Iron in PDB 3a16: Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
Enzymatic activity of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
All present enzymatic activity of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime:
4.99.1.5;
Protein crystallography data
The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime, PDB code: 3a16
was solved by
H.Sawai,
H.Sugimoto,
Y.Kato,
Y.Asano,
Y.Shiro,
S.Aono,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.81 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.710,
147.670,
78.910,
90.00,
90.01,
90.00
|
R / Rfree (%)
|
24.8 /
27.4
|
Other elements in 3a16:
The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
(pdb code 3a16). 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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime, PDB code: 3a16:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3a16
Go back to
Iron Binding Sites List in 3a16
Iron binding site 1 out
of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe354
b:8.3
occ:1.00
|
FE
|
A:HEM354
|
0.0
|
8.3
|
1.0
|
NC
|
A:HEM354
|
2.0
|
5.5
|
1.0
|
ND
|
A:HEM354
|
2.0
|
6.9
|
1.0
|
NB
|
A:HEM354
|
2.1
|
7.3
|
1.0
|
NA
|
A:HEM354
|
2.1
|
6.8
|
1.0
|
NE2
|
A:HIS299
|
2.2
|
8.4
|
1.0
|
N1
|
A:PXO355
|
2.5
|
12.1
|
1.0
|
C4C
|
A:HEM354
|
3.0
|
7.3
|
1.0
|
C1D
|
A:HEM354
|
3.0
|
6.0
|
1.0
|
C1C
|
A:HEM354
|
3.0
|
7.8
|
1.0
|
C4B
|
A:HEM354
|
3.1
|
7.0
|
1.0
|
C4D
|
A:HEM354
|
3.1
|
6.8
|
1.0
|
C4A
|
A:HEM354
|
3.1
|
8.8
|
1.0
|
C1A
|
A:HEM354
|
3.1
|
8.4
|
1.0
|
CE1
|
A:HIS299
|
3.1
|
7.3
|
1.0
|
C1B
|
A:HEM354
|
3.1
|
7.3
|
1.0
|
CD2
|
A:HIS299
|
3.2
|
6.5
|
1.0
|
O1
|
A:PXO355
|
3.2
|
8.7
|
1.0
|
CHD
|
A:HEM354
|
3.4
|
6.4
|
1.0
|
CHC
|
A:HEM354
|
3.4
|
7.8
|
1.0
|
C1
|
A:PXO355
|
3.4
|
12.6
|
1.0
|
CHA
|
A:HEM354
|
3.5
|
7.8
|
1.0
|
CHB
|
A:HEM354
|
3.5
|
8.3
|
1.0
|
C2C
|
A:HEM354
|
4.2
|
6.9
|
1.0
|
C3C
|
A:HEM354
|
4.2
|
6.9
|
1.0
|
ND1
|
A:HIS299
|
4.2
|
6.3
|
1.0
|
C2D
|
A:HEM354
|
4.3
|
6.4
|
1.0
|
C3B
|
A:HEM354
|
4.3
|
7.7
|
1.0
|
C3D
|
A:HEM354
|
4.3
|
5.7
|
1.0
|
C3A
|
A:HEM354
|
4.3
|
8.0
|
1.0
|
C2B
|
A:HEM354
|
4.3
|
7.6
|
1.0
|
C2A
|
A:HEM354
|
4.3
|
8.5
|
1.0
|
CG
|
A:HIS299
|
4.3
|
8.5
|
1.0
|
C2
|
A:PXO355
|
4.9
|
13.9
|
1.0
|
OG
|
A:SER219
|
4.9
|
5.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 3a16
Go back to
Iron Binding Sites List in 3a16
Iron binding site 2 out
of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe354
b:7.9
occ:1.00
|
FE
|
B:HEM354
|
0.0
|
7.9
|
1.0
|
NA
|
B:HEM354
|
2.0
|
6.4
|
1.0
|
NC
|
B:HEM354
|
2.0
|
5.0
|
1.0
|
ND
|
B:HEM354
|
2.0
|
5.5
|
1.0
|
NB
|
B:HEM354
|
2.1
|
6.0
|
1.0
|
NE2
|
B:HIS299
|
2.1
|
4.1
|
0.2
|
N1
|
B:PXO355
|
2.1
|
11.9
|
1.0
|
NE2
|
B:HIS299
|
2.2
|
9.1
|
0.8
|
CD2
|
B:HIS299
|
2.8
|
3.4
|
0.2
|
C1
|
B:PXO355
|
3.0
|
14.3
|
1.0
|
CE1
|
B:HIS299
|
3.0
|
7.7
|
0.8
|
C1D
|
B:HEM354
|
3.0
|
5.9
|
1.0
|
C1A
|
B:HEM354
|
3.0
|
7.1
|
1.0
|
C1C
|
B:HEM354
|
3.1
|
6.8
|
1.0
|
C4A
|
B:HEM354
|
3.1
|
7.9
|
1.0
|
C1B
|
B:HEM354
|
3.1
|
7.7
|
1.0
|
C4B
|
B:HEM354
|
3.1
|
6.8
|
1.0
|
C4C
|
B:HEM354
|
3.1
|
6.8
|
1.0
|
C4D
|
B:HEM354
|
3.1
|
6.0
|
1.0
|
O1
|
B:PXO355
|
3.1
|
8.7
|
1.0
|
CD2
|
B:HIS299
|
3.2
|
6.5
|
0.8
|
CE1
|
B:HIS299
|
3.3
|
3.5
|
0.2
|
CHD
|
B:HEM354
|
3.4
|
5.9
|
1.0
|
CHC
|
B:HEM354
|
3.4
|
6.2
|
1.0
|
CHB
|
B:HEM354
|
3.4
|
6.9
|
1.0
|
CHA
|
B:HEM354
|
3.4
|
6.8
|
1.0
|
CG
|
B:HIS299
|
4.1
|
2.9
|
0.2
|
ND1
|
B:HIS299
|
4.2
|
7.7
|
0.8
|
ND1
|
B:HIS299
|
4.3
|
2.9
|
0.2
|
C3A
|
B:HEM354
|
4.3
|
7.2
|
1.0
|
C2A
|
B:HEM354
|
4.3
|
7.2
|
1.0
|
C2C
|
B:HEM354
|
4.3
|
4.9
|
1.0
|
C2D
|
B:HEM354
|
4.3
|
5.2
|
1.0
|
C2B
|
B:HEM354
|
4.3
|
6.4
|
1.0
|
C3D
|
B:HEM354
|
4.3
|
6.3
|
1.0
|
C3B
|
B:HEM354
|
4.3
|
7.4
|
1.0
|
C3C
|
B:HEM354
|
4.3
|
5.3
|
1.0
|
CG
|
B:HIS299
|
4.3
|
7.8
|
0.8
|
C2
|
B:PXO355
|
4.4
|
16.2
|
1.0
|
OG
|
B:SER219
|
4.9
|
6.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 3a16
Go back to
Iron Binding Sites List in 3a16
Iron binding site 3 out
of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe354
b:9.1
occ:1.00
|
FE
|
C:HEM354
|
0.0
|
9.1
|
1.0
|
NA
|
C:HEM354
|
2.0
|
6.9
|
1.0
|
NB
|
C:HEM354
|
2.0
|
6.8
|
1.0
|
ND
|
C:HEM354
|
2.0
|
7.0
|
1.0
|
NC
|
C:HEM354
|
2.1
|
5.8
|
1.0
|
N1
|
C:PXO355
|
2.2
|
11.1
|
1.0
|
NE2
|
C:HIS299
|
2.3
|
10.8
|
1.0
|
C1
|
C:PXO355
|
3.0
|
11.4
|
1.0
|
C4D
|
C:HEM354
|
3.0
|
6.7
|
1.0
|
C1A
|
C:HEM354
|
3.0
|
8.8
|
1.0
|
C4A
|
C:HEM354
|
3.1
|
8.9
|
1.0
|
C4B
|
C:HEM354
|
3.1
|
7.4
|
1.0
|
C1C
|
C:HEM354
|
3.1
|
7.5
|
1.0
|
C1D
|
C:HEM354
|
3.1
|
6.4
|
1.0
|
C1B
|
C:HEM354
|
3.1
|
7.5
|
1.0
|
O1
|
C:PXO355
|
3.1
|
10.1
|
1.0
|
C4C
|
C:HEM354
|
3.1
|
7.5
|
1.0
|
CE1
|
C:HIS299
|
3.2
|
8.8
|
1.0
|
CD2
|
C:HIS299
|
3.3
|
7.8
|
1.0
|
CHA
|
C:HEM354
|
3.4
|
7.8
|
1.0
|
CHC
|
C:HEM354
|
3.4
|
7.9
|
1.0
|
CHB
|
C:HEM354
|
3.4
|
8.3
|
1.0
|
CHD
|
C:HEM354
|
3.5
|
6.5
|
1.0
|
C3A
|
C:HEM354
|
4.3
|
8.2
|
1.0
|
C2A
|
C:HEM354
|
4.3
|
8.5
|
1.0
|
C3D
|
C:HEM354
|
4.3
|
6.4
|
1.0
|
C2B
|
C:HEM354
|
4.3
|
7.6
|
1.0
|
C2D
|
C:HEM354
|
4.3
|
6.6
|
1.0
|
C2C
|
C:HEM354
|
4.3
|
7.1
|
1.0
|
C3B
|
C:HEM354
|
4.3
|
8.0
|
1.0
|
ND1
|
C:HIS299
|
4.3
|
7.8
|
1.0
|
C3C
|
C:HEM354
|
4.3
|
6.5
|
1.0
|
CG
|
C:HIS299
|
4.4
|
9.1
|
1.0
|
C2
|
C:PXO355
|
4.5
|
12.9
|
1.0
|
OG
|
C:SER219
|
4.9
|
5.3
|
1.0
|
|
Iron binding site 4 out
of 4 in 3a16
Go back to
Iron Binding Sites List in 3a16
Iron binding site 4 out
of 4 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime
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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe354
b:8.5
occ:1.00
|
FE
|
D:HEM354
|
0.0
|
8.5
|
1.0
|
NC
|
D:HEM354
|
2.0
|
5.0
|
1.0
|
ND
|
D:HEM354
|
2.0
|
6.0
|
1.0
|
NA
|
D:HEM354
|
2.1
|
6.1
|
1.0
|
NB
|
D:HEM354
|
2.1
|
6.0
|
1.0
|
NE2
|
D:HIS299
|
2.1
|
4.7
|
0.2
|
N1
|
D:PXO355
|
2.1
|
14.1
|
1.0
|
NE2
|
D:HIS299
|
2.2
|
9.2
|
0.8
|
CD2
|
D:HIS299
|
2.8
|
3.8
|
0.2
|
C1
|
D:PXO355
|
3.0
|
14.2
|
1.0
|
C1D
|
D:HEM354
|
3.0
|
5.7
|
1.0
|
CE1
|
D:HIS299
|
3.0
|
8.5
|
0.8
|
C1C
|
D:HEM354
|
3.0
|
7.0
|
1.0
|
O1
|
D:PXO355
|
3.0
|
7.7
|
1.0
|
C4C
|
D:HEM354
|
3.1
|
6.5
|
1.0
|
C4B
|
D:HEM354
|
3.1
|
6.9
|
1.0
|
C4A
|
D:HEM354
|
3.1
|
7.5
|
1.0
|
C1A
|
D:HEM354
|
3.1
|
7.3
|
1.0
|
C1B
|
D:HEM354
|
3.1
|
7.7
|
1.0
|
C4D
|
D:HEM354
|
3.1
|
6.2
|
1.0
|
CD2
|
D:HIS299
|
3.2
|
7.4
|
0.8
|
CE1
|
D:HIS299
|
3.3
|
4.5
|
0.2
|
CHD
|
D:HEM354
|
3.4
|
5.9
|
1.0
|
CHC
|
D:HEM354
|
3.4
|
6.1
|
1.0
|
CHB
|
D:HEM354
|
3.4
|
6.9
|
1.0
|
CHA
|
D:HEM354
|
3.5
|
6.8
|
1.0
|
CG
|
D:HIS299
|
4.1
|
3.1
|
0.2
|
ND1
|
D:HIS299
|
4.2
|
7.7
|
0.8
|
ND1
|
D:HIS299
|
4.3
|
3.1
|
0.2
|
C2C
|
D:HEM354
|
4.3
|
4.7
|
1.0
|
C2D
|
D:HEM354
|
4.3
|
5.3
|
1.0
|
C3C
|
D:HEM354
|
4.3
|
5.6
|
1.0
|
C3B
|
D:HEM354
|
4.3
|
7.4
|
1.0
|
C3A
|
D:HEM354
|
4.3
|
7.3
|
1.0
|
C2A
|
D:HEM354
|
4.3
|
7.0
|
1.0
|
C3D
|
D:HEM354
|
4.3
|
6.0
|
1.0
|
C2B
|
D:HEM354
|
4.3
|
6.1
|
1.0
|
CG
|
D:HIS299
|
4.3
|
8.4
|
0.8
|
C2
|
D:PXO355
|
4.4
|
15.4
|
1.0
|
CD1
|
D:ILE302
|
4.5
|
3.5
|
0.2
|
OG
|
D:SER219
|
4.9
|
6.5
|
1.0
|
|
Reference:
H.Sawai,
H.Sugimoto,
Y.Kato,
Y.Asano,
Y.Shiro,
S.Aono.
X-Ray Crystal Structure of Michaelis Complex of Aldoxime Dehydratase J.Biol.Chem. V. 284 32089 2009.
ISSN: ISSN 0021-9258
PubMed: 19740758
DOI: 10.1074/JBC.M109.018762
Page generated: Sun Aug 4 06:38:44 2024
|