Iron in PDB 4l1q: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex
Enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex
All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;
Protein crystallography data
The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 4l1q
was solved by
E.Y.Yukl,
C.M.Wilmot,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.35 /
1.92
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.530,
83.520,
107.780,
109.94,
91.54,
105.78
|
R / Rfree (%)
|
16 /
20.7
|
Other elements in 4l1q:
The structure of Crystal Structure of the E113Q-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 E113Q-Maug/Pre-Methylamine Dehydrogenase Complex
(pdb code 4l1q). 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 E113Q-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 4l1q:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4l1q
Go back to
Iron Binding Sites List in 4l1q
Iron binding site 1 out
of 4 in the Crystal Structure of the E113Q-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 E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:31.6
occ:1.00
|
FE
|
A:HEC402
|
0.0
|
31.6
|
1.0
|
ND
|
A:HEC402
|
2.0
|
31.4
|
1.0
|
NB
|
A:HEC402
|
2.0
|
29.6
|
1.0
|
NC
|
A:HEC402
|
2.1
|
29.1
|
1.0
|
NA
|
A:HEC402
|
2.1
|
30.9
|
1.0
|
NE2
|
A:HIS35
|
2.1
|
28.5
|
1.0
|
O
|
A:HOH757
|
2.9
|
43.4
|
1.0
|
C4D
|
A:HEC402
|
3.0
|
31.5
|
1.0
|
C4C
|
A:HEC402
|
3.0
|
31.0
|
1.0
|
C1D
|
A:HEC402
|
3.0
|
31.2
|
1.0
|
C1A
|
A:HEC402
|
3.0
|
29.2
|
1.0
|
C4A
|
A:HEC402
|
3.1
|
29.0
|
1.0
|
C1C
|
A:HEC402
|
3.1
|
28.9
|
1.0
|
C1B
|
A:HEC402
|
3.1
|
30.9
|
1.0
|
C4B
|
A:HEC402
|
3.1
|
31.5
|
1.0
|
CE1
|
A:HIS35
|
3.1
|
29.0
|
1.0
|
CD2
|
A:HIS35
|
3.1
|
30.1
|
1.0
|
CHD
|
A:HEC402
|
3.3
|
30.9
|
1.0
|
CHA
|
A:HEC402
|
3.4
|
31.0
|
1.0
|
CHB
|
A:HEC402
|
3.4
|
28.3
|
1.0
|
CHC
|
A:HEC402
|
3.5
|
28.5
|
1.0
|
NE2
|
A:GLN103
|
4.1
|
33.1
|
1.0
|
ND1
|
A:HIS35
|
4.2
|
29.1
|
1.0
|
CG
|
A:HIS35
|
4.3
|
29.3
|
1.0
|
CG
|
A:PRO107
|
4.3
|
36.5
|
1.0
|
C3D
|
A:HEC402
|
4.3
|
31.4
|
1.0
|
C2D
|
A:HEC402
|
4.3
|
31.7
|
1.0
|
C2B
|
A:HEC402
|
4.3
|
30.4
|
1.0
|
C2C
|
A:HEC402
|
4.4
|
28.6
|
1.0
|
C3C
|
A:HEC402
|
4.4
|
28.0
|
1.0
|
C3A
|
A:HEC402
|
4.4
|
28.9
|
1.0
|
C3B
|
A:HEC402
|
4.4
|
31.9
|
1.0
|
C2A
|
A:HEC402
|
4.4
|
29.3
|
1.0
|
CB
|
A:PRO107
|
5.0
|
34.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 4l1q
Go back to
Iron Binding Sites List in 4l1q
Iron binding site 2 out
of 4 in the Crystal Structure of the E113Q-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 E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe403
b:29.8
occ:1.00
|
FE
|
A:HEC403
|
0.0
|
29.8
|
1.0
|
OH
|
A:TYR294
|
1.9
|
31.2
|
1.0
|
ND
|
A:HEC403
|
2.0
|
28.3
|
1.0
|
NB
|
A:HEC403
|
2.0
|
27.4
|
1.0
|
NC
|
A:HEC403
|
2.0
|
29.2
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
27.1
|
1.0
|
NA
|
A:HEC403
|
2.1
|
27.9
|
1.0
|
CZ
|
A:TYR294
|
2.9
|
32.6
|
1.0
|
C1D
|
A:HEC403
|
3.0
|
32.6
|
1.0
|
C1B
|
A:HEC403
|
3.0
|
29.5
|
1.0
|
C4C
|
A:HEC403
|
3.0
|
29.4
|
1.0
|
C4B
|
A:HEC403
|
3.0
|
28.9
|
1.0
|
C4D
|
A:HEC403
|
3.0
|
30.2
|
1.0
|
C1C
|
A:HEC403
|
3.0
|
27.6
|
1.0
|
C4A
|
A:HEC403
|
3.1
|
30.2
|
1.0
|
CD2
|
A:HIS205
|
3.1
|
26.5
|
1.0
|
CE1
|
A:HIS205
|
3.1
|
25.0
|
1.0
|
C1A
|
A:HEC403
|
3.1
|
27.2
|
1.0
|
CHD
|
A:HEC403
|
3.3
|
27.9
|
1.0
|
CHB
|
A:HEC403
|
3.4
|
28.5
|
1.0
|
CHA
|
A:HEC403
|
3.4
|
27.8
|
1.0
|
CHC
|
A:HEC403
|
3.4
|
27.7
|
1.0
|
CE2
|
A:TYR294
|
3.6
|
31.3
|
1.0
|
CE1
|
A:TYR294
|
3.7
|
32.8
|
1.0
|
ND1
|
A:HIS205
|
4.2
|
26.9
|
1.0
|
CG
|
A:HIS205
|
4.2
|
27.5
|
1.0
|
C2D
|
A:HEC403
|
4.2
|
31.2
|
1.0
|
C3D
|
A:HEC403
|
4.3
|
29.3
|
1.0
|
C3B
|
A:HEC403
|
4.3
|
30.9
|
1.0
|
C3C
|
A:HEC403
|
4.3
|
27.6
|
1.0
|
C2B
|
A:HEC403
|
4.3
|
29.9
|
1.0
|
C2C
|
A:HEC403
|
4.3
|
26.7
|
1.0
|
C2A
|
A:HEC403
|
4.4
|
29.6
|
1.0
|
C3A
|
A:HEC403
|
4.4
|
30.1
|
1.0
|
CD2
|
A:TYR294
|
4.8
|
32.9
|
1.0
|
CD1
|
A:TYR294
|
4.9
|
33.5
|
1.0
|
CD1
|
A:ILE226
|
5.0
|
31.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 4l1q
Go back to
Iron Binding Sites List in 4l1q
Iron binding site 3 out
of 4 in the Crystal Structure of the E113Q-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 E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:23.6
occ:1.00
|
FE
|
B:HEC402
|
0.0
|
23.6
|
1.0
|
NC
|
B:HEC402
|
2.0
|
24.9
|
1.0
|
NA
|
B:HEC402
|
2.0
|
24.9
|
1.0
|
NB
|
B:HEC402
|
2.0
|
22.8
|
1.0
|
ND
|
B:HEC402
|
2.1
|
24.1
|
1.0
|
NE2
|
B:HIS35
|
2.1
|
23.1
|
1.0
|
C4A
|
B:HEC402
|
3.0
|
22.2
|
1.0
|
C4C
|
B:HEC402
|
3.0
|
24.9
|
1.0
|
C4D
|
B:HEC402
|
3.0
|
20.4
|
1.0
|
C4B
|
B:HEC402
|
3.0
|
24.4
|
1.0
|
C1C
|
B:HEC402
|
3.0
|
22.5
|
1.0
|
C1B
|
B:HEC402
|
3.0
|
23.2
|
1.0
|
C1D
|
B:HEC402
|
3.0
|
24.1
|
1.0
|
C1A
|
B:HEC402
|
3.1
|
19.8
|
1.0
|
CD2
|
B:HIS35
|
3.1
|
26.1
|
1.0
|
CE1
|
B:HIS35
|
3.1
|
24.2
|
1.0
|
CHD
|
B:HEC402
|
3.4
|
24.2
|
1.0
|
CHB
|
B:HEC402
|
3.4
|
22.7
|
1.0
|
CHA
|
B:HEC402
|
3.4
|
19.7
|
1.0
|
CHC
|
B:HEC402
|
3.4
|
23.5
|
1.0
|
O
|
B:HOH880
|
3.6
|
50.8
|
1.0
|
NE2
|
B:GLN103
|
4.1
|
23.9
|
1.0
|
ND1
|
B:HIS35
|
4.2
|
23.2
|
1.0
|
CG
|
B:HIS35
|
4.3
|
23.4
|
1.0
|
CG
|
B:PRO107
|
4.3
|
30.5
|
1.0
|
C2C
|
B:HEC402
|
4.3
|
25.1
|
1.0
|
C3A
|
B:HEC402
|
4.3
|
21.9
|
1.0
|
C3C
|
B:HEC402
|
4.3
|
26.4
|
1.0
|
C2A
|
B:HEC402
|
4.3
|
22.8
|
1.0
|
C3D
|
B:HEC402
|
4.3
|
22.6
|
1.0
|
C2B
|
B:HEC402
|
4.3
|
23.3
|
1.0
|
C2D
|
B:HEC402
|
4.3
|
21.4
|
1.0
|
C3B
|
B:HEC402
|
4.3
|
22.7
|
1.0
|
CB
|
B:PRO107
|
4.8
|
29.0
|
1.0
|
CG2
|
B:THR67
|
4.9
|
22.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 4l1q
Go back to
Iron Binding Sites List in 4l1q
Iron binding site 4 out
of 4 in the Crystal Structure of the E113Q-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 E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:18.2
occ:1.00
|
FE
|
B:HEC403
|
0.0
|
18.2
|
1.0
|
ND
|
B:HEC403
|
2.0
|
16.3
|
1.0
|
NB
|
B:HEC403
|
2.0
|
16.2
|
1.0
|
NC
|
B:HEC403
|
2.0
|
16.2
|
1.0
|
OH
|
B:TYR294
|
2.0
|
16.9
|
1.0
|
NA
|
B:HEC403
|
2.0
|
18.1
|
1.0
|
NE2
|
B:HIS205
|
2.1
|
15.8
|
1.0
|
CZ
|
B:TYR294
|
2.9
|
18.7
|
1.0
|
C1B
|
B:HEC403
|
2.9
|
18.3
|
1.0
|
C1D
|
B:HEC403
|
3.0
|
16.6
|
1.0
|
CD2
|
B:HIS205
|
3.0
|
16.3
|
1.0
|
C4C
|
B:HEC403
|
3.0
|
16.6
|
1.0
|
C4A
|
B:HEC403
|
3.0
|
18.0
|
1.0
|
C1C
|
B:HEC403
|
3.0
|
16.0
|
1.0
|
C4D
|
B:HEC403
|
3.0
|
16.0
|
1.0
|
C1A
|
B:HEC403
|
3.1
|
16.4
|
1.0
|
C4B
|
B:HEC403
|
3.1
|
15.4
|
1.0
|
CE1
|
B:HIS205
|
3.1
|
18.3
|
1.0
|
CHB
|
B:HEC403
|
3.3
|
18.0
|
1.0
|
CHD
|
B:HEC403
|
3.4
|
16.0
|
1.0
|
CHA
|
B:HEC403
|
3.4
|
16.0
|
1.0
|
CHC
|
B:HEC403
|
3.5
|
17.4
|
1.0
|
CE2
|
B:TYR294
|
3.6
|
19.2
|
1.0
|
CE1
|
B:TYR294
|
3.8
|
16.8
|
1.0
|
CG
|
B:HIS205
|
4.2
|
18.7
|
1.0
|
ND1
|
B:HIS205
|
4.2
|
18.0
|
1.0
|
C2D
|
B:HEC403
|
4.2
|
16.2
|
1.0
|
C2B
|
B:HEC403
|
4.2
|
18.5
|
1.0
|
C3B
|
B:HEC403
|
4.3
|
17.5
|
1.0
|
C3C
|
B:HEC403
|
4.3
|
16.7
|
1.0
|
C3D
|
B:HEC403
|
4.3
|
17.2
|
1.0
|
C2C
|
B:HEC403
|
4.3
|
18.9
|
1.0
|
C2A
|
B:HEC403
|
4.3
|
18.3
|
1.0
|
C3A
|
B:HEC403
|
4.3
|
17.2
|
1.0
|
CD2
|
B:TYR294
|
4.9
|
17.4
|
1.0
|
CD1
|
B:TYR294
|
4.9
|
17.6
|
1.0
|
|
Reference:
N.Abu Tarboush,
E.T.Yukl,
S.Shin,
M.Feng,
C.M.Wilmot,
V.L.Davidson.
Carboxyl Group of GLU113 Is Required For Stabilization of the Diferrous and Bis-Fe(IV) States of Maug. Biochemistry V. 52 6358 2013.
ISSN: ISSN 0006-2960
PubMed: 23952537
DOI: 10.1021/BI400905S
Page generated: Mon Aug 5 06:01:25 2024
|