Iron in PDB 3sjl: Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex
Enzymatic activity of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex
All present enzymatic activity of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;
Protein crystallography data
The structure of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3sjl
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)
|
29.39 /
1.63
|
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 (%)
|
14.2 /
18
|
Other elements in 3sjl:
The structure of Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex
(pdb code 3sjl). 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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3sjl:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3sjl
Go back to
Iron Binding Sites List in 3sjl
Iron binding site 1 out
of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:15.6
occ:1.00
|
FE
|
A:HEC500
|
0.0
|
15.6
|
1.0
|
NC
|
A:HEC500
|
2.0
|
13.7
|
1.0
|
NB
|
A:HEC500
|
2.0
|
15.1
|
1.0
|
ND
|
A:HEC500
|
2.0
|
14.7
|
1.0
|
NA
|
A:HEC500
|
2.0
|
14.6
|
1.0
|
OE2
|
A:GLU113
|
2.1
|
16.2
|
1.0
|
NE2
|
A:HIS35
|
2.1
|
17.7
|
1.0
|
C4B
|
A:HEC500
|
3.0
|
16.5
|
1.0
|
C4D
|
A:HEC500
|
3.0
|
13.5
|
1.0
|
C1C
|
A:HEC500
|
3.0
|
14.1
|
1.0
|
C1D
|
A:HEC500
|
3.0
|
16.1
|
1.0
|
C4C
|
A:HEC500
|
3.0
|
14.9
|
1.0
|
C1B
|
A:HEC500
|
3.0
|
14.3
|
1.0
|
CD2
|
A:HIS35
|
3.1
|
17.7
|
1.0
|
C4A
|
A:HEC500
|
3.1
|
13.2
|
1.0
|
C1A
|
A:HEC500
|
3.1
|
14.1
|
1.0
|
CE1
|
A:HIS35
|
3.1
|
17.4
|
1.0
|
CD
|
A:GLU113
|
3.2
|
14.9
|
1.0
|
CHD
|
A:HEC500
|
3.4
|
14.7
|
1.0
|
CHA
|
A:HEC500
|
3.4
|
15.0
|
1.0
|
CHC
|
A:HEC500
|
3.5
|
14.8
|
1.0
|
CHB
|
A:HEC500
|
3.5
|
14.7
|
1.0
|
CG
|
A:GLU113
|
3.7
|
15.1
|
1.0
|
ND1
|
A:HIS35
|
4.2
|
16.1
|
1.0
|
CG
|
A:HIS35
|
4.2
|
17.8
|
1.0
|
NE2
|
A:GLN103
|
4.2
|
15.5
|
1.0
|
OE1
|
A:GLU113
|
4.2
|
15.5
|
1.0
|
C2B
|
A:HEC500
|
4.3
|
14.6
|
1.0
|
OG
|
A:SER107
|
4.3
|
13.1
|
1.0
|
C3B
|
A:HEC500
|
4.3
|
14.8
|
1.0
|
C3D
|
A:HEC500
|
4.3
|
14.7
|
1.0
|
C2D
|
A:HEC500
|
4.3
|
15.9
|
1.0
|
C3C
|
A:HEC500
|
4.3
|
14.4
|
1.0
|
C2A
|
A:HEC500
|
4.3
|
15.5
|
1.0
|
C2C
|
A:HEC500
|
4.3
|
13.8
|
1.0
|
C3A
|
A:HEC500
|
4.4
|
15.2
|
1.0
|
CB
|
A:GLU113
|
4.6
|
18.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 3sjl
Go back to
Iron Binding Sites List in 3sjl
Iron binding site 2 out
of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe600
b:17.1
occ:1.00
|
FE
|
A:HEC600
|
0.0
|
17.1
|
1.0
|
NC
|
A:HEC600
|
1.9
|
15.6
|
1.0
|
OH
|
A:TYR294
|
2.0
|
15.1
|
1.0
|
NA
|
A:HEC600
|
2.0
|
13.3
|
1.0
|
NB
|
A:HEC600
|
2.0
|
16.8
|
1.0
|
ND
|
A:HEC600
|
2.0
|
15.5
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
14.3
|
1.0
|
CZ
|
A:TYR294
|
3.0
|
15.6
|
1.0
|
C1C
|
A:HEC600
|
3.0
|
17.8
|
1.0
|
C4C
|
A:HEC600
|
3.0
|
14.1
|
1.0
|
C1A
|
A:HEC600
|
3.0
|
17.1
|
1.0
|
C1B
|
A:HEC600
|
3.0
|
16.5
|
1.0
|
C1D
|
A:HEC600
|
3.0
|
14.1
|
1.0
|
CE1
|
A:HIS205
|
3.0
|
15.1
|
1.0
|
CD2
|
A:HIS205
|
3.0
|
15.2
|
1.0
|
C4D
|
A:HEC600
|
3.0
|
13.7
|
1.0
|
C4A
|
A:HEC600
|
3.1
|
17.2
|
1.0
|
C4B
|
A:HEC600
|
3.1
|
15.7
|
1.0
|
CHB
|
A:HEC600
|
3.4
|
16.5
|
1.0
|
CHD
|
A:HEC600
|
3.4
|
14.3
|
1.0
|
CHC
|
A:HEC600
|
3.4
|
15.3
|
1.0
|
CHA
|
A:HEC600
|
3.5
|
13.4
|
1.0
|
CE1
|
A:TYR294
|
3.7
|
15.2
|
1.0
|
CE2
|
A:TYR294
|
3.7
|
16.9
|
1.0
|
ND1
|
A:HIS205
|
4.1
|
15.8
|
1.0
|
CG
|
A:HIS205
|
4.2
|
15.9
|
1.0
|
C2C
|
A:HEC600
|
4.2
|
16.8
|
1.0
|
C2A
|
A:HEC600
|
4.3
|
15.4
|
1.0
|
C3C
|
A:HEC600
|
4.3
|
17.0
|
1.0
|
C2B
|
A:HEC600
|
4.3
|
17.8
|
1.0
|
C3A
|
A:HEC600
|
4.3
|
17.1
|
1.0
|
C3D
|
A:HEC600
|
4.3
|
14.0
|
1.0
|
C2D
|
A:HEC600
|
4.3
|
13.8
|
1.0
|
C3B
|
A:HEC600
|
4.4
|
16.8
|
1.0
|
CD1
|
A:TYR294
|
4.9
|
16.6
|
1.0
|
CD1
|
A:ILE226
|
5.0
|
17.5
|
1.0
|
CD2
|
A:TYR294
|
5.0
|
17.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 3sjl
Go back to
Iron Binding Sites List in 3sjl
Iron binding site 3 out
of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:16.6
occ:1.00
|
FE
|
B:HEC500
|
0.0
|
16.6
|
1.0
|
ND
|
B:HEC500
|
2.0
|
15.5
|
1.0
|
NE2
|
B:HIS35
|
2.0
|
14.3
|
1.0
|
NA
|
B:HEC500
|
2.0
|
15.3
|
1.0
|
NB
|
B:HEC500
|
2.0
|
14.8
|
1.0
|
NC
|
B:HEC500
|
2.1
|
16.1
|
1.0
|
OE2
|
B:GLU113
|
2.1
|
17.3
|
1.0
|
C4D
|
B:HEC500
|
3.0
|
13.6
|
1.0
|
C4B
|
B:HEC500
|
3.0
|
15.5
|
1.0
|
CD2
|
B:HIS35
|
3.0
|
16.8
|
1.0
|
C1B
|
B:HEC500
|
3.0
|
16.4
|
1.0
|
CE1
|
B:HIS35
|
3.0
|
14.8
|
1.0
|
C4C
|
B:HEC500
|
3.1
|
16.4
|
1.0
|
C4A
|
B:HEC500
|
3.1
|
14.1
|
1.0
|
C1A
|
B:HEC500
|
3.1
|
16.4
|
1.0
|
C1D
|
B:HEC500
|
3.1
|
16.3
|
1.0
|
C1C
|
B:HEC500
|
3.1
|
16.8
|
1.0
|
CD
|
B:GLU113
|
3.2
|
17.6
|
1.0
|
CHA
|
B:HEC500
|
3.4
|
12.9
|
1.0
|
CHD
|
B:HEC500
|
3.5
|
16.5
|
1.0
|
CHB
|
B:HEC500
|
3.5
|
13.3
|
1.0
|
CHC
|
B:HEC500
|
3.5
|
16.6
|
1.0
|
CG
|
B:GLU113
|
3.7
|
18.0
|
1.0
|
ND1
|
B:HIS35
|
4.2
|
15.3
|
1.0
|
CG
|
B:HIS35
|
4.2
|
14.2
|
1.0
|
OG
|
B:SER107
|
4.2
|
18.0
|
1.0
|
NE2
|
B:GLN103
|
4.2
|
16.6
|
1.0
|
OE1
|
B:GLU113
|
4.2
|
16.9
|
1.0
|
C3B
|
B:HEC500
|
4.3
|
16.5
|
1.0
|
C3D
|
B:HEC500
|
4.3
|
15.8
|
1.0
|
C2B
|
B:HEC500
|
4.3
|
16.3
|
1.0
|
C2D
|
B:HEC500
|
4.3
|
14.9
|
1.0
|
C3A
|
B:HEC500
|
4.3
|
14.9
|
1.0
|
C2C
|
B:HEC500
|
4.3
|
20.3
|
1.0
|
C2A
|
B:HEC500
|
4.3
|
14.8
|
1.0
|
C3C
|
B:HEC500
|
4.4
|
19.2
|
1.0
|
CB
|
B:GLU113
|
4.6
|
15.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 3sjl
Go back to
Iron Binding Sites List in 3sjl
Iron binding site 4 out
of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe600
b:14.1
occ:1.00
|
FE
|
B:HEC600
|
0.0
|
14.1
|
1.0
|
OH
|
B:TYR294
|
1.9
|
12.5
|
1.0
|
NA
|
B:HEC600
|
2.0
|
13.1
|
1.0
|
ND
|
B:HEC600
|
2.0
|
12.7
|
1.0
|
NC
|
B:HEC600
|
2.0
|
11.1
|
1.0
|
NB
|
B:HEC600
|
2.0
|
14.1
|
1.0
|
NE2
|
B:HIS205
|
2.1
|
14.0
|
1.0
|
CZ
|
B:TYR294
|
2.9
|
13.9
|
1.0
|
C4C
|
B:HEC600
|
3.0
|
11.5
|
1.0
|
C4A
|
B:HEC600
|
3.0
|
13.5
|
1.0
|
C1A
|
B:HEC600
|
3.0
|
12.3
|
1.0
|
C1D
|
B:HEC600
|
3.0
|
12.3
|
1.0
|
CD2
|
B:HIS205
|
3.0
|
13.0
|
1.0
|
C4D
|
B:HEC600
|
3.0
|
13.1
|
1.0
|
C4B
|
B:HEC600
|
3.0
|
14.3
|
1.0
|
C1B
|
B:HEC600
|
3.0
|
14.3
|
1.0
|
C1C
|
B:HEC600
|
3.0
|
12.3
|
1.0
|
CE1
|
B:HIS205
|
3.1
|
14.2
|
1.0
|
CHD
|
B:HEC600
|
3.4
|
13.7
|
1.0
|
CHA
|
B:HEC600
|
3.4
|
9.7
|
1.0
|
CHB
|
B:HEC600
|
3.4
|
12.8
|
1.0
|
CHC
|
B:HEC600
|
3.5
|
12.5
|
1.0
|
CE1
|
B:TYR294
|
3.6
|
14.8
|
1.0
|
CE2
|
B:TYR294
|
3.8
|
12.2
|
1.0
|
CG
|
B:HIS205
|
4.2
|
13.0
|
1.0
|
ND1
|
B:HIS205
|
4.2
|
13.7
|
1.0
|
C3A
|
B:HEC600
|
4.3
|
14.3
|
1.0
|
C3D
|
B:HEC600
|
4.3
|
12.3
|
1.0
|
C3C
|
B:HEC600
|
4.3
|
11.8
|
1.0
|
C2D
|
B:HEC600
|
4.3
|
14.2
|
1.0
|
C2A
|
B:HEC600
|
4.3
|
16.4
|
1.0
|
C2C
|
B:HEC600
|
4.3
|
13.1
|
1.0
|
C3B
|
B:HEC600
|
4.3
|
13.7
|
1.0
|
C2B
|
B:HEC600
|
4.3
|
14.8
|
1.0
|
CD1
|
B:TYR294
|
4.9
|
12.8
|
1.0
|
CD1
|
B:ILE226
|
4.9
|
15.0
|
1.0
|
CD2
|
B:TYR294
|
5.0
|
12.4
|
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 19:58:31 2024
|