Magnesium in PDB 6fpi: Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
Enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q:
1.12.99.6;
Protein crystallography data
The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q, PDB code: 6fpi
was solved by
S.B.Carr,
F.A.Armstrong,
R.M.Evans,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
83.51 /
1.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.820,
97.730,
183.200,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.5 /
16.7
|
Other elements in 6fpi:
The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
(pdb code 6fpi). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q, PDB code: 6fpi:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6fpi
Go back to
Magnesium Binding Sites List in 6fpi
Magnesium binding site 1 out
of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg602
b:12.2
occ:1.00
|
HE2
|
L:HIS582
|
1.4
|
13.6
|
0.0
|
O
|
L:HOH721
|
2.1
|
16.1
|
1.0
|
O
|
L:CYS528
|
2.1
|
15.8
|
1.0
|
O
|
L:HOH731
|
2.1
|
14.5
|
1.0
|
OE1
|
L:GLU57
|
2.1
|
14.9
|
1.0
|
O
|
L:HOH711
|
2.1
|
16.6
|
1.0
|
NE2
|
L:HIS582
|
2.2
|
13.8
|
1.0
|
H
|
L:CYS528
|
3.0
|
15.3
|
1.0
|
CD
|
L:GLU57
|
3.1
|
15.1
|
1.0
|
CE1
|
L:HIS582
|
3.2
|
15.1
|
1.0
|
CD2
|
L:HIS582
|
3.2
|
14.9
|
1.0
|
C
|
L:CYS528
|
3.3
|
14.9
|
1.0
|
HE1
|
L:HIS582
|
3.3
|
14.8
|
1.0
|
OE2
|
L:GLU57
|
3.4
|
15.9
|
1.0
|
HZ1
|
L:LYS399
|
3.4
|
17.2
|
1.0
|
HD2
|
L:HIS582
|
3.4
|
14.6
|
1.0
|
HB2
|
L:CYS528
|
3.6
|
16.9
|
1.0
|
HD2
|
L:LYS399
|
3.7
|
16.1
|
1.0
|
N
|
L:CYS528
|
3.8
|
14.6
|
1.0
|
HA
|
L:VAL529
|
4.0
|
15.5
|
1.0
|
CA
|
L:CYS528
|
4.0
|
16.7
|
1.0
|
OE2
|
L:GLU347
|
4.0
|
19.2
|
1.0
|
OE1
|
L:GLU347
|
4.1
|
20.2
|
1.0
|
HG21
|
L:VAL529
|
4.2
|
16.7
|
1.0
|
OE1
|
L:GLN527
|
4.2
|
19.7
|
1.0
|
O
|
L:HOH944
|
4.3
|
15.0
|
1.0
|
ND1
|
L:HIS582
|
4.3
|
15.3
|
1.0
|
CB
|
L:CYS528
|
4.3
|
16.0
|
1.0
|
O
|
L:HOH825
|
4.3
|
15.2
|
1.0
|
NZ
|
L:LYS399
|
4.3
|
17.4
|
1.0
|
N
|
L:VAL529
|
4.4
|
15.1
|
1.0
|
CG
|
L:HIS582
|
4.4
|
14.4
|
1.0
|
CG
|
L:GLU57
|
4.4
|
15.4
|
1.0
|
CD
|
L:GLU347
|
4.5
|
18.2
|
1.0
|
HE3
|
L:LYS399
|
4.6
|
16.8
|
1.0
|
HG2
|
L:GLU57
|
4.6
|
15.5
|
1.0
|
CD
|
L:LYS399
|
4.6
|
16.3
|
1.0
|
HG3
|
L:GLU57
|
4.6
|
15.5
|
1.0
|
CA
|
L:VAL529
|
4.6
|
15.4
|
1.0
|
HG1
|
L:THR370
|
4.6
|
17.6
|
0.0
|
HA
|
L:GLN527
|
4.6
|
15.2
|
1.0
|
HB3
|
L:GLN527
|
4.7
|
16.1
|
1.0
|
CE
|
L:LYS399
|
4.7
|
16.8
|
1.0
|
HZ2
|
L:LYS399
|
4.8
|
17.2
|
1.0
|
HB3
|
L:CYS528
|
4.8
|
16.9
|
1.0
|
HZ3
|
L:LYS399
|
4.8
|
17.2
|
1.0
|
HG22
|
L:THR533
|
4.9
|
15.6
|
1.0
|
C
|
L:GLN527
|
4.9
|
15.8
|
1.0
|
HA
|
L:CYS528
|
4.9
|
15.8
|
1.0
|
HG23
|
L:VAL530
|
5.0
|
17.0
|
1.0
|
HG1
|
L:THR533
|
5.0
|
14.5
|
0.0
|
HG3
|
L:LYS399
|
5.0
|
15.7
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6fpi
Go back to
Magnesium Binding Sites List in 6fpi
Magnesium binding site 2 out
of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg602
b:11.5
occ:1.00
|
HE2
|
M:HIS582
|
1.4
|
15.1
|
0.0
|
O
|
M:HOH723
|
2.1
|
15.0
|
1.0
|
O
|
M:CYS528
|
2.1
|
15.6
|
1.0
|
O
|
M:HOH736
|
2.1
|
15.3
|
1.0
|
O
|
M:HOH722
|
2.2
|
16.2
|
1.0
|
OE1
|
M:GLU57
|
2.2
|
14.6
|
1.0
|
NE2
|
M:HIS582
|
2.2
|
15.2
|
1.0
|
H
|
M:CYS528
|
3.1
|
15.8
|
1.0
|
CD
|
M:GLU57
|
3.1
|
15.6
|
1.0
|
CE1
|
M:HIS582
|
3.2
|
15.5
|
1.0
|
CD2
|
M:HIS582
|
3.2
|
16.3
|
1.0
|
C
|
M:CYS528
|
3.3
|
15.4
|
1.0
|
HE1
|
M:HIS582
|
3.3
|
15.3
|
1.0
|
HZ1
|
M:LYS399
|
3.3
|
17.5
|
1.0
|
OE2
|
M:GLU57
|
3.4
|
16.2
|
1.0
|
HD2
|
M:HIS582
|
3.4
|
16.0
|
1.0
|
HB2
|
M:CYS528
|
3.6
|
17.1
|
1.0
|
HD2
|
M:LYS399
|
3.8
|
15.7
|
1.0
|
N
|
M:CYS528
|
3.8
|
15.1
|
1.0
|
CA
|
M:CYS528
|
4.0
|
16.9
|
1.0
|
HA
|
M:VAL529
|
4.0
|
16.0
|
1.0
|
OE2
|
M:GLU347
|
4.1
|
18.8
|
1.0
|
HG21
|
M:VAL529
|
4.1
|
16.9
|
1.0
|
OE1
|
M:GLU347
|
4.2
|
19.6
|
1.0
|
OE1
|
M:GLN527
|
4.2
|
20.0
|
1.0
|
NZ
|
M:LYS399
|
4.2
|
17.9
|
1.0
|
O
|
M:HOH966
|
4.3
|
14.8
|
1.0
|
CB
|
M:CYS528
|
4.3
|
16.8
|
1.0
|
ND1
|
M:HIS582
|
4.3
|
14.8
|
1.0
|
O
|
M:HOH804
|
4.3
|
15.4
|
1.0
|
HE3
|
M:LYS399
|
4.3
|
16.6
|
1.0
|
N
|
M:VAL529
|
4.3
|
15.5
|
1.0
|
CG
|
M:HIS582
|
4.4
|
16.4
|
1.0
|
CG
|
M:GLU57
|
4.5
|
15.4
|
1.0
|
CD
|
M:GLU347
|
4.6
|
17.0
|
1.0
|
HA
|
M:GLN527
|
4.6
|
15.6
|
1.0
|
CD
|
M:LYS399
|
4.6
|
15.5
|
1.0
|
HG1
|
M:THR370
|
4.6
|
17.1
|
0.0
|
CE
|
M:LYS399
|
4.6
|
16.6
|
1.0
|
HB3
|
M:GLN527
|
4.6
|
15.8
|
1.0
|
CA
|
M:VAL529
|
4.6
|
15.8
|
1.0
|
HZ2
|
M:LYS399
|
4.6
|
17.5
|
1.0
|
HG2
|
M:GLU57
|
4.7
|
15.4
|
1.0
|
HG3
|
M:GLU57
|
4.7
|
15.4
|
1.0
|
HB3
|
M:CYS528
|
4.8
|
17.1
|
1.0
|
HZ3
|
M:LYS399
|
4.8
|
17.5
|
1.0
|
C
|
M:GLN527
|
4.9
|
16.1
|
1.0
|
HG22
|
M:THR533
|
4.9
|
14.6
|
1.0
|
HG3
|
M:LYS399
|
4.9
|
15.5
|
1.0
|
HG23
|
M:VAL530
|
4.9
|
18.6
|
1.0
|
HA
|
M:CYS528
|
4.9
|
16.2
|
1.0
|
HG1
|
M:THR533
|
5.0
|
14.3
|
0.0
|
|
Reference:
R.M.Evans,
P.A.Ash,
S.E.Beaton,
E.J.Brooke,
K.A.Vincent,
S.B.Carr,
F.A.Armstrong.
Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Tue Oct 1 00:35:23 2024
|