Iron in PDB 3orv: Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex
Enzymatic activity of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex
All present enzymatic activity of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;
Protein crystallography data
The structure of Crystal Structure of the Y294H-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3orv
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)
|
44.49 /
1.91
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.527,
83.524,
107.782,
109.94,
91.54,
105.78
|
R / Rfree (%)
|
13.9 /
18.7
|
Other elements in 3orv:
The structure of Crystal Structure of the Y294H-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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex
(pdb code 3orv). 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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3orv:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3orv
Go back to
Iron Binding Sites List in 3orv
Iron binding site 1 out
of 4 in the Crystal Structure of the Y294H-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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:21.9
occ:1.00
|
FE
|
A:HEC500
|
0.0
|
21.9
|
1.0
|
NA
|
A:HEC500
|
2.1
|
23.6
|
1.0
|
ND
|
A:HEC500
|
2.1
|
23.2
|
1.0
|
NC
|
A:HEC500
|
2.1
|
22.1
|
1.0
|
NB
|
A:HEC500
|
2.1
|
25.4
|
1.0
|
NE2
|
A:HIS35
|
2.1
|
21.0
|
1.0
|
C1A
|
A:HEC500
|
3.0
|
22.7
|
1.0
|
C1C
|
A:HEC500
|
3.1
|
22.8
|
1.0
|
CD2
|
A:HIS35
|
3.1
|
24.9
|
1.0
|
C4D
|
A:HEC500
|
3.1
|
22.2
|
1.0
|
C4B
|
A:HEC500
|
3.1
|
23.2
|
1.0
|
C1D
|
A:HEC500
|
3.1
|
21.1
|
1.0
|
C4C
|
A:HEC500
|
3.1
|
21.9
|
1.0
|
C4A
|
A:HEC500
|
3.1
|
25.1
|
1.0
|
C1B
|
A:HEC500
|
3.1
|
24.1
|
1.0
|
CE1
|
A:HIS35
|
3.2
|
20.4
|
1.0
|
CHC
|
A:HEC500
|
3.4
|
20.0
|
1.0
|
CHA
|
A:HEC500
|
3.4
|
21.3
|
1.0
|
CHD
|
A:HEC500
|
3.5
|
21.8
|
1.0
|
CHB
|
A:HEC500
|
3.5
|
22.3
|
1.0
|
O
|
A:HOH436
|
3.8
|
32.2
|
1.0
|
NE2
|
A:GLN103
|
4.2
|
21.8
|
1.0
|
CG
|
A:HIS35
|
4.3
|
21.9
|
1.0
|
ND1
|
A:HIS35
|
4.3
|
19.7
|
1.0
|
CG
|
A:PRO107
|
4.3
|
25.0
|
1.0
|
C2A
|
A:HEC500
|
4.3
|
20.7
|
1.0
|
C2C
|
A:HEC500
|
4.4
|
20.6
|
1.0
|
C2D
|
A:HEC500
|
4.4
|
22.4
|
1.0
|
C3D
|
A:HEC500
|
4.4
|
22.3
|
1.0
|
C3C
|
A:HEC500
|
4.4
|
23.4
|
1.0
|
C3A
|
A:HEC500
|
4.4
|
24.3
|
1.0
|
C3B
|
A:HEC500
|
4.4
|
20.1
|
1.0
|
C2B
|
A:HEC500
|
4.4
|
25.4
|
1.0
|
CB
|
A:PRO107
|
4.9
|
25.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 3orv
Go back to
Iron Binding Sites List in 3orv
Iron binding site 2 out
of 4 in the Crystal Structure of the Y294H-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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe600
b:21.5
occ:1.00
|
FE
|
A:HEC600
|
0.0
|
21.5
|
1.0
|
NB
|
A:HEC600
|
2.0
|
20.9
|
1.0
|
NC
|
A:HEC600
|
2.1
|
23.0
|
1.0
|
ND
|
A:HEC600
|
2.1
|
24.4
|
1.0
|
NE2
|
A:HIS205
|
2.1
|
21.7
|
1.0
|
NA
|
A:HEC600
|
2.1
|
23.3
|
1.0
|
NE2
|
A:HIS294
|
2.1
|
24.1
|
1.0
|
C4B
|
A:HEC600
|
3.0
|
20.9
|
1.0
|
C1B
|
A:HEC600
|
3.0
|
22.1
|
1.0
|
C1C
|
A:HEC600
|
3.0
|
23.2
|
1.0
|
C4C
|
A:HEC600
|
3.0
|
19.1
|
1.0
|
CD2
|
A:HIS205
|
3.0
|
19.1
|
1.0
|
CE1
|
A:HIS294
|
3.1
|
20.8
|
1.0
|
C1D
|
A:HEC600
|
3.1
|
21.0
|
1.0
|
C4A
|
A:HEC600
|
3.1
|
21.1
|
1.0
|
C4D
|
A:HEC600
|
3.1
|
20.8
|
1.0
|
CD2
|
A:HIS294
|
3.1
|
24.1
|
1.0
|
C1A
|
A:HEC600
|
3.1
|
22.5
|
1.0
|
CE1
|
A:HIS205
|
3.1
|
20.8
|
1.0
|
CHC
|
A:HEC600
|
3.4
|
20.8
|
1.0
|
CHB
|
A:HEC600
|
3.4
|
21.3
|
1.0
|
CHD
|
A:HEC600
|
3.4
|
18.4
|
1.0
|
CHA
|
A:HEC600
|
3.5
|
18.9
|
1.0
|
ND1
|
A:HIS294
|
4.1
|
21.0
|
1.0
|
CG
|
A:HIS294
|
4.2
|
23.7
|
1.0
|
CG
|
A:HIS205
|
4.2
|
23.3
|
1.0
|
ND1
|
A:HIS205
|
4.2
|
24.9
|
1.0
|
C3B
|
A:HEC600
|
4.3
|
19.1
|
1.0
|
C2B
|
A:HEC600
|
4.3
|
21.0
|
1.0
|
C2C
|
A:HEC600
|
4.3
|
20.5
|
1.0
|
C3C
|
A:HEC600
|
4.3
|
20.3
|
1.0
|
C3D
|
A:HEC600
|
4.4
|
21.1
|
1.0
|
C2D
|
A:HEC600
|
4.4
|
20.3
|
1.0
|
C3A
|
A:HEC600
|
4.4
|
23.9
|
1.0
|
C2A
|
A:HEC600
|
4.4
|
21.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 3orv
Go back to
Iron Binding Sites List in 3orv
Iron binding site 3 out
of 4 in the Crystal Structure of the Y294H-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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:19.5
occ:1.00
|
FE
|
B:HEC500
|
0.0
|
19.5
|
1.0
|
NB
|
B:HEC500
|
2.0
|
18.5
|
1.0
|
NE2
|
B:HIS35
|
2.0
|
17.0
|
1.0
|
ND
|
B:HEC500
|
2.0
|
21.2
|
1.0
|
NC
|
B:HEC500
|
2.1
|
19.2
|
1.0
|
NA
|
B:HEC500
|
2.1
|
19.6
|
1.0
|
CE1
|
B:HIS35
|
3.0
|
17.7
|
1.0
|
C1B
|
B:HEC500
|
3.0
|
18.9
|
1.0
|
C1C
|
B:HEC500
|
3.0
|
16.3
|
1.0
|
C4C
|
B:HEC500
|
3.0
|
21.7
|
1.0
|
C1D
|
B:HEC500
|
3.1
|
20.6
|
1.0
|
CD2
|
B:HIS35
|
3.1
|
16.8
|
1.0
|
C1A
|
B:HEC500
|
3.1
|
19.3
|
1.0
|
C4B
|
B:HEC500
|
3.1
|
19.5
|
1.0
|
C4D
|
B:HEC500
|
3.1
|
20.2
|
1.0
|
C4A
|
B:HEC500
|
3.1
|
20.1
|
1.0
|
CHB
|
B:HEC500
|
3.4
|
16.0
|
1.0
|
CHD
|
B:HEC500
|
3.4
|
18.3
|
1.0
|
CHC
|
B:HEC500
|
3.4
|
17.7
|
1.0
|
CHA
|
B:HEC500
|
3.5
|
16.7
|
1.0
|
O
|
B:HOH406
|
3.7
|
29.5
|
1.0
|
NE2
|
B:GLN103
|
4.1
|
18.8
|
1.0
|
ND1
|
B:HIS35
|
4.1
|
19.9
|
1.0
|
CG
|
B:HIS35
|
4.2
|
18.4
|
1.0
|
CG
|
B:PRO107
|
4.3
|
25.5
|
1.0
|
C2B
|
B:HEC500
|
4.3
|
14.8
|
1.0
|
C2C
|
B:HEC500
|
4.3
|
18.1
|
1.0
|
C3B
|
B:HEC500
|
4.3
|
18.2
|
1.0
|
C3C
|
B:HEC500
|
4.3
|
18.7
|
1.0
|
C2D
|
B:HEC500
|
4.4
|
22.2
|
1.0
|
C2A
|
B:HEC500
|
4.4
|
19.2
|
1.0
|
C3A
|
B:HEC500
|
4.4
|
18.9
|
1.0
|
C3D
|
B:HEC500
|
4.4
|
19.6
|
1.0
|
CB
|
B:PRO107
|
4.9
|
24.6
|
1.0
|
CD2
|
B:LEU70
|
5.0
|
19.6
|
1.0
|
|
Iron binding site 4 out
of 4 in 3orv
Go back to
Iron Binding Sites List in 3orv
Iron binding site 4 out
of 4 in the Crystal Structure of the Y294H-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 Y294H-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe600
b:17.9
occ:1.00
|
FE
|
B:HEC600
|
0.0
|
17.9
|
1.0
|
NE2
|
B:HIS205
|
2.0
|
18.4
|
1.0
|
ND
|
B:HEC600
|
2.1
|
19.3
|
1.0
|
NC
|
B:HEC600
|
2.1
|
18.7
|
1.0
|
NB
|
B:HEC600
|
2.1
|
18.7
|
1.0
|
NA
|
B:HEC600
|
2.1
|
17.9
|
1.0
|
NE2
|
B:HIS294
|
2.1
|
16.2
|
1.0
|
CE1
|
B:HIS294
|
3.0
|
17.4
|
1.0
|
CD2
|
B:HIS205
|
3.0
|
15.9
|
1.0
|
CE1
|
B:HIS205
|
3.0
|
17.9
|
1.0
|
C1A
|
B:HEC600
|
3.1
|
16.8
|
1.0
|
C1D
|
B:HEC600
|
3.1
|
16.7
|
1.0
|
C4C
|
B:HEC600
|
3.1
|
16.1
|
1.0
|
C1C
|
B:HEC600
|
3.1
|
14.9
|
1.0
|
C4D
|
B:HEC600
|
3.1
|
13.7
|
1.0
|
C4B
|
B:HEC600
|
3.1
|
15.2
|
1.0
|
C4A
|
B:HEC600
|
3.1
|
16.2
|
1.0
|
C1B
|
B:HEC600
|
3.1
|
17.4
|
1.0
|
CD2
|
B:HIS294
|
3.1
|
17.4
|
1.0
|
CHD
|
B:HEC600
|
3.4
|
17.0
|
1.0
|
CHA
|
B:HEC600
|
3.5
|
12.8
|
1.0
|
CHB
|
B:HEC600
|
3.5
|
16.4
|
1.0
|
CHC
|
B:HEC600
|
3.5
|
12.7
|
1.0
|
ND1
|
B:HIS294
|
4.0
|
17.4
|
1.0
|
CG
|
B:HIS294
|
4.1
|
17.2
|
1.0
|
ND1
|
B:HIS205
|
4.1
|
16.5
|
1.0
|
CG
|
B:HIS205
|
4.2
|
16.0
|
1.0
|
C2D
|
B:HEC600
|
4.3
|
19.2
|
1.0
|
C3D
|
B:HEC600
|
4.3
|
14.5
|
1.0
|
C2A
|
B:HEC600
|
4.4
|
16.8
|
1.0
|
C2C
|
B:HEC600
|
4.4
|
17.0
|
1.0
|
C3B
|
B:HEC600
|
4.4
|
16.6
|
1.0
|
C3C
|
B:HEC600
|
4.4
|
14.8
|
1.0
|
C3A
|
B:HEC600
|
4.4
|
16.9
|
1.0
|
C2B
|
B:HEC600
|
4.4
|
17.4
|
1.0
|
|
Reference:
N.Abu Tarboush,
L.M.Jensen,
M.Feng,
H.Tachikawa,
C.M.Wilmot,
V.L.Davidson.
Functional Importance of Tyrosine 294 and the Catalytic Selectivity For the Bis-Fe(IV) State of Maug Revealed By Replacement of This Axial Heme Ligand with Histidine . Biochemistry V. 49 9783 2010.
ISSN: ISSN 0006-2960
PubMed: 20929212
DOI: 10.1021/BI101254P
Page generated: Sun Aug 4 17:14:37 2024
|