Nickel in PDB 6gal: Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10
Enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10
All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10:
1.12.99.6;
Protein crystallography data
The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10, PDB code: 6gal
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)
|
92.12 /
1.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.906,
95.224,
183.910,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
12 /
14.7
|
Other elements in 6gal:
The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10
(pdb code 6gal). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the
Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10, PDB code: 6gal:
Jump to Nickel binding site number:
1;
2;
Nickel binding site 1 out
of 2 in 6gal
Go back to
Nickel Binding Sites List in 6gal
Nickel binding site 1 out
of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni601
b:9.2
occ:1.00
|
NI
|
L:EJ2601
|
0.0
|
9.2
|
1.0
|
H
|
L:EJ2601
|
1.6
|
8.1
|
1.0
|
SG
|
L:CYS576
|
2.1
|
11.3
|
1.0
|
SG
|
L:CYS76
|
2.2
|
8.3
|
1.0
|
SG
|
L:CYS79
|
2.3
|
7.5
|
1.0
|
SG
|
L:CYS579
|
2.4
|
7.9
|
1.0
|
FE
|
L:EJ2601
|
2.6
|
7.0
|
1.0
|
H
|
L:CYS79
|
2.9
|
7.5
|
1.0
|
HB2
|
L:CYS76
|
3.1
|
7.3
|
1.0
|
CB
|
L:CYS76
|
3.1
|
7.2
|
1.0
|
HB3
|
L:CYS76
|
3.1
|
7.2
|
1.0
|
CB
|
L:CYS576
|
3.3
|
8.5
|
1.0
|
HB2
|
L:CYS579
|
3.3
|
6.1
|
1.0
|
HB3
|
L:CYS576
|
3.4
|
8.8
|
1.0
|
HB2
|
L:CYS576
|
3.4
|
8.6
|
1.0
|
HB3
|
L:CYS79
|
3.4
|
7.8
|
1.0
|
CB
|
L:CYS79
|
3.5
|
7.5
|
1.0
|
CB
|
L:CYS579
|
3.5
|
6.1
|
1.0
|
C1
|
L:EJ2601
|
3.6
|
6.8
|
1.0
|
N
|
L:CYS79
|
3.8
|
7.8
|
1.0
|
HB
|
L:VAL78
|
3.8
|
8.5
|
1.0
|
C2
|
L:EJ2601
|
3.8
|
6.2
|
1.0
|
H
|
L:CYS579
|
3.9
|
6.1
|
1.0
|
HD2
|
L:ARG509
|
4.0
|
8.5
|
1.0
|
HB3
|
L:CYS579
|
4.2
|
6.5
|
1.0
|
HH11
|
L:ARG509
|
4.2
|
8.7
|
1.0
|
CA
|
L:CYS79
|
4.2
|
8.0
|
1.0
|
C3
|
L:EJ2601
|
4.2
|
7.3
|
1.0
|
HB2
|
L:CYS79
|
4.3
|
7.6
|
1.0
|
O
|
L:HOH895
|
4.3
|
30.7
|
1.0
|
NH1
|
L:ARG509
|
4.3
|
9.3
|
1.0
|
H
|
L:VAL78
|
4.3
|
7.0
|
1.0
|
HE2
|
L:HIS83
|
4.4
|
7.3
|
0.0
|
CA
|
L:CYS76
|
4.5
|
6.7
|
1.0
|
HH12
|
L:ARG509
|
4.5
|
9.1
|
1.0
|
CA
|
L:CYS579
|
4.5
|
6.2
|
1.0
|
N1
|
L:EJ2601
|
4.6
|
6.8
|
1.0
|
CZ
|
L:ARG509
|
4.6
|
8.0
|
1.0
|
N
|
L:CYS579
|
4.6
|
5.8
|
1.0
|
CA
|
L:CYS576
|
4.6
|
7.7
|
1.0
|
HG3
|
L:GLN28
|
4.7
|
12.8
|
1.0
|
HA
|
L:CYS579
|
4.7
|
6.1
|
1.0
|
NE
|
L:ARG509
|
4.7
|
8.1
|
1.0
|
CB
|
L:VAL78
|
4.7
|
8.6
|
1.0
|
CD
|
L:ARG509
|
4.7
|
8.6
|
1.0
|
HA
|
L:CYS76
|
4.7
|
6.8
|
1.0
|
N2
|
L:EJ2601
|
4.8
|
6.3
|
1.0
|
HA
|
L:CYS576
|
4.8
|
7.7
|
1.0
|
C
|
L:VAL78
|
4.9
|
8.5
|
1.0
|
HD3
|
L:ARG509
|
4.9
|
8.3
|
1.0
|
HA
|
L:CYS79
|
4.9
|
8.1
|
1.0
|
|
Nickel binding site 2 out
of 2 in 6gal
Go back to
Nickel Binding Sites List in 6gal
Nickel binding site 2 out
of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q Collected at pH 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Ni602
b:9.5
occ:1.00
|
NI
|
M:EJ2602
|
0.0
|
9.5
|
1.0
|
H
|
M:EJ2602
|
1.6
|
8.7
|
1.0
|
SG
|
M:CYS576
|
2.2
|
11.4
|
1.0
|
SG
|
M:CYS76
|
2.3
|
8.8
|
1.0
|
SG
|
M:CYS79
|
2.3
|
8.4
|
1.0
|
SG
|
M:CYS579
|
2.5
|
8.2
|
1.0
|
FE
|
M:EJ2602
|
2.6
|
7.8
|
1.0
|
H
|
M:CYS79
|
2.9
|
8.1
|
1.0
|
CB
|
M:CYS76
|
3.1
|
8.4
|
1.0
|
HB2
|
M:CYS76
|
3.1
|
8.3
|
1.0
|
HB3
|
M:CYS76
|
3.1
|
8.2
|
1.0
|
CB
|
M:CYS576
|
3.3
|
8.7
|
1.0
|
HB2
|
M:CYS579
|
3.3
|
7.1
|
1.0
|
HB3
|
M:CYS576
|
3.3
|
8.6
|
1.0
|
HB2
|
M:CYS576
|
3.4
|
8.6
|
1.0
|
HB3
|
M:CYS79
|
3.4
|
8.2
|
1.0
|
CB
|
M:CYS79
|
3.5
|
8.1
|
1.0
|
CB
|
M:CYS579
|
3.5
|
7.3
|
1.0
|
C1
|
M:EJ2602
|
3.6
|
8.0
|
1.0
|
C2
|
M:EJ2602
|
3.7
|
6.9
|
1.0
|
N
|
M:CYS79
|
3.8
|
7.9
|
1.0
|
HB
|
M:VAL78
|
3.8
|
9.1
|
1.0
|
H
|
M:CYS579
|
3.9
|
6.4
|
1.0
|
HD2
|
M:ARG509
|
4.0
|
8.5
|
1.0
|
O
|
M:HOH881
|
4.1
|
35.6
|
1.0
|
HB3
|
M:CYS579
|
4.2
|
7.4
|
1.0
|
CA
|
M:CYS79
|
4.2
|
8.4
|
1.0
|
HH11
|
M:ARG509
|
4.2
|
9.3
|
1.0
|
C3
|
M:EJ2602
|
4.2
|
8.2
|
1.0
|
HB2
|
M:CYS79
|
4.3
|
8.1
|
1.0
|
NH1
|
M:ARG509
|
4.3
|
10.1
|
1.0
|
H
|
M:VAL78
|
4.3
|
7.7
|
1.0
|
HE2
|
M:HIS83
|
4.4
|
7.6
|
0.0
|
CA
|
M:CYS76
|
4.5
|
7.1
|
1.0
|
CA
|
M:CYS579
|
4.5
|
6.8
|
1.0
|
N
|
M:CYS579
|
4.6
|
6.4
|
1.0
|
HH12
|
M:ARG509
|
4.6
|
9.8
|
1.0
|
N1
|
M:EJ2602
|
4.6
|
7.6
|
1.0
|
CZ
|
M:ARG509
|
4.6
|
9.5
|
1.0
|
CA
|
M:CYS576
|
4.6
|
6.6
|
1.0
|
HA
|
M:CYS579
|
4.7
|
6.6
|
1.0
|
HG3
|
M:GLN28
|
4.7
|
11.9
|
1.0
|
N2
|
M:EJ2602
|
4.7
|
7.5
|
1.0
|
CB
|
M:VAL78
|
4.7
|
9.2
|
1.0
|
CD
|
M:ARG509
|
4.7
|
8.4
|
1.0
|
HA
|
M:CYS76
|
4.7
|
7.2
|
1.0
|
NE
|
M:ARG509
|
4.8
|
8.8
|
1.0
|
HA
|
M:CYS576
|
4.8
|
6.5
|
1.0
|
C
|
M:VAL78
|
4.8
|
8.4
|
1.0
|
HD3
|
M:ARG509
|
5.0
|
8.6
|
1.0
|
HA
|
M:CYS79
|
5.0
|
8.8
|
1.0
|
|
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: Thu Oct 10 08:28:45 2024
|