545
|
3.1
|
11.3
|
1.0
|
CE1
|
A:HIS541
|
3.1
|
8.1
|
1.0
|
CE1
|
A:HIS366
|
3.1
|
10.4
|
1.0
|
CD2
|
A:HIS541
|
3.1
|
8.1
|
1.0
|
C
|
A:ILE663
|
3.2
|
9.2
|
1.0
|
CD2
|
A:HIS366
|
3.2
|
9.5
|
1.0
|
CG
|
A:HIS545
|
3.4
|
7.9
|
1.0
|
CD2
|
A:HIS361
|
3.4
|
10.2
|
1.0
|
O
|
A:ILE663
|
3.5
|
11.4
|
1.0
|
CB
|
A:HIS545
|
3.8
|
6.6
|
1.0
|
ND1
|
A:HIS541
|
4.2
|
8.5
|
1.0
|
NE2
|
A:HIS545
|
4.2
|
13.1
|
1.0
|
ND1
|
A:HIS361
|
4.2
|
6.7
|
1.0
|
ND1
|
A:HIS366
|
4.3
|
8.6
|
1.0
|
CG
|
A:HIS541
|
4.3
|
8.7
|
1.0
|
CG
|
A:HIS366
|
4.3
|
10.7
|
1.0
|
C13
|
A:OYP664
|
4.4
|
9.8
|
1.0
|
CD2
|
A:HIS545
|
4.4
|
11.5
|
1.0
|
CG
|
A:HIS361
|
4.4
|
8.0
|
1.0
|
CA
|
A:ILE663
|
4.6
|
7.6
|
1.0
|
C14
|
A:OYP664
|
4.6
|
8.7
|
1.0
|
C12
|
A:OYP664
|
4.6
|
12.4
|
1.0
|
CG1
|
A:VAL661
|
4.8
|
4.5
|
1.0
|
N
|
A:ILE663
|
4.9
|
9.6
|
1.0
|
CA
|
A:HIS545
|
4.9
|
9.5
|
1.0
|
CG2
|
A:ILE663
|
4.9
|
10.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 3rde
Go back to
Iron Binding Sites List in 3rde
Iron binding site 2 out
of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
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 the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe2
b:9.3
occ:1.00
|
NE2
|
B:HIS361
|
2.2
|
6.8
|
1.0
|
NE2
|
B:HIS541
|
2.2
|
7.1
|
1.0
|
NE2
|
B:HIS366
|
2.2
|
10.8
|
1.0
|
O
|
B:HOH6
|
2.2
|
12.7
|
1.0
|
ND1
|
B:HIS545
|
2.3
|
9.5
|
1.0
|
OXT
|
B:ILE663
|
2.3
|
9.4
|
1.0
|
CE1
|
B:HIS361
|
3.0
|
8.7
|
1.0
|
CE1
|
B:HIS545
|
3.1
|
10.9
|
1.0
|
CE1
|
B:HIS541
|
3.2
|
9.5
|
1.0
|
CD2
|
B:HIS541
|
3.2
|
8.8
|
1.0
|
CD2
|
B:HIS366
|
3.2
|
9.7
|
1.0
|
CE1
|
B:HIS366
|
3.2
|
10.4
|
1.0
|
C
|
B:ILE663
|
3.2
|
10.7
|
1.0
|
CD2
|
B:HIS361
|
3.3
|
6.1
|
1.0
|
CG
|
B:HIS545
|
3.4
|
9.6
|
1.0
|
O
|
B:ILE663
|
3.5
|
9.2
|
1.0
|
CB
|
B:HIS545
|
3.9
|
9.4
|
1.0
|
ND1
|
B:HIS361
|
4.2
|
7.1
|
1.0
|
NE2
|
B:HIS545
|
4.3
|
12.1
|
1.0
|
ND1
|
B:HIS541
|
4.3
|
9.5
|
1.0
|
ND1
|
B:HIS366
|
4.3
|
8.6
|
1.0
|
CG
|
B:HIS541
|
4.3
|
10.9
|
1.0
|
CG
|
B:HIS366
|
4.3
|
9.8
|
1.0
|
CG
|
B:HIS361
|
4.3
|
5.9
|
1.0
|
C13
|
B:OYP664
|
4.4
|
12.3
|
1.0
|
CD2
|
B:HIS545
|
4.4
|
14.0
|
1.0
|
C14
|
B:OYP664
|
4.6
|
13.1
|
1.0
|
C12
|
B:OYP664
|
4.6
|
15.1
|
1.0
|
CA
|
B:ILE663
|
4.7
|
11.6
|
1.0
|
CG1
|
B:VAL661
|
4.9
|
12.2
|
1.0
|
CA
|
B:HIS545
|
4.9
|
9.2
|
1.0
|
N
|
B:ILE663
|
5.0
|
11.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 3rde
Go back to
Iron Binding Sites List in 3rde
Iron binding site 3 out
of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
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 the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe3
b:17.3
occ:1.00
|
NE2
|
C:HIS361
|
2.1
|
7.5
|
1.0
|
NE2
|
C:HIS541
|
2.2
|
15.8
|
1.0
|
OXT
|
C:ILE663
|
2.3
|
17.7
|
1.0
|
NE2
|
C:HIS366
|
2.3
|
15.7
|
1.0
|
O
|
C:HOH7
|
2.3
|
18.2
|
1.0
|
ND1
|
C:HIS545
|
2.3
|
19.8
|
1.0
|
CE1
|
C:HIS361
|
3.0
|
17.6
|
1.0
|
CE1
|
C:HIS545
|
3.1
|
22.7
|
1.0
|
CD2
|
C:HIS541
|
3.1
|
18.9
|
1.0
|
CD2
|
C:HIS361
|
3.1
|
20.1
|
1.0
|
CE1
|
C:HIS366
|
3.2
|
17.7
|
1.0
|
C
|
C:ILE663
|
3.2
|
18.3
|
1.0
|
CE1
|
C:HIS541
|
3.3
|
18.2
|
1.0
|
CD2
|
C:HIS366
|
3.3
|
14.5
|
1.0
|
O
|
C:ILE663
|
3.4
|
18.8
|
1.0
|
CG
|
C:HIS545
|
3.4
|
17.7
|
1.0
|
CB
|
C:HIS545
|
3.9
|
19.6
|
1.0
|
ND1
|
C:HIS361
|
4.1
|
13.6
|
1.0
|
CG
|
C:HIS361
|
4.2
|
16.0
|
1.0
|
NE2
|
C:HIS545
|
4.3
|
22.0
|
1.0
|
CG
|
C:HIS541
|
4.3
|
17.2
|
1.0
|
ND1
|
C:HIS366
|
4.3
|
18.4
|
1.0
|
ND1
|
C:HIS541
|
4.4
|
16.1
|
1.0
|
CG
|
C:HIS366
|
4.4
|
16.5
|
1.0
|
C13
|
C:OYP664
|
4.4
|
16.0
|
1.0
|
CD2
|
C:HIS545
|
4.5
|
19.0
|
1.0
|
CA
|
C:ILE663
|
4.6
|
17.7
|
1.0
|
C14
|
C:OYP664
|
4.6
|
15.8
|
1.0
|
C12
|
C:OYP664
|
4.7
|
16.6
|
1.0
|
CG2
|
C:ILE663
|
4.7
|
19.2
|
1.0
|
CG1
|
C:VAL661
|
4.8
|
18.1
|
1.0
|
CA
|
C:HIS545
|
4.9
|
18.8
|
1.0
|
N
|
C:ILE663
|
4.9
|
16.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 3rde
Go back to
Iron Binding Sites List in 3rde
Iron binding site 4 out
of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase
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 the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe4
b:12.0
occ:1.00
|
NE2
|
D:HIS541
|
2.1
|
9.3
|
1.0
|
NE2
|
D:HIS361
|
2.2
|
10.7
|
1.0
|
O
|
D:HOH8
|
2.2
|
13.7
|
1.0
|
NE2
|
D:HIS366
|
2.2
|
11.9
|
1.0
|
OXT
|
D:ILE663
|
2.3
|
13.2
|
1.0
|
ND1
|
D:HIS545
|
2.3
|
13.7
|
1.0
|
CE1
|
D:HIS361
|
3.0
|
14.6
|
1.0
|
CE1
|
D:HIS541
|
3.1
|
13.9
|
1.0
|
CD2
|
D:HIS541
|
3.1
|
10.5
|
1.0
|
CE1
|
D:HIS545
|
3.1
|
13.9
|
1.0
|
CE1
|
D:HIS366
|
3.2
|
12.7
|
1.0
|
CD2
|
D:HIS366
|
3.2
|
16.0
|
1.0
|
C
|
D:ILE663
|
3.3
|
14.8
|
1.0
|
CD2
|
D:HIS361
|
3.3
|
13.5
|
1.0
|
CG
|
D:HIS545
|
3.4
|
12.0
|
1.0
|
O
|
D:ILE663
|
3.5
|
12.3
|
1.0
|
CB
|
D:HIS545
|
3.8
|
11.6
|
1.0
|
ND1
|
D:HIS361
|
4.2
|
14.0
|
1.0
|
ND1
|
D:HIS541
|
4.2
|
10.4
|
1.0
|
CG
|
D:HIS541
|
4.2
|
9.1
|
1.0
|
NE2
|
D:HIS545
|
4.3
|
18.0
|
1.0
|
ND1
|
D:HIS366
|
4.3
|
13.7
|
1.0
|
CG
|
D:HIS361
|
4.4
|
10.7
|
1.0
|
CG
|
D:HIS366
|
4.4
|
13.8
|
1.0
|
C13
|
D:OYP664
|
4.4
|
15.1
|
1.0
|
CD2
|
D:HIS545
|
4.4
|
17.1
|
1.0
|
C12
|
D:OYP664
|
4.6
|
17.3
|
1.0
|
C14
|
D:OYP664
|
4.6
|
15.6
|
1.0
|
CA
|
D:ILE663
|
4.7
|
13.5
|
1.0
|
CG1
|
D:VAL661
|
4.7
|
10.2
|
1.0
|
CA
|
D:HIS545
|
4.9
|
10.4
|
1.0
|
N
|
D:ILE663
|
5.0
|
14.4
|
1.0
|
|
Reference:
S.Xu,
T.C.Mueser,
L.J.Marnett,
M.O.Funk.
Crystal Structure of 12-Lipoxygenase Catalytic-Domain-Inhibitor Complex Identifies A Substrate-Binding Channel For Catalysis. Structure V. 20 1490 2012.
ISSN: ISSN 0969-2126
PubMed: 22795085
DOI: 10.1016/J.STR.2012.06.003
Page generated: Sun Aug 4 19:13:07 2024
|