Iron in PDB 4l3g: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days
Enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days
All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days:
1.4.99.3;
Protein crystallography data
The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days, PDB code: 4l3g
was solved by
E.T.Yukl,
C.M.Wilmot,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.62 /
2.05
|
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 (%)
|
15.8 /
21
|
Other elements in 4l3g:
The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days 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 Aged 120 Days
(pdb code 4l3g). 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 Aged 120 Days, PDB code: 4l3g:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4l3g
Go back to
Iron Binding Sites List in 4l3g
Iron binding site 1 out
of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days
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 Aged 120 Days within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:34.8
occ:1.00
|
FE
|
A:HEC402
|
0.0
|
34.8
|
1.0
|
NB
|
A:HEC402
|
2.0
|
32.6
|
1.0
|
ND
|
A:HEC402
|
2.1
|
33.4
|
1.0
|
NA
|
A:HEC402
|
2.1
|
33.1
|
1.0
|
NC
|
A:HEC402
|
2.1
|
36.4
|
1.0
|
NE2
|
A:HIS35
|
2.2
|
36.9
|
1.0
|
OD1
|
A:HYP107
|
2.9
|
44.8
|
1.0
|
C4B
|
A:HEC402
|
3.0
|
35.0
|
1.0
|
C4D
|
A:HEC402
|
3.0
|
33.3
|
1.0
|
C1A
|
A:HEC402
|
3.0
|
30.7
|
1.0
|
C1B
|
A:HEC402
|
3.0
|
33.7
|
1.0
|
C4A
|
A:HEC402
|
3.1
|
34.6
|
1.0
|
C1C
|
A:HEC402
|
3.1
|
36.2
|
1.0
|
C1D
|
A:HEC402
|
3.1
|
34.1
|
1.0
|
C4C
|
A:HEC402
|
3.1
|
36.9
|
1.0
|
CD2
|
A:HIS35
|
3.2
|
37.7
|
1.0
|
CE1
|
A:HIS35
|
3.2
|
37.7
|
1.0
|
O
|
A:HOH657
|
3.2
|
38.4
|
0.5
|
CHA
|
A:HEC402
|
3.4
|
32.1
|
1.0
|
CHC
|
A:HEC402
|
3.4
|
34.9
|
1.0
|
CHD
|
A:HEC402
|
3.4
|
37.4
|
1.0
|
CHB
|
A:HEC402
|
3.4
|
31.5
|
1.0
|
NE2
|
A:GLN103
|
4.1
|
35.1
|
1.0
|
CG
|
A:HYP107
|
4.1
|
42.6
|
1.0
|
C3D
|
A:HEC402
|
4.3
|
32.8
|
1.0
|
ND1
|
A:HIS35
|
4.3
|
34.9
|
1.0
|
C3B
|
A:HEC402
|
4.3
|
32.2
|
1.0
|
C2D
|
A:HEC402
|
4.3
|
30.6
|
1.0
|
C2B
|
A:HEC402
|
4.3
|
32.1
|
1.0
|
CG
|
A:HIS35
|
4.3
|
35.0
|
1.0
|
C2C
|
A:HEC402
|
4.4
|
37.7
|
1.0
|
C2A
|
A:HEC402
|
4.4
|
34.3
|
1.0
|
C3A
|
A:HEC402
|
4.4
|
34.9
|
1.0
|
C3C
|
A:HEC402
|
4.4
|
39.1
|
1.0
|
CB
|
A:HYP107
|
4.7
|
43.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 4l3g
Go back to
Iron Binding Sites List in 4l3g
Iron binding site 2 out
of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days
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 Aged 120 Days within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe403
b:32.8
occ:1.00
|
FE
|
A:HEC403
|
0.0
|
32.8
|
1.0
|
OH
|
A:TYR294
|
1.9
|
28.3
|
1.0
|
ND
|
A:HEC403
|
2.0
|
31.1
|
1.0
|
NB
|
A:HEC403
|
2.0
|
32.7
|
1.0
|
NA
|
A:HEC403
|
2.1
|
32.5
|
1.0
|
NC
|
A:HEC403
|
2.1
|
32.5
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
30.3
|
1.0
|
CZ
|
A:TYR294
|
2.8
|
29.8
|
1.0
|
C1B
|
A:HEC403
|
3.0
|
32.0
|
1.0
|
C4B
|
A:HEC403
|
3.0
|
31.3
|
1.0
|
C1D
|
A:HEC403
|
3.0
|
32.8
|
1.0
|
C4D
|
A:HEC403
|
3.0
|
32.6
|
1.0
|
C1C
|
A:HEC403
|
3.0
|
31.2
|
1.0
|
C4A
|
A:HEC403
|
3.1
|
33.1
|
1.0
|
C1A
|
A:HEC403
|
3.1
|
33.0
|
1.0
|
C4C
|
A:HEC403
|
3.1
|
32.2
|
1.0
|
CD2
|
A:HIS205
|
3.1
|
29.7
|
1.0
|
CE1
|
A:HIS205
|
3.1
|
29.2
|
1.0
|
CHB
|
A:HEC403
|
3.4
|
32.0
|
1.0
|
CHC
|
A:HEC403
|
3.4
|
30.7
|
1.0
|
CHD
|
A:HEC403
|
3.4
|
30.7
|
1.0
|
CHA
|
A:HEC403
|
3.4
|
31.2
|
1.0
|
CE2
|
A:TYR294
|
3.6
|
29.6
|
1.0
|
CE1
|
A:TYR294
|
3.7
|
29.1
|
1.0
|
ND1
|
A:HIS205
|
4.2
|
30.3
|
1.0
|
CG
|
A:HIS205
|
4.2
|
28.8
|
1.0
|
C2B
|
A:HEC403
|
4.3
|
34.1
|
1.0
|
C3B
|
A:HEC403
|
4.3
|
34.2
|
1.0
|
C2D
|
A:HEC403
|
4.3
|
32.1
|
1.0
|
C3D
|
A:HEC403
|
4.3
|
31.0
|
1.0
|
C2C
|
A:HEC403
|
4.3
|
32.5
|
1.0
|
C3A
|
A:HEC403
|
4.4
|
34.0
|
1.0
|
C2A
|
A:HEC403
|
4.4
|
32.0
|
1.0
|
C3C
|
A:HEC403
|
4.4
|
34.0
|
1.0
|
CD2
|
A:TYR294
|
4.8
|
30.5
|
1.0
|
CD1
|
A:TYR294
|
4.9
|
30.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 4l3g
Go back to
Iron Binding Sites List in 4l3g
Iron binding site 3 out
of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days
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 Aged 120 Days within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:29.9
occ:1.00
|
FE
|
B:HEC402
|
0.0
|
29.9
|
1.0
|
NA
|
B:HEC402
|
2.0
|
32.0
|
1.0
|
ND
|
B:HEC402
|
2.0
|
33.0
|
1.0
|
NC
|
B:HEC402
|
2.1
|
33.7
|
1.0
|
NB
|
B:HEC402
|
2.1
|
32.7
|
1.0
|
NE2
|
B:HIS35
|
2.2
|
28.9
|
1.0
|
OD1
|
B:HYP107
|
2.9
|
48.2
|
1.0
|
C1A
|
B:HEC402
|
3.0
|
30.6
|
1.0
|
C4D
|
B:HEC402
|
3.0
|
30.6
|
1.0
|
C1C
|
B:HEC402
|
3.0
|
33.3
|
1.0
|
C1D
|
B:HEC402
|
3.0
|
34.9
|
1.0
|
C4C
|
B:HEC402
|
3.1
|
33.1
|
1.0
|
C4B
|
B:HEC402
|
3.1
|
32.0
|
1.0
|
C4A
|
B:HEC402
|
3.1
|
30.3
|
1.0
|
C1B
|
B:HEC402
|
3.1
|
32.2
|
1.0
|
CE1
|
B:HIS35
|
3.1
|
30.4
|
1.0
|
CD2
|
B:HIS35
|
3.2
|
29.2
|
1.0
|
CHA
|
B:HEC402
|
3.4
|
29.1
|
1.0
|
CHC
|
B:HEC402
|
3.4
|
32.9
|
1.0
|
CHD
|
B:HEC402
|
3.4
|
32.0
|
1.0
|
CHB
|
B:HEC402
|
3.5
|
30.3
|
1.0
|
O
|
B:HOH736
|
3.6
|
31.1
|
0.5
|
CG
|
B:HYP107
|
4.2
|
39.2
|
1.0
|
NE2
|
B:GLN103
|
4.2
|
35.6
|
1.0
|
ND1
|
B:HIS35
|
4.3
|
30.7
|
1.0
|
C2C
|
B:HEC402
|
4.3
|
33.3
|
1.0
|
C3D
|
B:HEC402
|
4.3
|
32.9
|
1.0
|
CG
|
B:HIS35
|
4.3
|
30.0
|
1.0
|
C2D
|
B:HEC402
|
4.3
|
33.0
|
1.0
|
C3C
|
B:HEC402
|
4.3
|
32.0
|
1.0
|
C2A
|
B:HEC402
|
4.3
|
31.1
|
1.0
|
C3A
|
B:HEC402
|
4.4
|
30.3
|
1.0
|
C3B
|
B:HEC402
|
4.4
|
30.6
|
1.0
|
C2B
|
B:HEC402
|
4.4
|
31.0
|
1.0
|
CB
|
B:HYP107
|
4.8
|
37.8
|
1.0
|
CD2
|
B:LEU70
|
5.0
|
29.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 4l3g
Go back to
Iron Binding Sites List in 4l3g
Iron binding site 4 out
of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days
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 Aged 120 Days within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:24.6
occ:1.00
|
FE
|
B:HEC403
|
0.0
|
24.6
|
1.0
|
OH
|
B:TYR294
|
1.8
|
22.0
|
1.0
|
NE2
|
B:HIS205
|
2.0
|
23.4
|
1.0
|
ND
|
B:HEC403
|
2.0
|
25.7
|
1.0
|
NC
|
B:HEC403
|
2.1
|
26.2
|
1.0
|
NB
|
B:HEC403
|
2.1
|
27.2
|
1.0
|
NA
|
B:HEC403
|
2.1
|
27.8
|
1.0
|
CZ
|
B:TYR294
|
2.8
|
22.9
|
1.0
|
C1D
|
B:HEC403
|
3.0
|
25.4
|
1.0
|
CE1
|
B:HIS205
|
3.0
|
21.0
|
1.0
|
C1B
|
B:HEC403
|
3.0
|
26.2
|
1.0
|
C4A
|
B:HEC403
|
3.0
|
26.9
|
1.0
|
C4C
|
B:HEC403
|
3.0
|
25.3
|
1.0
|
C4D
|
B:HEC403
|
3.1
|
24.3
|
1.0
|
CD2
|
B:HIS205
|
3.1
|
21.4
|
1.0
|
C4B
|
B:HEC403
|
3.1
|
24.2
|
1.0
|
C1C
|
B:HEC403
|
3.1
|
26.3
|
1.0
|
C1A
|
B:HEC403
|
3.1
|
26.8
|
1.0
|
CHD
|
B:HEC403
|
3.3
|
24.7
|
1.0
|
CHB
|
B:HEC403
|
3.4
|
25.6
|
1.0
|
CHA
|
B:HEC403
|
3.5
|
24.2
|
1.0
|
CHC
|
B:HEC403
|
3.5
|
23.9
|
1.0
|
CE2
|
B:TYR294
|
3.6
|
24.4
|
1.0
|
CE1
|
B:TYR294
|
3.7
|
23.1
|
1.0
|
ND1
|
B:HIS205
|
4.1
|
21.8
|
1.0
|
CG
|
B:HIS205
|
4.2
|
21.8
|
1.0
|
C2D
|
B:HEC403
|
4.3
|
25.2
|
1.0
|
C2B
|
B:HEC403
|
4.3
|
26.1
|
1.0
|
C3D
|
B:HEC403
|
4.3
|
23.6
|
1.0
|
C3B
|
B:HEC403
|
4.3
|
24.6
|
1.0
|
C3A
|
B:HEC403
|
4.3
|
28.2
|
1.0
|
C2A
|
B:HEC403
|
4.4
|
25.2
|
1.0
|
C3C
|
B:HEC403
|
4.4
|
24.9
|
1.0
|
C2C
|
B:HEC403
|
4.4
|
25.8
|
1.0
|
CD2
|
B:TYR294
|
4.8
|
24.0
|
1.0
|
CD1
|
B:TYR294
|
4.9
|
25.4
|
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 06:04:23 2024
|