Iron in PDB 3svw: Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
Enzymatic activity of Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
All present enzymatic activity of Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;
Protein crystallography data
The structure of Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3svw
was solved by
L.M.R.Jensen,
C.M.Wilmot,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.89 /
1.86
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.606,
89.001,
104.812,
67.05,
79.51,
79.72
|
R / Rfree (%)
|
13.1 /
17.4
|
Other elements in 3svw:
The structure of Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
(pdb code 3svw). 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 P107V-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3svw:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3svw
Go back to
Iron Binding Sites List in 3svw
Iron binding site 1 out
of 4 in the Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
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 P107V-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:12.7
occ:1.00
|
FE
|
A:HEC500
|
0.0
|
12.7
|
1.0
|
NC
|
A:HEC500
|
2.0
|
11.3
|
1.0
|
ND
|
A:HEC500
|
2.0
|
13.2
|
1.0
|
NB
|
A:HEC500
|
2.0
|
13.0
|
1.0
|
NA
|
A:HEC500
|
2.1
|
14.2
|
1.0
|
NE2
|
A:HIS35
|
2.2
|
14.1
|
1.0
|
C1C
|
A:HEC500
|
3.0
|
12.8
|
1.0
|
C4D
|
A:HEC500
|
3.0
|
12.1
|
1.0
|
C4B
|
A:HEC500
|
3.0
|
13.6
|
1.0
|
C4C
|
A:HEC500
|
3.0
|
12.7
|
1.0
|
C1B
|
A:HEC500
|
3.1
|
13.4
|
1.0
|
C1A
|
A:HEC500
|
3.1
|
12.6
|
1.0
|
C1D
|
A:HEC500
|
3.1
|
13.4
|
1.0
|
C4A
|
A:HEC500
|
3.1
|
11.2
|
1.0
|
CD2
|
A:HIS35
|
3.1
|
14.2
|
1.0
|
CE1
|
A:HIS35
|
3.3
|
9.8
|
1.0
|
CHC
|
A:HEC500
|
3.4
|
10.8
|
1.0
|
CHD
|
A:HEC500
|
3.4
|
12.5
|
1.0
|
CHA
|
A:HEC500
|
3.4
|
11.3
|
1.0
|
CHB
|
A:HEC500
|
3.4
|
10.7
|
1.0
|
CG2
|
A:VAL107
|
3.9
|
16.8
|
1.0
|
NE2
|
A:GLN103
|
4.2
|
12.8
|
1.0
|
C2C
|
A:HEC500
|
4.3
|
11.0
|
1.0
|
C3C
|
A:HEC500
|
4.3
|
10.5
|
1.0
|
CG
|
A:HIS35
|
4.3
|
15.2
|
1.0
|
C3D
|
A:HEC500
|
4.3
|
10.8
|
1.0
|
C3B
|
A:HEC500
|
4.3
|
9.8
|
1.0
|
C2B
|
A:HEC500
|
4.3
|
10.2
|
1.0
|
ND1
|
A:HIS35
|
4.4
|
14.5
|
1.0
|
C2D
|
A:HEC500
|
4.4
|
13.3
|
1.0
|
C2A
|
A:HEC500
|
4.4
|
10.2
|
1.0
|
C3A
|
A:HEC500
|
4.4
|
10.1
|
1.0
|
CG
|
A:GLU113
|
4.9
|
27.0
|
1.0
|
CB
|
A:VAL107
|
5.0
|
15.9
|
1.0
|
CD2
|
A:LEU70
|
5.0
|
15.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 3svw
Go back to
Iron Binding Sites List in 3svw
Iron binding site 2 out
of 4 in the Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
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 P107V-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe600
b:14.2
occ:1.00
|
FE
|
A:HEC600
|
0.0
|
14.2
|
1.0
|
OH
|
A:TYR294
|
2.0
|
13.1
|
1.0
|
NE2
|
A:HIS205
|
2.0
|
13.2
|
1.0
|
NA
|
A:HEC600
|
2.1
|
14.2
|
1.0
|
NC
|
A:HEC600
|
2.1
|
15.0
|
1.0
|
NB
|
A:HEC600
|
2.1
|
14.6
|
1.0
|
ND
|
A:HEC600
|
2.1
|
10.6
|
1.0
|
CZ
|
A:TYR294
|
2.9
|
14.2
|
1.0
|
CE1
|
A:HIS205
|
3.0
|
11.2
|
1.0
|
CD2
|
A:HIS205
|
3.0
|
12.5
|
1.0
|
C1B
|
A:HEC600
|
3.0
|
15.7
|
1.0
|
C1A
|
A:HEC600
|
3.0
|
13.9
|
1.0
|
C1C
|
A:HEC600
|
3.0
|
12.7
|
1.0
|
C1D
|
A:HEC600
|
3.1
|
15.1
|
1.0
|
C4C
|
A:HEC600
|
3.1
|
15.6
|
1.0
|
C4A
|
A:HEC600
|
3.1
|
14.5
|
1.0
|
C4D
|
A:HEC600
|
3.1
|
12.6
|
1.0
|
C4B
|
A:HEC600
|
3.1
|
14.3
|
1.0
|
CHD
|
A:HEC600
|
3.4
|
14.6
|
1.0
|
CHB
|
A:HEC600
|
3.4
|
12.9
|
1.0
|
CHA
|
A:HEC600
|
3.4
|
10.7
|
1.0
|
CHC
|
A:HEC600
|
3.4
|
10.7
|
1.0
|
CE1
|
A:TYR294
|
3.7
|
12.5
|
1.0
|
CE2
|
A:TYR294
|
3.8
|
14.9
|
1.0
|
ND1
|
A:HIS205
|
4.1
|
12.8
|
1.0
|
CG
|
A:HIS205
|
4.2
|
14.0
|
1.0
|
C2C
|
A:HEC600
|
4.3
|
12.2
|
1.0
|
C2B
|
A:HEC600
|
4.3
|
14.4
|
1.0
|
C3B
|
A:HEC600
|
4.3
|
14.5
|
1.0
|
C2A
|
A:HEC600
|
4.3
|
14.0
|
1.0
|
C3C
|
A:HEC600
|
4.4
|
13.6
|
1.0
|
C3A
|
A:HEC600
|
4.4
|
12.5
|
1.0
|
C2D
|
A:HEC600
|
4.4
|
11.7
|
1.0
|
C3D
|
A:HEC600
|
4.4
|
12.1
|
1.0
|
CD1
|
A:ILE226
|
4.9
|
13.0
|
1.0
|
CD1
|
A:TYR294
|
4.9
|
16.7
|
1.0
|
CD2
|
A:TYR294
|
5.0
|
17.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 3svw
Go back to
Iron Binding Sites List in 3svw
Iron binding site 3 out
of 4 in the Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
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 P107V-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:13.2
occ:1.00
|
FE
|
B:HEC500
|
0.0
|
13.2
|
1.0
|
NC
|
B:HEC500
|
2.0
|
14.1
|
1.0
|
NE2
|
B:HIS35
|
2.0
|
10.7
|
1.0
|
ND
|
B:HEC500
|
2.0
|
13.7
|
1.0
|
NA
|
B:HEC500
|
2.1
|
11.6
|
1.0
|
NB
|
B:HEC500
|
2.1
|
12.9
|
1.0
|
C4D
|
B:HEC500
|
3.0
|
13.6
|
1.0
|
CE1
|
B:HIS35
|
3.0
|
10.3
|
1.0
|
C1C
|
B:HEC500
|
3.0
|
12.9
|
1.0
|
CD2
|
B:HIS35
|
3.0
|
13.7
|
1.0
|
C4C
|
B:HEC500
|
3.0
|
14.8
|
1.0
|
C4B
|
B:HEC500
|
3.0
|
10.9
|
1.0
|
C4A
|
B:HEC500
|
3.0
|
11.1
|
1.0
|
C1D
|
B:HEC500
|
3.1
|
12.4
|
1.0
|
C1A
|
B:HEC500
|
3.1
|
10.8
|
1.0
|
C1B
|
B:HEC500
|
3.1
|
11.3
|
1.0
|
CHD
|
B:HEC500
|
3.4
|
12.8
|
1.0
|
CHA
|
B:HEC500
|
3.4
|
10.5
|
1.0
|
CHC
|
B:HEC500
|
3.4
|
11.7
|
1.0
|
CHB
|
B:HEC500
|
3.5
|
9.8
|
1.0
|
O
|
B:HOH2289
|
3.9
|
20.1
|
1.0
|
NE2
|
B:GLN103
|
4.0
|
10.9
|
1.0
|
ND1
|
B:HIS35
|
4.2
|
13.4
|
1.0
|
CG
|
B:HIS35
|
4.2
|
13.2
|
1.0
|
C3C
|
B:HEC500
|
4.3
|
12.5
|
1.0
|
C2C
|
B:HEC500
|
4.3
|
13.2
|
1.0
|
C3D
|
B:HEC500
|
4.3
|
10.9
|
1.0
|
C3A
|
B:HEC500
|
4.3
|
8.1
|
1.0
|
C2D
|
B:HEC500
|
4.4
|
12.5
|
1.0
|
C3B
|
B:HEC500
|
4.4
|
8.2
|
1.0
|
C2A
|
B:HEC500
|
4.4
|
9.2
|
1.0
|
C2B
|
B:HEC500
|
4.4
|
11.7
|
1.0
|
CG2
|
B:VAL107
|
4.4
|
16.4
|
1.0
|
CB
|
B:VAL107
|
4.9
|
14.6
|
1.0
|
CD
|
B:GLN103
|
5.0
|
10.2
|
1.0
|
CG1
|
B:VAL107
|
5.0
|
13.2
|
1.0
|
CD2
|
B:LEU70
|
5.0
|
11.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 3svw
Go back to
Iron Binding Sites List in 3svw
Iron binding site 4 out
of 4 in the Crystal Structure of the P107V-Maug/Pre-Methylamine Dehydrogenase Complex
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 P107V-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe600
b:11.2
occ:1.00
|
FE
|
B:HEC600
|
0.0
|
11.2
|
1.0
|
OH
|
B:TYR294
|
1.9
|
7.8
|
1.0
|
ND
|
B:HEC600
|
2.0
|
8.4
|
1.0
|
NA
|
B:HEC600
|
2.0
|
10.1
|
1.0
|
NC
|
B:HEC600
|
2.0
|
10.2
|
1.0
|
NB
|
B:HEC600
|
2.1
|
10.7
|
1.0
|
NE2
|
B:HIS205
|
2.1
|
9.0
|
1.0
|
CZ
|
B:TYR294
|
2.9
|
11.0
|
1.0
|
CD2
|
B:HIS205
|
3.0
|
9.8
|
1.0
|
C1B
|
B:HEC600
|
3.0
|
9.4
|
1.0
|
C1D
|
B:HEC600
|
3.0
|
7.8
|
1.0
|
C4D
|
B:HEC600
|
3.0
|
8.9
|
1.0
|
C4A
|
B:HEC600
|
3.0
|
11.4
|
1.0
|
C4C
|
B:HEC600
|
3.0
|
8.8
|
1.0
|
C1C
|
B:HEC600
|
3.0
|
9.1
|
1.0
|
C4B
|
B:HEC600
|
3.1
|
9.3
|
1.0
|
C1A
|
B:HEC600
|
3.1
|
8.4
|
1.0
|
CE1
|
B:HIS205
|
3.1
|
9.1
|
1.0
|
CHB
|
B:HEC600
|
3.4
|
10.1
|
1.0
|
CHD
|
B:HEC600
|
3.4
|
4.8
|
1.0
|
CHC
|
B:HEC600
|
3.4
|
8.1
|
1.0
|
CHA
|
B:HEC600
|
3.4
|
6.8
|
1.0
|
CE1
|
B:TYR294
|
3.6
|
11.1
|
1.0
|
CE2
|
B:TYR294
|
3.8
|
10.3
|
1.0
|
CG
|
B:HIS205
|
4.1
|
10.8
|
1.0
|
ND1
|
B:HIS205
|
4.2
|
7.7
|
1.0
|
C2B
|
B:HEC600
|
4.3
|
11.0
|
1.0
|
C2D
|
B:HEC600
|
4.3
|
10.7
|
1.0
|
C3D
|
B:HEC600
|
4.3
|
9.3
|
1.0
|
C3B
|
B:HEC600
|
4.3
|
10.7
|
1.0
|
C3C
|
B:HEC600
|
4.3
|
8.2
|
1.0
|
C3A
|
B:HEC600
|
4.3
|
11.2
|
1.0
|
C2C
|
B:HEC600
|
4.3
|
10.2
|
1.0
|
C2A
|
B:HEC600
|
4.3
|
8.3
|
1.0
|
CD1
|
B:TYR294
|
4.9
|
10.2
|
1.0
|
CD2
|
B:TYR294
|
5.0
|
11.2
|
1.0
|
|
Reference:
M.Feng,
L.M.Jensen,
E.T.Yukl,
X.Wei,
A.Liu,
C.M.Wilmot,
V.L.Davidson.
Proline 107 Is A Major Determinant in Maintaining the Structure of the Distal Pocket and Reactivity of the High-Spin Heme of Maug. Biochemistry V. 51 1598 2012.
ISSN: ISSN 0006-2960
PubMed: 22299652
DOI: 10.1021/BI201882E
Page generated: Sun Aug 4 20:02:56 2024
|