Iron in PDB 5tqn: Lipoxygenase-1 (Soybean) L546A Mutant at 293K
Enzymatic activity of Lipoxygenase-1 (Soybean) L546A Mutant at 293K
All present enzymatic activity of Lipoxygenase-1 (Soybean) L546A Mutant at 293K:
1.13.11.12;
Protein crystallography data
The structure of Lipoxygenase-1 (Soybean) L546A Mutant at 293K, PDB code: 5tqn
was solved by
E.M.Poss,
J.S.Fraser,
C.Gee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.97 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.519,
92.656,
100.751,
90.00,
93.47,
90.00
|
R / Rfree (%)
|
14.5 /
16.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Lipoxygenase-1 (Soybean) L546A Mutant at 293K
(pdb code 5tqn). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Lipoxygenase-1 (Soybean) L546A Mutant at 293K, PDB code: 5tqn:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 5tqn
Go back to
Iron Binding Sites List in 5tqn
Iron binding site 1 out
of 2 in the Lipoxygenase-1 (Soybean) L546A Mutant at 293K
![](/pictures/FE/pdb/tq/5tqn-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/tq/5tqn-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Lipoxygenase-1 (Soybean) L546A Mutant at 293K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe901
b:27.2
occ:1.00
|
HE1
|
A:HIS499
|
1.9
|
20.9
|
0.6
|
NE2
|
A:HIS504
|
2.2
|
18.6
|
0.6
|
O
|
A:HOH1028
|
2.3
|
35.2
|
1.0
|
OXT
|
A:ILE839
|
2.3
|
18.5
|
1.0
|
NE2
|
A:HIS690
|
2.3
|
12.7
|
0.9
|
NE2
|
A:HIS504
|
2.4
|
19.1
|
0.4
|
NE2
|
A:HIS499
|
2.4
|
16.3
|
0.4
|
CE1
|
A:HIS499
|
2.5
|
17.4
|
0.6
|
OD1
|
A:ASN694
|
2.6
|
15.8
|
0.2
|
NE2
|
A:HIS690
|
2.6
|
12.8
|
0.1
|
NE2
|
A:HIS499
|
2.9
|
17.8
|
0.6
|
HE1
|
A:HIS504
|
2.9
|
23.3
|
0.6
|
CE1
|
A:HIS504
|
2.9
|
19.4
|
0.6
|
HD2
|
A:HIS504
|
3.0
|
21.7
|
0.4
|
CD2
|
A:HIS504
|
3.1
|
18.1
|
0.4
|
HD2
|
A:HIS690
|
3.2
|
15.1
|
0.1
|
C
|
A:ILE839
|
3.2
|
20.1
|
1.0
|
CD2
|
A:HIS690
|
3.3
|
12.6
|
0.1
|
CD2
|
A:HIS690
|
3.3
|
13.0
|
0.9
|
OD1
|
A:ASN694
|
3.3
|
17.8
|
0.8
|
CD2
|
A:HIS499
|
3.3
|
17.7
|
0.4
|
CE1
|
A:HIS690
|
3.3
|
13.3
|
0.9
|
CE1
|
A:HIS499
|
3.4
|
17.6
|
0.4
|
HD2
|
A:HIS690
|
3.4
|
15.6
|
0.9
|
O
|
A:ILE839
|
3.4
|
21.0
|
1.0
|
CD2
|
A:HIS504
|
3.4
|
17.3
|
0.6
|
HD2
|
A:HIS499
|
3.4
|
21.3
|
0.4
|
CE1
|
A:HIS504
|
3.5
|
19.8
|
0.4
|
HE1
|
A:HIS690
|
3.5
|
16.0
|
0.9
|
HE1
|
A:HIS499
|
3.5
|
21.1
|
0.4
|
HG23
|
A:ILE837
|
3.6
|
18.6
|
1.0
|
ND1
|
A:HIS499
|
3.6
|
19.4
|
0.6
|
CG
|
A:ASN694
|
3.7
|
15.2
|
0.2
|
HD2
|
A:HIS504
|
3.7
|
20.8
|
0.6
|
CE1
|
A:HIS690
|
3.8
|
13.3
|
0.1
|
HE1
|
A:HIS504
|
3.8
|
23.8
|
0.4
|
CG
|
A:ASN694
|
3.8
|
15.2
|
0.8
|
HB2
|
A:ASN694
|
3.8
|
17.9
|
0.8
|
HB2
|
A:ASN694
|
3.9
|
17.3
|
0.2
|
HE1
|
A:HIS690
|
4.1
|
16.0
|
0.1
|
CD2
|
A:HIS499
|
4.1
|
17.4
|
0.6
|
ND1
|
A:HIS504
|
4.1
|
19.3
|
0.6
|
H
|
A:ILE839
|
4.3
|
21.2
|
1.0
|
CG
|
A:HIS504
|
4.3
|
17.2
|
0.4
|
HG23
|
A:ILE839
|
4.3
|
28.8
|
1.0
|
HD23
|
A:LEU754
|
4.3
|
19.5
|
0.3
|
CB
|
A:ASN694
|
4.4
|
14.4
|
0.2
|
CB
|
A:ASN694
|
4.4
|
14.9
|
0.8
|
CG2
|
A:ILE837
|
4.4
|
15.5
|
1.0
|
CG
|
A:HIS504
|
4.4
|
17.1
|
0.6
|
HG22
|
A:ILE837
|
4.4
|
18.6
|
1.0
|
CG
|
A:HIS690
|
4.4
|
12.3
|
0.9
|
ND1
|
A:HIS690
|
4.4
|
13.1
|
0.9
|
ND1
|
A:HIS499
|
4.5
|
16.9
|
0.4
|
CG
|
A:HIS499
|
4.5
|
17.6
|
0.4
|
ND1
|
A:HIS504
|
4.5
|
19.0
|
0.4
|
ND2
|
A:ASN694
|
4.5
|
15.1
|
0.8
|
CG
|
A:HIS499
|
4.5
|
17.8
|
0.6
|
CG
|
A:HIS690
|
4.5
|
12.4
|
0.1
|
HG
|
A:LEU754
|
4.5
|
23.7
|
0.3
|
HD21
|
A:ASN694
|
4.6
|
18.2
|
0.8
|
HG21
|
A:ILE837
|
4.6
|
18.6
|
1.0
|
CA
|
A:ILE839
|
4.6
|
18.5
|
1.0
|
ND2
|
A:ASN694
|
4.7
|
14.9
|
0.2
|
HD21
|
A:ASN694
|
4.7
|
17.9
|
0.2
|
HD22
|
A:LEU754
|
4.7
|
27.2
|
0.7
|
ND1
|
A:HIS690
|
4.7
|
13.0
|
0.1
|
HD21
|
A:LEU754
|
4.8
|
19.5
|
0.3
|
HD2
|
A:HIS499
|
4.8
|
20.9
|
0.6
|
N
|
A:ILE839
|
4.9
|
17.7
|
1.0
|
HB3
|
A:ASN694
|
4.9
|
17.9
|
0.8
|
CD2
|
A:LEU754
|
4.9
|
16.2
|
0.3
|
OG1
|
A:THR503
|
4.9
|
13.0
|
0.6
|
HD13
|
A:LEU754
|
4.9
|
24.8
|
0.7
|
HB3
|
A:LEU754
|
5.0
|
21.1
|
0.7
|
|
Iron binding site 2 out
of 2 in 5tqn
Go back to
Iron Binding Sites List in 5tqn
Iron binding site 2 out
of 2 in the Lipoxygenase-1 (Soybean) L546A Mutant at 293K
![](/pictures/FE/pdb/tq/5tqn-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/tq/5tqn-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Lipoxygenase-1 (Soybean) L546A Mutant at 293K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe901
b:27.1
occ:1.00
|
HE1
|
B:HIS499
|
2.1
|
34.5
|
0.3
|
O
|
B:HOH1069
|
2.2
|
28.8
|
1.0
|
NE2
|
B:HIS504
|
2.3
|
14.7
|
0.3
|
OXT
|
B:ILE839
|
2.3
|
18.8
|
1.0
|
NE2
|
B:HIS504
|
2.3
|
15.1
|
0.7
|
NE2
|
B:HIS499
|
2.3
|
27.6
|
0.7
|
NE2
|
B:HIS690
|
2.4
|
10.8
|
0.2
|
NE2
|
B:HIS690
|
2.4
|
10.6
|
0.8
|
CE1
|
B:HIS499
|
2.7
|
28.7
|
0.3
|
HE1
|
B:HIS504
|
2.7
|
17.8
|
0.3
|
CE1
|
B:HIS504
|
2.8
|
14.8
|
0.3
|
OD1
|
B:ASN694
|
2.9
|
15.8
|
0.7
|
NE2
|
B:HIS499
|
3.1
|
29.2
|
0.3
|
CE1
|
B:HIS690
|
3.2
|
11.3
|
0.2
|
HE1
|
B:HIS690
|
3.2
|
13.5
|
0.2
|
C
|
B:ILE839
|
3.2
|
23.3
|
1.0
|
CD2
|
B:HIS690
|
3.2
|
12.3
|
0.8
|
CD2
|
B:HIS504
|
3.2
|
14.2
|
0.7
|
CE1
|
B:HIS499
|
3.3
|
29.6
|
0.7
|
CE1
|
B:HIS504
|
3.3
|
15.5
|
0.7
|
HD2
|
B:HIS690
|
3.3
|
14.8
|
0.8
|
CD2
|
B:HIS499
|
3.3
|
27.9
|
0.7
|
O
|
B:ILE839
|
3.4
|
24.4
|
1.0
|
HE1
|
B:HIS499
|
3.4
|
35.5
|
0.7
|
HD2
|
B:HIS504
|
3.4
|
17.0
|
0.7
|
CE1
|
B:HIS690
|
3.4
|
11.6
|
0.8
|
CD2
|
B:HIS690
|
3.4
|
11.3
|
0.2
|
HE1
|
B:HIS504
|
3.4
|
18.6
|
0.7
|
HD2
|
B:HIS499
|
3.5
|
33.5
|
0.7
|
CD2
|
B:HIS504
|
3.5
|
14.0
|
0.3
|
HE1
|
B:HIS690
|
3.6
|
13.9
|
0.8
|
HG23
|
B:ILE837
|
3.7
|
18.3
|
1.0
|
HD2
|
B:HIS690
|
3.7
|
13.6
|
0.2
|
HB2
|
B:ASN694
|
3.7
|
16.8
|
0.3
|
CG
|
B:ASN694
|
3.7
|
15.1
|
0.7
|
ND1
|
B:HIS499
|
3.8
|
27.5
|
0.3
|
HB2
|
B:ASN694
|
3.9
|
16.3
|
0.7
|
OD1
|
B:ASN694
|
3.9
|
14.6
|
0.3
|
HD2
|
B:HIS504
|
3.9
|
16.8
|
0.3
|
CG
|
B:ASN694
|
4.0
|
14.8
|
0.3
|
ND1
|
B:HIS504
|
4.1
|
15.4
|
0.3
|
H
|
B:ILE839
|
4.3
|
23.2
|
1.0
|
HG23
|
B:ILE839
|
4.3
|
29.9
|
1.0
|
CB
|
B:ASN694
|
4.3
|
14.0
|
0.3
|
ND1
|
B:HIS690
|
4.3
|
11.8
|
0.2
|
CD2
|
B:HIS499
|
4.4
|
28.3
|
0.3
|
ND1
|
B:HIS504
|
4.4
|
16.2
|
0.7
|
CB
|
B:ASN694
|
4.4
|
13.6
|
0.7
|
CG
|
B:HIS504
|
4.4
|
14.0
|
0.7
|
ND1
|
B:HIS499
|
4.4
|
28.1
|
0.7
|
ND2
|
B:ASN694
|
4.4
|
15.7
|
0.3
|
CG
|
B:HIS690
|
4.4
|
11.8
|
0.8
|
CG
|
B:HIS504
|
4.5
|
13.9
|
0.3
|
CG2
|
B:ILE837
|
4.5
|
15.2
|
1.0
|
CG
|
B:HIS499
|
4.5
|
24.3
|
0.7
|
ND1
|
B:HIS690
|
4.5
|
12.5
|
0.8
|
CG
|
B:HIS690
|
4.5
|
12.0
|
0.2
|
HG22
|
B:ILE837
|
4.5
|
18.3
|
1.0
|
ND2
|
B:ASN694
|
4.5
|
16.2
|
0.7
|
HD21
|
B:ASN694
|
4.6
|
19.4
|
0.7
|
HD21
|
B:ASN694
|
4.6
|
18.8
|
0.3
|
CA
|
B:ILE839
|
4.6
|
19.7
|
1.0
|
CG
|
B:HIS499
|
4.7
|
24.5
|
0.3
|
HB3
|
B:ASN694
|
4.7
|
16.8
|
0.3
|
HG21
|
B:ILE837
|
4.7
|
18.3
|
1.0
|
HD13
|
B:LEU754
|
4.8
|
30.1
|
1.0
|
HD22
|
B:ASN694
|
4.8
|
18.8
|
0.3
|
N
|
B:ILE839
|
4.8
|
19.4
|
1.0
|
HD22
|
B:LEU754
|
4.8
|
28.9
|
1.0
|
HB3
|
B:LEU754
|
4.9
|
21.7
|
1.0
|
HB3
|
B:ASN694
|
5.0
|
16.3
|
0.7
|
|
Reference:
S.Hu,
A.R.Offenbacher,
E.M.Thompson,
C.L.Gee,
J.Wilcoxen,
C.A.M.Carr,
D.M.Prigozhin,
V.Yang,
T.Alber,
R.D.Britt,
J.S.Fraser,
J.P.Klinman.
Biophysical Characterization of A Disabled Double Mutant of Soybean Lipoxygenase: the "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and An Identified Dynamical Network. J.Am.Chem.Soc. V. 141 1555 2019.
ISSN: ESSN 1520-5126
PubMed: 30645119
DOI: 10.1021/JACS.8B10992
Page generated: Tue Aug 6 09:41:16 2024
|