Nickel in PDB 8w6x: Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State
Enzymatic activity of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State
All present enzymatic activity of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State:
1.12.2.1;
Protein crystallography data
The structure of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x
was solved by
T.Hiromoto,
T.Tamada,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
N/A /
1.04
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.705,
98.485,
126.86,
90,
90,
90
|
|
R / Rfree (%)
|
18.9 /
22
|
Other elements in 8w6x:
The structure of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State
(pdb code 8w6x). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the
Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State, PDB code: 8w6x:
Jump to Nickel binding site number:
1;
2;
Nickel binding site 1 out
of 2 in 8w6x
Go back to
Nickel Binding Sites List in 8w6x
Nickel binding site 1 out
of 2 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni601
b:9.6
occ:0.68
|
NI
|
L:NFU601
|
0.0
|
9.6
|
0.7
|
|
SG
|
L:CYS546
|
1.6
|
10.7
|
0.3
|
|
OD
|
L:CYS546
|
1.6
|
11.7
|
0.3
|
|
O
|
L:OH608
|
1.7
|
8.1
|
0.7
|
|
SG
|
L:CYS81
|
1.8
|
10.4
|
0.3
|
|
SG
|
L:CYS81
|
2.2
|
10.3
|
0.7
|
|
SG
|
L:CYS546
|
2.2
|
8.9
|
0.7
|
|
NI
|
L:NFU601
|
2.4
|
11.1
|
0.3
|
|
SG
|
L:CYS549
|
2.6
|
7.6
|
0.7
|
|
SG
|
L:CYS84
|
2.7
|
9.3
|
1.0
|
|
H
|
L:CYS84
|
2.7
|
4.5
|
0.8
|
|
D
|
L:CYS84
|
2.7
|
13.9
|
0.2
|
|
OE1
|
L:GLU34
|
2.9
|
10.5
|
0.3
|
|
FE
|
L:NFU601
|
2.9
|
7.8
|
1.0
|
|
SG
|
L:CYS549
|
2.9
|
12.9
|
0.3
|
|
CB
|
L:CYS81
|
3.0
|
8.2
|
0.7
|
|
HB3
|
L:CYS81
|
3.0
|
7.1
|
0.7
|
|
OE2
|
L:GLU34
|
3.1
|
10.0
|
0.3
|
|
HB2
|
L:CYS81
|
3.2
|
5.5
|
0.7
|
|
CD
|
L:GLU34
|
3.2
|
9.9
|
0.3
|
|
CB
|
L:CYS546
|
3.2
|
8.7
|
0.7
|
|
CB
|
L:CYS546
|
3.3
|
8.7
|
0.3
|
|
HB2
|
L:CYS549
|
3.3
|
9.5
|
0.7
|
|
HB3
|
L:CYS546
|
3.3
|
7.5
|
0.7
|
|
HB3
|
L:CYS84
|
3.3
|
5.2
|
1.0
|
|
HB2
|
L:CYS546
|
3.4
|
10.1
|
0.7
|
|
CB
|
L:CYS81
|
3.4
|
10.0
|
0.3
|
|
HB
|
L:VAL83
|
3.4
|
8.6
|
0.7
|
|
HB
|
L:VAL83
|
3.5
|
7.1
|
0.3
|
|
HB3
|
L:CYS546
|
3.5
|
10.1
|
0.3
|
|
HB3
|
L:CYS549
|
3.5
|
11.1
|
0.3
|
|
CB
|
L:CYS84
|
3.5
|
8.8
|
1.0
|
|
CB
|
L:CYS549
|
3.6
|
9.3
|
0.7
|
|
HB2
|
L:CYS81
|
3.7
|
9.6
|
0.3
|
|
N
|
L:CYS84
|
3.7
|
8.1
|
1.0
|
|
HB2
|
L:CYS546
|
3.7
|
8.7
|
0.3
|
|
H
|
L:CYS549
|
3.8
|
14.2
|
0.6
|
|
HA
|
L:CYS81
|
3.9
|
6.5
|
0.3
|
|
CB
|
L:CYS549
|
3.9
|
12.3
|
0.3
|
|
D
|
L:VAL83
|
3.9
|
8.6
|
0.3
|
|
C1
|
L:NFU601
|
4.0
|
9.1
|
1.0
|
|
HB3
|
L:CYS81
|
4.1
|
11.8
|
0.3
|
|
HD2
|
L:ARG479
|
4.1
|
3.0
|
1.0
|
|
HG3
|
L:GLU34
|
4.1
|
7.7
|
0.7
|
|
C2
|
L:NFU601
|
4.2
|
8.8
|
1.0
|
|
CA
|
L:CYS84
|
4.2
|
9.5
|
1.0
|
|
CA
|
L:CYS81
|
4.2
|
8.7
|
0.3
|
|
HB3
|
L:GLU34
|
4.3
|
8.8
|
0.3
|
|
H
|
L:VAL83
|
4.3
|
12.2
|
0.7
|
|
HA
|
L:CYS546
|
4.3
|
9.2
|
0.3
|
|
HB3
|
L:CYS549
|
4.3
|
13.4
|
0.7
|
|
CA
|
L:CYS546
|
4.4
|
8.1
|
0.3
|
|
HE2
|
L:HIS88
|
4.4
|
4.6
|
0.9
|
|
DE2
|
L:HIS88
|
4.4
|
20.5
|
0.1
|
|
C3
|
L:NFU601
|
4.4
|
10.0
|
1.0
|
|
DH11
|
L:ARG479
|
4.5
|
5.3
|
0.8
|
|
HH11
|
L:ARG479
|
4.5
|
9.1
|
0.2
|
|
CB
|
L:VAL83
|
4.5
|
9.5
|
0.7
|
|
N
|
L:CYS549
|
4.5
|
8.1
|
0.7
|
|
CA
|
L:CYS81
|
4.5
|
7.9
|
0.7
|
|
HB2
|
L:CYS84
|
4.5
|
10.5
|
1.0
|
|
CB
|
L:VAL83
|
4.5
|
8.6
|
0.3
|
|
CG
|
L:GLU34
|
4.5
|
9.5
|
0.3
|
|
N
|
L:CYS549
|
4.5
|
9.5
|
0.3
|
|
CA
|
L:CYS549
|
4.5
|
8.0
|
0.7
|
|
NH1
|
L:ARG479
|
4.6
|
9.4
|
1.0
|
|
HB3
|
L:GLU34
|
4.6
|
10.4
|
0.7
|
|
CA
|
L:CYS546
|
4.6
|
6.8
|
0.7
|
|
HG12
|
L:VAL83
|
4.7
|
11.7
|
0.7
|
|
N
|
L:VAL83
|
4.7
|
8.2
|
0.3
|
|
HB2
|
L:CYS549
|
4.7
|
12.6
|
0.3
|
|
C
|
L:VAL83
|
4.7
|
8.5
|
0.3
|
|
HB2
|
L:GLU34
|
4.7
|
9.3
|
0.3
|
|
HA
|
L:CYS549
|
4.7
|
11.8
|
0.7
|
|
CB
|
L:GLU34
|
4.8
|
8.9
|
0.3
|
|
C
|
L:VAL83
|
4.8
|
8.1
|
0.7
|
|
HG12
|
L:VAL83
|
4.8
|
10.4
|
0.3
|
|
N1
|
L:NFU601
|
4.8
|
9.1
|
1.0
|
|
CZ
|
L:ARG479
|
4.8
|
8.1
|
1.0
|
|
C
|
L:CYS81
|
4.9
|
8.3
|
0.3
|
|
CA
|
L:VAL83
|
4.9
|
8.4
|
0.3
|
|
HA
|
L:CYS81
|
4.9
|
9.2
|
0.7
|
|
CA
|
L:CYS549
|
4.9
|
10.8
|
0.3
|
|
NE
|
L:ARG479
|
4.9
|
9.1
|
1.0
|
|
HA
|
L:CYS546
|
4.9
|
2.5
|
0.7
|
|
N
|
L:VAL83
|
4.9
|
8.8
|
0.7
|
|
D
|
L:GLY82
|
4.9
|
8.8
|
0.1
|
|
CD
|
L:ARG479
|
4.9
|
9.3
|
1.0
|
|
C
|
L:CYS546
|
4.9
|
7.2
|
0.3
|
|
CA
|
L:VAL83
|
4.9
|
8.6
|
0.7
|
|
HG3
|
L:GLU34
|
5.0
|
9.0
|
0.3
|
|
C
|
L:CYS84
|
5.0
|
8.2
|
1.0
|
|
DH12
|
L:ARG479
|
5.0
|
4.0
|
0.5
|
|
HH12
|
L:ARG479
|
5.0
|
15.2
|
0.5
|
|
C
|
L:CYS81
|
5.0
|
7.7
|
0.7
|
|
CG
|
L:GLU34
|
5.0
|
8.6
|
0.7
|
|
Nickel binding site 2 out
of 2 in 8w6x
Go back to
Nickel Binding Sites List in 8w6x
Nickel binding site 2 out
of 2 in the Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Neutron Structure of [Nife]-Hydrogenase From D. Vulgaris Miyazaki F in Its Oxidized State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni601
b:11.1
occ:0.32
|
NI
|
L:NFU601
|
0.0
|
11.1
|
0.3
|
|
H
|
L:CYS549
|
1.5
|
14.2
|
0.6
|
|
HB2
|
L:CYS549
|
1.7
|
9.5
|
0.7
|
|
SG
|
L:CYS546
|
1.8
|
8.9
|
0.7
|
|
OE2
|
L:GLU34
|
1.8
|
10.0
|
0.3
|
|
CB
|
L:CYS549
|
2.1
|
9.3
|
0.7
|
|
SG
|
L:CYS549
|
2.1
|
12.9
|
0.3
|
|
N
|
L:CYS549
|
2.2
|
8.1
|
0.7
|
|
SG
|
L:CYS546
|
2.2
|
10.7
|
0.3
|
|
N
|
L:CYS549
|
2.3
|
9.5
|
0.3
|
|
SG
|
L:CYS549
|
2.3
|
7.6
|
0.7
|
|
NI
|
L:NFU601
|
2.4
|
9.6
|
0.7
|
|
CA
|
L:CYS549
|
2.6
|
8.0
|
0.7
|
|
HB2
|
L:CYS81
|
2.7
|
5.5
|
0.7
|
|
CB
|
L:CYS549
|
2.7
|
12.3
|
0.3
|
|
HB3
|
L:CYS549
|
2.8
|
11.1
|
0.3
|
|
CD
|
L:GLU34
|
2.8
|
9.9
|
0.3
|
|
HB3
|
L:CYS546
|
2.9
|
7.5
|
0.7
|
|
CB
|
L:CYS546
|
3.0
|
8.7
|
0.7
|
|
HB3
|
L:CYS546
|
3.0
|
10.1
|
0.3
|
|
SG
|
L:CYS81
|
3.0
|
10.3
|
0.7
|
|
CA
|
L:CYS549
|
3.0
|
10.8
|
0.3
|
|
HA
|
L:CYS549
|
3.1
|
11.8
|
0.7
|
|
CB
|
L:CYS546
|
3.1
|
8.7
|
0.3
|
|
OE1
|
L:GLU34
|
3.1
|
10.5
|
0.3
|
|
HB3
|
L:CYS549
|
3.2
|
13.4
|
0.7
|
|
SG
|
L:CYS81
|
3.2
|
10.4
|
0.3
|
|
CB
|
L:CYS81
|
3.3
|
8.2
|
0.7
|
|
O
|
L:OH608
|
3.3
|
8.1
|
0.7
|
|
D
|
L:ALA548
|
3.3
|
8.3
|
0.5
|
|
O
|
L:CYS546
|
3.4
|
6.2
|
0.3
|
|
H
|
L:GLY550
|
3.4
|
11.1
|
0.4
|
|
C
|
L:ALA548
|
3.4
|
7.7
|
0.7
|
|
C
|
L:CYS546
|
3.4
|
7.2
|
0.3
|
|
C
|
L:ALA548
|
3.5
|
9.4
|
0.3
|
|
HB3
|
L:ALA548
|
3.5
|
7.9
|
0.3
|
|
OD
|
L:CYS546
|
3.5
|
11.7
|
0.3
|
|
O
|
L:CYS546
|
3.5
|
8.5
|
0.7
|
|
CA
|
L:CYS546
|
3.6
|
8.1
|
0.3
|
|
N
|
L:ALA548
|
3.6
|
7.3
|
0.3
|
|
C
|
L:CYS546
|
3.6
|
7.4
|
0.7
|
|
HB2
|
L:ALA548
|
3.7
|
8.6
|
0.7
|
|
HA
|
L:CYS546
|
3.7
|
9.2
|
0.3
|
|
HB2
|
L:ALA548
|
3.7
|
8.9
|
0.3
|
|
HB2
|
L:CYS81
|
3.8
|
9.6
|
0.3
|
|
HB2
|
L:CYS546
|
3.8
|
10.1
|
0.7
|
|
HB2
|
L:CYS549
|
3.8
|
12.6
|
0.3
|
|
CA
|
L:CYS546
|
3.8
|
6.8
|
0.7
|
|
HA
|
L:CYS81
|
3.8
|
6.5
|
0.3
|
|
HB3
|
L:CYS81
|
3.8
|
7.1
|
0.7
|
|
CA
|
L:ALA548
|
3.8
|
8.2
|
0.3
|
|
OE2
|
L:GLU34
|
3.8
|
8.8
|
0.7
|
|
H
|
L:GLY550
|
3.9
|
9.6
|
0.6
|
|
HA
|
L:CYS549
|
3.9
|
10.6
|
0.3
|
|
CB
|
L:ALA548
|
3.9
|
8.0
|
0.3
|
|
H
|
L:ALA548
|
3.9
|
17.4
|
0.6
|
|
C
|
L:CYS549
|
3.9
|
7.9
|
0.7
|
|
N
|
L:GLY550
|
3.9
|
10.3
|
0.3
|
|
C
|
L:CYS549
|
3.9
|
9.9
|
0.3
|
|
N
|
L:ALA548
|
4.0
|
8.7
|
0.7
|
|
HB1
|
L:ALA548
|
4.0
|
7.1
|
0.7
|
|
FE
|
L:NFU601
|
4.0
|
7.8
|
1.0
|
|
CA
|
L:ALA548
|
4.0
|
7.5
|
0.7
|
|
CB
|
L:CYS81
|
4.0
|
10.0
|
0.3
|
|
N
|
L:ILE547
|
4.1
|
8.4
|
0.3
|
|
HB2
|
L:CYS546
|
4.1
|
8.7
|
0.3
|
|
CB
|
L:ALA548
|
4.1
|
8.2
|
0.7
|
|
HB3
|
L:GLU34
|
4.1
|
8.8
|
0.3
|
|
CG
|
L:GLU34
|
4.2
|
9.5
|
0.3
|
|
HA
|
L:CYS546
|
4.2
|
2.5
|
0.7
|
|
N
|
L:GLY550
|
4.3
|
7.7
|
0.7
|
|
HG3
|
L:GLU34
|
4.3
|
7.7
|
0.7
|
|
C1
|
L:NFU601
|
4.3
|
9.1
|
1.0
|
|
N
|
L:ILE547
|
4.3
|
6.7
|
0.7
|
|
O
|
L:ALA548
|
4.3
|
7.5
|
0.7
|
|
C
|
L:ILE547
|
4.4
|
7.7
|
0.3
|
|
O
|
L:THR80
|
4.4
|
9.1
|
0.3
|
|
HG22
|
L:THR80
|
4.4
|
8.2
|
0.7
|
|
HB3
|
L:GLU34
|
4.4
|
10.4
|
0.7
|
|
HE2
|
L:HIS88
|
4.4
|
4.6
|
0.9
|
|
DE2
|
L:HIS88
|
4.4
|
20.5
|
0.1
|
|
HG2
|
L:GLU34
|
4.4
|
8.9
|
0.3
|
|
SG
|
L:CYS84
|
4.4
|
9.3
|
1.0
|
|
CA
|
L:CYS81
|
4.4
|
8.7
|
0.3
|
|
CD
|
L:GLU34
|
4.5
|
8.8
|
0.7
|
|
D
|
L:ILE547
|
4.5
|
13.5
|
0.1
|
|
O
|
L:THR80
|
4.5
|
8.8
|
0.7
|
|
HG21
|
L:THR80
|
4.5
|
8.8
|
0.7
|
|
O
|
L:ALA548
|
4.5
|
9.9
|
0.3
|
|
C
|
L:ILE547
|
4.6
|
8.2
|
0.7
|
|
CA
|
L:CYS81
|
4.6
|
7.9
|
0.7
|
|
HG11
|
L:VAL500
|
4.6
|
10.7
|
1.0
|
|
HA
|
L:CYS81
|
4.7
|
9.2
|
0.7
|
|
CB
|
L:GLU34
|
4.7
|
8.9
|
0.3
|
|
H
|
L:ILE547
|
4.8
|
5.7
|
0.9
|
|
CA
|
L:ILE547
|
4.8
|
7.7
|
0.3
|
|
N1
|
L:NFU601
|
4.8
|
9.1
|
1.0
|
|
CG
|
L:GLU34
|
4.8
|
8.6
|
0.7
|
|
D
|
L:CYS84
|
4.9
|
13.9
|
0.2
|
|
H
|
L:CYS84
|
4.9
|
4.5
|
0.8
|
|
HA
|
L:ALA548
|
4.9
|
8.4
|
0.3
|
|
O
|
L:CYS549
|
5.0
|
7.1
|
0.7
|
|
HG3
|
L:GLU34
|
5.0
|
9.0
|
0.3
|
|
HB1
|
L:ALA548
|
5.0
|
7.2
|
0.3
|
|
CG2
|
L:THR80
|
5.0
|
7.3
|
0.7
|
|
Reference:
T.Hiromoto,
K.Nishikawa,
S.Inoue,
H.Ogata,
Y.Hori,
K.Kusaka,
Y.Hirano,
K.Kurihara,
Y.Shigeta,
T.Tamada,
Y.Higuchi.
New Insights Into the Oxidation Process From Neutron and X-Ray Crystal Structures of An O2-Sensitive [Nife]-Hydrogenase. Chemical Science 2023.
DOI: 10.1039/D3SC02156D
Page generated: Thu Dec 28 11:57:06 2023
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