Nickel in PDB 2frv: Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
Enzymatic activity of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
All present enzymatic activity of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase:
1.18.99.1;
Protein crystallography data
The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 2frv
was solved by
A.Volbeda,
M.Frey,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.54
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.780,
113.160,
133.910,
90.03,
90.02,
119.99
|
R / Rfree (%)
|
22.4 /
23.9
|
Other elements in 2frv:
The structure of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
(pdb code 2frv). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the
Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 2frv:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
Nickel binding site 1 out
of 6 in 2frv
Go back to
Nickel Binding Sites List in 2frv
Nickel binding site 1 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/NI/pdb/fr/2frv-NI-sphere_01.jpg) Mono view
![](/pictures/NI/pdb/fr/2frv-NI-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni538
b:7.6
occ:1.00
|
O
|
L:O539
|
1.7
|
7.6
|
1.0
|
SG
|
L:CYS65
|
2.2
|
4.0
|
1.0
|
SG
|
L:CYS530
|
2.3
|
10.1
|
1.0
|
SG
|
L:CYS68
|
2.6
|
2.0
|
1.0
|
SG
|
L:CYS533
|
2.6
|
2.0
|
1.0
|
FE
|
L:FCO537
|
2.9
|
2.0
|
1.0
|
CB
|
L:CYS65
|
3.0
|
2.0
|
1.0
|
CB
|
L:CYS530
|
3.3
|
2.0
|
1.0
|
CB
|
L:CYS68
|
3.6
|
2.0
|
1.0
|
CB
|
L:CYS533
|
3.7
|
2.0
|
1.0
|
N
|
L:CYS68
|
3.8
|
2.5
|
1.0
|
C2
|
L:FCO537
|
3.9
|
2.7
|
1.0
|
C1
|
L:FCO537
|
4.0
|
2.3
|
1.0
|
CA
|
L:CYS68
|
4.3
|
3.6
|
1.0
|
CA
|
L:CYS65
|
4.4
|
2.0
|
1.0
|
CB
|
L:VAL67
|
4.5
|
4.7
|
1.0
|
N
|
L:CYS533
|
4.6
|
2.0
|
1.0
|
C3
|
L:FCO537
|
4.6
|
2.6
|
1.0
|
CA
|
L:CYS530
|
4.6
|
2.6
|
1.0
|
CA
|
L:CYS533
|
4.6
|
2.0
|
1.0
|
N2
|
L:FCO537
|
4.8
|
7.5
|
1.0
|
NH1
|
L:ARG463
|
4.8
|
5.7
|
1.0
|
C
|
L:VAL67
|
4.8
|
3.4
|
1.0
|
N1
|
L:FCO537
|
4.9
|
3.8
|
1.0
|
C
|
L:CYS65
|
4.9
|
2.0
|
1.0
|
CZ
|
L:ARG463
|
4.9
|
6.3
|
1.0
|
N
|
L:VAL67
|
4.9
|
2.0
|
1.0
|
CG
|
L:GLU18
|
4.9
|
5.5
|
1.0
|
C
|
L:CYS68
|
5.0
|
5.3
|
1.0
|
NE
|
L:ARG463
|
5.0
|
4.0
|
1.0
|
|
Nickel binding site 2 out
of 6 in 2frv
Go back to
Nickel Binding Sites List in 2frv
Nickel binding site 2 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/NI/pdb/fr/2frv-NI-sphere_02.jpg) Mono view
![](/pictures/NI/pdb/fr/2frv-NI-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni538
b:7.6
occ:1.00
|
O
|
B:O539
|
1.7
|
7.6
|
1.0
|
SG
|
B:CYS65
|
2.2
|
4.0
|
1.0
|
SG
|
B:CYS530
|
2.3
|
10.1
|
1.0
|
SG
|
B:CYS68
|
2.6
|
2.0
|
1.0
|
SG
|
B:CYS533
|
2.6
|
2.0
|
1.0
|
FE
|
B:FCO537
|
2.9
|
2.0
|
1.0
|
CB
|
B:CYS65
|
3.0
|
2.0
|
1.0
|
CB
|
B:CYS530
|
3.3
|
2.0
|
1.0
|
CB
|
B:CYS68
|
3.6
|
2.0
|
1.0
|
CB
|
B:CYS533
|
3.7
|
2.0
|
1.0
|
N
|
B:CYS68
|
3.8
|
2.5
|
1.0
|
C2
|
B:FCO537
|
3.9
|
2.7
|
1.0
|
C1
|
B:FCO537
|
4.0
|
2.3
|
1.0
|
CA
|
B:CYS68
|
4.3
|
3.6
|
1.0
|
CA
|
B:CYS65
|
4.4
|
2.0
|
1.0
|
CB
|
B:VAL67
|
4.5
|
4.7
|
1.0
|
N
|
B:CYS533
|
4.6
|
2.0
|
1.0
|
C3
|
B:FCO537
|
4.6
|
2.6
|
1.0
|
CA
|
B:CYS530
|
4.6
|
2.6
|
1.0
|
CA
|
B:CYS533
|
4.6
|
2.0
|
1.0
|
N2
|
B:FCO537
|
4.8
|
7.5
|
1.0
|
NH1
|
B:ARG463
|
4.8
|
5.7
|
1.0
|
C
|
B:VAL67
|
4.8
|
3.4
|
1.0
|
N1
|
B:FCO537
|
4.9
|
3.8
|
1.0
|
C
|
B:CYS65
|
4.9
|
2.0
|
1.0
|
CZ
|
B:ARG463
|
4.9
|
6.3
|
1.0
|
N
|
B:VAL67
|
4.9
|
2.0
|
1.0
|
CG
|
B:GLU18
|
4.9
|
5.5
|
1.0
|
C
|
B:CYS68
|
5.0
|
5.3
|
1.0
|
NE
|
B:ARG463
|
5.0
|
4.0
|
1.0
|
|
Nickel binding site 3 out
of 6 in 2frv
Go back to
Nickel Binding Sites List in 2frv
Nickel binding site 3 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/NI/pdb/fr/2frv-NI-sphere_03.jpg) Mono view
![](/pictures/NI/pdb/fr/2frv-NI-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni538
b:7.6
occ:1.00
|
O
|
D:O539
|
1.7
|
7.6
|
1.0
|
SG
|
D:CYS65
|
2.2
|
4.0
|
1.0
|
SG
|
D:CYS530
|
2.3
|
10.1
|
1.0
|
SG
|
D:CYS68
|
2.6
|
2.0
|
1.0
|
SG
|
D:CYS533
|
2.6
|
2.0
|
1.0
|
FE
|
D:FCO537
|
2.9
|
2.0
|
1.0
|
CB
|
D:CYS65
|
3.0
|
2.0
|
1.0
|
CB
|
D:CYS530
|
3.3
|
2.0
|
1.0
|
CB
|
D:CYS68
|
3.6
|
2.0
|
1.0
|
CB
|
D:CYS533
|
3.7
|
2.0
|
1.0
|
N
|
D:CYS68
|
3.8
|
2.5
|
1.0
|
C2
|
D:FCO537
|
3.9
|
2.7
|
1.0
|
C1
|
D:FCO537
|
4.0
|
2.3
|
1.0
|
CA
|
D:CYS68
|
4.3
|
3.6
|
1.0
|
CA
|
D:CYS65
|
4.4
|
2.0
|
1.0
|
CB
|
D:VAL67
|
4.5
|
4.7
|
1.0
|
N
|
D:CYS533
|
4.6
|
2.0
|
1.0
|
CA
|
D:CYS530
|
4.6
|
2.6
|
1.0
|
C3
|
D:FCO537
|
4.6
|
2.6
|
1.0
|
CA
|
D:CYS533
|
4.6
|
2.0
|
1.0
|
N2
|
D:FCO537
|
4.8
|
7.5
|
1.0
|
NH1
|
D:ARG463
|
4.8
|
5.7
|
1.0
|
C
|
D:VAL67
|
4.8
|
3.4
|
1.0
|
N1
|
D:FCO537
|
4.9
|
3.8
|
1.0
|
C
|
D:CYS65
|
4.9
|
2.0
|
1.0
|
CZ
|
D:ARG463
|
4.9
|
6.3
|
1.0
|
N
|
D:VAL67
|
4.9
|
2.0
|
1.0
|
CG
|
D:GLU18
|
4.9
|
5.5
|
1.0
|
C
|
D:CYS68
|
5.0
|
5.3
|
1.0
|
NE
|
D:ARG463
|
5.0
|
4.0
|
1.0
|
|
Nickel binding site 4 out
of 6 in 2frv
Go back to
Nickel Binding Sites List in 2frv
Nickel binding site 4 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/NI/pdb/fr/2frv-NI-sphere_04.jpg) Mono view
![](/pictures/NI/pdb/fr/2frv-NI-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni538
b:7.6
occ:1.00
|
O
|
F:O539
|
1.7
|
7.6
|
1.0
|
SG
|
F:CYS65
|
2.2
|
4.0
|
1.0
|
SG
|
F:CYS530
|
2.3
|
10.1
|
1.0
|
SG
|
F:CYS68
|
2.6
|
2.0
|
1.0
|
SG
|
F:CYS533
|
2.6
|
2.0
|
1.0
|
FE
|
F:FCO537
|
2.9
|
2.0
|
1.0
|
CB
|
F:CYS65
|
3.0
|
2.0
|
1.0
|
CB
|
F:CYS530
|
3.3
|
2.0
|
1.0
|
CB
|
F:CYS68
|
3.6
|
2.0
|
1.0
|
CB
|
F:CYS533
|
3.7
|
2.0
|
1.0
|
N
|
F:CYS68
|
3.8
|
2.5
|
1.0
|
C2
|
F:FCO537
|
3.9
|
2.7
|
1.0
|
C1
|
F:FCO537
|
4.0
|
2.3
|
1.0
|
CA
|
F:CYS68
|
4.3
|
3.6
|
1.0
|
CA
|
F:CYS65
|
4.4
|
2.0
|
1.0
|
CB
|
F:VAL67
|
4.5
|
4.7
|
1.0
|
N
|
F:CYS533
|
4.6
|
2.0
|
1.0
|
C3
|
F:FCO537
|
4.6
|
2.6
|
1.0
|
CA
|
F:CYS530
|
4.6
|
2.6
|
1.0
|
CA
|
F:CYS533
|
4.6
|
2.0
|
1.0
|
N2
|
F:FCO537
|
4.8
|
7.5
|
1.0
|
NH1
|
F:ARG463
|
4.8
|
5.7
|
1.0
|
C
|
F:VAL67
|
4.8
|
3.4
|
1.0
|
N1
|
F:FCO537
|
4.9
|
3.8
|
1.0
|
C
|
F:CYS65
|
4.9
|
2.0
|
1.0
|
CZ
|
F:ARG463
|
4.9
|
6.3
|
1.0
|
N
|
F:VAL67
|
4.9
|
2.0
|
1.0
|
CG
|
F:GLU18
|
4.9
|
5.5
|
1.0
|
C
|
F:CYS68
|
5.0
|
5.3
|
1.0
|
NE
|
F:ARG463
|
5.0
|
4.0
|
1.0
|
|
Nickel binding site 5 out
of 6 in 2frv
Go back to
Nickel Binding Sites List in 2frv
Nickel binding site 5 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/NI/pdb/fr/2frv-NI-sphere_05.jpg) Mono view
![](/pictures/NI/pdb/fr/2frv-NI-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ni538
b:7.6
occ:1.00
|
O
|
H:O539
|
1.7
|
7.6
|
1.0
|
SG
|
H:CYS65
|
2.2
|
4.0
|
1.0
|
SG
|
H:CYS530
|
2.3
|
10.1
|
1.0
|
SG
|
H:CYS68
|
2.6
|
2.0
|
1.0
|
SG
|
H:CYS533
|
2.6
|
2.0
|
1.0
|
FE
|
H:FCO537
|
2.9
|
2.0
|
1.0
|
CB
|
H:CYS65
|
3.0
|
2.0
|
1.0
|
CB
|
H:CYS530
|
3.3
|
2.0
|
1.0
|
CB
|
H:CYS68
|
3.6
|
2.0
|
1.0
|
CB
|
H:CYS533
|
3.7
|
2.0
|
1.0
|
N
|
H:CYS68
|
3.8
|
2.5
|
1.0
|
C2
|
H:FCO537
|
3.9
|
2.7
|
1.0
|
C1
|
H:FCO537
|
4.0
|
2.3
|
1.0
|
CA
|
H:CYS68
|
4.3
|
3.6
|
1.0
|
CA
|
H:CYS65
|
4.4
|
2.0
|
1.0
|
CB
|
H:VAL67
|
4.5
|
4.7
|
1.0
|
N
|
H:CYS533
|
4.6
|
2.0
|
1.0
|
C3
|
H:FCO537
|
4.6
|
2.6
|
1.0
|
CA
|
H:CYS530
|
4.6
|
2.6
|
1.0
|
CA
|
H:CYS533
|
4.6
|
2.0
|
1.0
|
N2
|
H:FCO537
|
4.8
|
7.5
|
1.0
|
NH1
|
H:ARG463
|
4.8
|
5.7
|
1.0
|
C
|
H:VAL67
|
4.8
|
3.4
|
1.0
|
N1
|
H:FCO537
|
4.9
|
3.8
|
1.0
|
C
|
H:CYS65
|
4.9
|
2.0
|
1.0
|
CZ
|
H:ARG463
|
4.9
|
6.3
|
1.0
|
N
|
H:VAL67
|
4.9
|
2.0
|
1.0
|
CG
|
H:GLU18
|
4.9
|
5.5
|
1.0
|
C
|
H:CYS68
|
5.0
|
5.3
|
1.0
|
NE
|
H:ARG463
|
5.0
|
4.0
|
1.0
|
|
Nickel binding site 6 out
of 6 in 2frv
Go back to
Nickel Binding Sites List in 2frv
Nickel binding site 6 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/NI/pdb/fr/2frv-NI-sphere_06.jpg) Mono view
![](/pictures/NI/pdb/fr/2frv-NI-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ni538
b:7.6
occ:1.00
|
O
|
J:O539
|
1.7
|
7.6
|
1.0
|
SG
|
J:CYS65
|
2.2
|
4.0
|
1.0
|
SG
|
J:CYS530
|
2.3
|
10.1
|
1.0
|
SG
|
J:CYS68
|
2.6
|
2.0
|
1.0
|
SG
|
J:CYS533
|
2.6
|
2.0
|
1.0
|
FE
|
J:FCO537
|
2.9
|
2.0
|
1.0
|
CB
|
J:CYS65
|
3.0
|
2.0
|
1.0
|
CB
|
J:CYS530
|
3.3
|
2.0
|
1.0
|
CB
|
J:CYS68
|
3.6
|
2.0
|
1.0
|
CB
|
J:CYS533
|
3.7
|
2.0
|
1.0
|
N
|
J:CYS68
|
3.8
|
2.5
|
1.0
|
C2
|
J:FCO537
|
3.9
|
2.7
|
1.0
|
C1
|
J:FCO537
|
4.0
|
2.3
|
1.0
|
CA
|
J:CYS68
|
4.3
|
3.6
|
1.0
|
CA
|
J:CYS65
|
4.4
|
2.0
|
1.0
|
CB
|
J:VAL67
|
4.5
|
4.7
|
1.0
|
N
|
J:CYS533
|
4.6
|
2.0
|
1.0
|
C3
|
J:FCO537
|
4.6
|
2.6
|
1.0
|
CA
|
J:CYS530
|
4.6
|
2.6
|
1.0
|
CA
|
J:CYS533
|
4.6
|
2.0
|
1.0
|
N2
|
J:FCO537
|
4.8
|
7.5
|
1.0
|
NH1
|
J:ARG463
|
4.8
|
5.7
|
1.0
|
C
|
J:VAL67
|
4.8
|
3.4
|
1.0
|
N1
|
J:FCO537
|
4.9
|
3.8
|
1.0
|
C
|
J:CYS65
|
4.9
|
2.0
|
1.0
|
CZ
|
J:ARG463
|
4.9
|
6.3
|
1.0
|
N
|
J:VAL67
|
4.9
|
2.0
|
1.0
|
CG
|
J:GLU18
|
4.9
|
5.5
|
1.0
|
C
|
J:CYS68
|
5.0
|
5.3
|
1.0
|
NE
|
J:ARG463
|
5.0
|
4.0
|
1.0
|
|
Reference:
A.Volbeda,
E.Garcin,
C.Piras,
A.L.De Lacey,
V.M.Fernandez,
E.C.Hatchikian,
M.Frey,
J.C.Fontecilla-Camps.
Structure of the [Nife] Hydrogenase Active Site: Evidence For Biologically Uncommon Fe Ligands J.Am.Chem.Soc. V. 118 12989 1996.
ISSN: ISSN 0002-7863
Page generated: Wed Dec 16 01:18:14 2020
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