Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase, PDB code: 2frv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 2frv
Go back to
Magnesium Binding Sites List in 2frv
Magnesium binding site 1 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/MG/pdb/fr/2frv-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/fr/2frv-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg540
b:2.0
occ:1.00
|
O
|
L:HOH5013
|
1.9
|
3.5
|
1.0
|
O
|
L:HOH5012
|
1.9
|
2.0
|
1.0
|
OE2
|
L:GLU46
|
2.0
|
4.1
|
1.0
|
O
|
L:HOH5011
|
2.2
|
2.0
|
1.0
|
O
|
L:LEU482
|
2.2
|
2.0
|
1.0
|
NE2
|
L:HIS536
|
2.3
|
2.0
|
1.0
|
CD
|
L:GLU46
|
3.1
|
4.1
|
1.0
|
CD2
|
L:HIS536
|
3.2
|
2.0
|
1.0
|
CE1
|
L:HIS536
|
3.3
|
2.0
|
1.0
|
C
|
L:LEU482
|
3.4
|
2.0
|
1.0
|
OE1
|
L:GLU46
|
3.7
|
6.8
|
1.0
|
N
|
L:LEU482
|
3.9
|
2.0
|
1.0
|
OE1
|
L:GLU321
|
4.0
|
16.4
|
1.0
|
OE2
|
L:GLU321
|
4.0
|
14.2
|
1.0
|
CA
|
L:LEU482
|
4.1
|
2.0
|
1.0
|
O
|
L:HOH5056
|
4.1
|
2.0
|
1.0
|
O
|
L:HOH5084
|
4.2
|
5.5
|
1.0
|
NE2
|
L:GLN481
|
4.3
|
2.7
|
1.0
|
CG
|
L:GLU46
|
4.4
|
2.3
|
1.0
|
ND1
|
L:HIS536
|
4.4
|
2.0
|
1.0
|
CG
|
L:HIS536
|
4.4
|
2.0
|
1.0
|
CD
|
L:GLU321
|
4.5
|
13.2
|
1.0
|
N
|
L:VAL483
|
4.5
|
2.0
|
1.0
|
CB
|
L:LEU482
|
4.5
|
2.0
|
1.0
|
NZ
|
L:LYS358
|
4.5
|
2.0
|
1.0
|
CA
|
L:VAL483
|
4.8
|
2.0
|
1.0
|
CD
|
L:LYS358
|
4.9
|
2.0
|
1.0
|
C
|
L:GLN481
|
4.9
|
2.0
|
1.0
|
CE
|
L:LYS358
|
5.0
|
2.0
|
1.0
|
CG
|
L:LEU482
|
5.0
|
2.6
|
1.0
|
CG2
|
L:VAL483
|
5.0
|
2.0
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 2frv
Go back to
Magnesium Binding Sites List in 2frv
Magnesium binding site 2 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/MG/pdb/fr/2frv-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/fr/2frv-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg540
b:2.0
occ:1.00
|
O
|
B:HOH5026
|
1.9
|
3.5
|
1.0
|
O
|
B:HOH5025
|
1.9
|
2.0
|
1.0
|
OE2
|
B:GLU46
|
2.0
|
4.1
|
1.0
|
O
|
B:HOH5024
|
2.2
|
2.0
|
1.0
|
O
|
B:LEU482
|
2.2
|
2.0
|
1.0
|
NE2
|
B:HIS536
|
2.3
|
2.0
|
1.0
|
CD
|
B:GLU46
|
3.1
|
4.1
|
1.0
|
CD2
|
B:HIS536
|
3.2
|
2.0
|
1.0
|
CE1
|
B:HIS536
|
3.3
|
2.0
|
1.0
|
C
|
B:LEU482
|
3.4
|
2.0
|
1.0
|
OE1
|
B:GLU46
|
3.7
|
6.8
|
1.0
|
N
|
B:LEU482
|
3.9
|
2.0
|
1.0
|
OE1
|
B:GLU321
|
4.0
|
16.4
|
1.0
|
OE2
|
B:GLU321
|
4.0
|
14.2
|
1.0
|
CA
|
B:LEU482
|
4.1
|
2.0
|
1.0
|
O
|
B:HOH5071
|
4.1
|
2.0
|
1.0
|
O
|
B:HOH5099
|
4.2
|
5.5
|
1.0
|
NE2
|
B:GLN481
|
4.3
|
2.7
|
1.0
|
CG
|
B:GLU46
|
4.4
|
2.3
|
1.0
|
ND1
|
B:HIS536
|
4.4
|
2.0
|
1.0
|
CG
|
B:HIS536
|
4.4
|
2.0
|
1.0
|
CD
|
B:GLU321
|
4.5
|
13.2
|
1.0
|
N
|
B:VAL483
|
4.5
|
2.0
|
1.0
|
CB
|
B:LEU482
|
4.5
|
2.0
|
1.0
|
NZ
|
B:LYS358
|
4.5
|
2.0
|
1.0
|
CA
|
B:VAL483
|
4.8
|
2.0
|
1.0
|
CD
|
B:LYS358
|
4.9
|
2.0
|
1.0
|
C
|
B:GLN481
|
4.9
|
2.0
|
1.0
|
CE
|
B:LYS358
|
5.0
|
2.0
|
1.0
|
CG
|
B:LEU482
|
5.0
|
2.6
|
1.0
|
CG2
|
B:VAL483
|
5.0
|
2.0
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 2frv
Go back to
Magnesium Binding Sites List in 2frv
Magnesium binding site 3 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/MG/pdb/fr/2frv-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/fr/2frv-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg540
b:2.0
occ:1.00
|
O
|
D:HOH5039
|
1.9
|
3.5
|
1.0
|
O
|
D:HOH5038
|
2.0
|
2.0
|
1.0
|
OE2
|
D:GLU46
|
2.0
|
4.1
|
1.0
|
O
|
D:HOH5037
|
2.2
|
2.0
|
1.0
|
O
|
D:LEU482
|
2.2
|
2.0
|
1.0
|
NE2
|
D:HIS536
|
2.3
|
2.0
|
1.0
|
CD
|
D:GLU46
|
3.1
|
4.1
|
1.0
|
CD2
|
D:HIS536
|
3.2
|
2.0
|
1.0
|
CE1
|
D:HIS536
|
3.3
|
2.0
|
1.0
|
C
|
D:LEU482
|
3.4
|
2.0
|
1.0
|
OE1
|
D:GLU46
|
3.7
|
6.8
|
1.0
|
N
|
D:LEU482
|
3.9
|
2.0
|
1.0
|
OE1
|
D:GLU321
|
4.0
|
16.4
|
1.0
|
OE2
|
D:GLU321
|
4.0
|
14.2
|
1.0
|
CA
|
D:LEU482
|
4.1
|
2.0
|
1.0
|
O
|
D:HOH5085
|
4.1
|
2.0
|
1.0
|
O
|
D:HOH5113
|
4.2
|
5.5
|
1.0
|
NE2
|
D:GLN481
|
4.3
|
2.7
|
1.0
|
CG
|
D:GLU46
|
4.4
|
2.3
|
1.0
|
ND1
|
D:HIS536
|
4.4
|
2.0
|
1.0
|
CG
|
D:HIS536
|
4.4
|
2.0
|
1.0
|
CD
|
D:GLU321
|
4.5
|
13.2
|
1.0
|
CB
|
D:LEU482
|
4.5
|
2.0
|
1.0
|
N
|
D:VAL483
|
4.5
|
2.0
|
1.0
|
NZ
|
D:LYS358
|
4.5
|
2.0
|
1.0
|
CA
|
D:VAL483
|
4.8
|
2.0
|
1.0
|
CD
|
D:LYS358
|
4.9
|
2.0
|
1.0
|
C
|
D:GLN481
|
4.9
|
2.0
|
1.0
|
CE
|
D:LYS358
|
5.0
|
2.0
|
1.0
|
CG
|
D:LEU482
|
5.0
|
2.6
|
1.0
|
CG2
|
D:VAL483
|
5.0
|
2.0
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 2frv
Go back to
Magnesium Binding Sites List in 2frv
Magnesium binding site 4 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/MG/pdb/fr/2frv-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/fr/2frv-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg540
b:2.0
occ:1.00
|
O
|
F:HOH5052
|
1.9
|
3.5
|
1.0
|
O
|
F:HOH5051
|
2.0
|
2.0
|
1.0
|
OE2
|
F:GLU46
|
2.0
|
4.1
|
1.0
|
O
|
F:HOH5050
|
2.2
|
2.0
|
1.0
|
O
|
F:LEU482
|
2.2
|
2.0
|
1.0
|
NE2
|
F:HIS536
|
2.3
|
2.0
|
1.0
|
CD
|
F:GLU46
|
3.1
|
4.1
|
1.0
|
CD2
|
F:HIS536
|
3.2
|
2.0
|
1.0
|
CE1
|
F:HIS536
|
3.3
|
2.0
|
1.0
|
C
|
F:LEU482
|
3.4
|
2.0
|
1.0
|
OE1
|
F:GLU46
|
3.7
|
6.8
|
1.0
|
N
|
F:LEU482
|
3.9
|
2.0
|
1.0
|
OE1
|
F:GLU321
|
4.0
|
16.4
|
1.0
|
OE2
|
F:GLU321
|
4.0
|
14.2
|
1.0
|
CA
|
F:LEU482
|
4.1
|
2.0
|
1.0
|
O
|
F:HOH684
|
4.1
|
2.0
|
1.0
|
O
|
F:HOH712
|
4.2
|
5.5
|
1.0
|
NE2
|
F:GLN481
|
4.3
|
2.7
|
1.0
|
CG
|
F:GLU46
|
4.4
|
2.3
|
1.0
|
ND1
|
F:HIS536
|
4.4
|
2.0
|
1.0
|
CG
|
F:HIS536
|
4.4
|
2.0
|
1.0
|
CD
|
F:GLU321
|
4.5
|
13.2
|
1.0
|
N
|
F:VAL483
|
4.5
|
2.0
|
1.0
|
CB
|
F:LEU482
|
4.5
|
2.0
|
1.0
|
NZ
|
F:LYS358
|
4.5
|
2.0
|
1.0
|
CA
|
F:VAL483
|
4.8
|
2.0
|
1.0
|
CD
|
F:LYS358
|
4.9
|
2.0
|
1.0
|
C
|
F:GLN481
|
4.9
|
2.0
|
1.0
|
CE
|
F:LYS358
|
5.0
|
2.0
|
1.0
|
CG
|
F:LEU482
|
5.0
|
2.6
|
1.0
|
CG2
|
F:VAL483
|
5.0
|
2.0
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 2frv
Go back to
Magnesium Binding Sites List in 2frv
Magnesium binding site 5 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/MG/pdb/fr/2frv-MG-sphere_05.jpg) Mono view
![](/pictures/MG/pdb/fr/2frv-MG-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg540
b:2.0
occ:1.00
|
O
|
H:HOH5065
|
1.9
|
3.5
|
1.0
|
O
|
H:HOH5064
|
1.9
|
2.0
|
1.0
|
OE2
|
H:GLU46
|
2.0
|
4.1
|
1.0
|
O
|
H:HOH5063
|
2.2
|
2.0
|
1.0
|
O
|
H:LEU482
|
2.2
|
2.0
|
1.0
|
NE2
|
H:HIS536
|
2.3
|
2.0
|
1.0
|
CD
|
H:GLU46
|
3.1
|
4.1
|
1.0
|
CD2
|
H:HIS536
|
3.2
|
2.0
|
1.0
|
CE1
|
H:HIS536
|
3.3
|
2.0
|
1.0
|
C
|
H:LEU482
|
3.4
|
2.0
|
1.0
|
OE1
|
H:GLU46
|
3.6
|
6.8
|
1.0
|
N
|
H:LEU482
|
3.9
|
2.0
|
1.0
|
OE1
|
H:GLU321
|
4.0
|
16.4
|
1.0
|
OE2
|
H:GLU321
|
4.0
|
14.2
|
1.0
|
CA
|
H:LEU482
|
4.1
|
2.0
|
1.0
|
O
|
H:HOH872
|
4.1
|
2.0
|
1.0
|
O
|
H:HOH900
|
4.2
|
5.5
|
1.0
|
NE2
|
H:GLN481
|
4.3
|
2.7
|
1.0
|
CG
|
H:GLU46
|
4.4
|
2.3
|
1.0
|
ND1
|
H:HIS536
|
4.4
|
2.0
|
1.0
|
CG
|
H:HIS536
|
4.4
|
2.0
|
1.0
|
CD
|
H:GLU321
|
4.5
|
13.2
|
1.0
|
N
|
H:VAL483
|
4.5
|
2.0
|
1.0
|
CB
|
H:LEU482
|
4.5
|
2.0
|
1.0
|
NZ
|
H:LYS358
|
4.5
|
2.0
|
1.0
|
CA
|
H:VAL483
|
4.8
|
2.0
|
1.0
|
CD
|
H:LYS358
|
4.9
|
2.0
|
1.0
|
C
|
H:GLN481
|
4.9
|
2.0
|
1.0
|
CE
|
H:LYS358
|
5.0
|
2.0
|
1.0
|
CG
|
H:LEU482
|
5.0
|
2.6
|
1.0
|
CG2
|
H:VAL483
|
5.0
|
2.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 2frv
Go back to
Magnesium Binding Sites List in 2frv
Magnesium binding site 6 out
of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase
![](/pictures/MG/pdb/fr/2frv-MG-sphere_06.jpg) Mono view
![](/pictures/MG/pdb/fr/2frv-MG-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg540
b:2.0
occ:1.00
|
O
|
J:HOH5078
|
1.9
|
3.5
|
1.0
|
O
|
J:HOH5077
|
1.9
|
2.0
|
1.0
|
OE2
|
J:GLU46
|
2.0
|
4.1
|
1.0
|
O
|
J:HOH5076
|
2.2
|
2.0
|
1.0
|
O
|
J:LEU482
|
2.2
|
2.0
|
1.0
|
NE2
|
J:HIS536
|
2.3
|
2.0
|
1.0
|
CD
|
J:GLU46
|
3.1
|
4.1
|
1.0
|
CD2
|
J:HIS536
|
3.2
|
2.0
|
1.0
|
CE1
|
J:HIS536
|
3.3
|
2.0
|
1.0
|
C
|
J:LEU482
|
3.4
|
2.0
|
1.0
|
OE1
|
J:GLU46
|
3.7
|
6.8
|
1.0
|
N
|
J:LEU482
|
3.9
|
2.0
|
1.0
|
OE1
|
J:GLU321
|
4.0
|
16.4
|
1.0
|
OE2
|
J:GLU321
|
4.0
|
14.2
|
1.0
|
CA
|
J:LEU482
|
4.1
|
2.0
|
1.0
|
O
|
J:HOH1060
|
4.1
|
2.0
|
1.0
|
O
|
J:HOH1088
|
4.2
|
5.5
|
1.0
|
NE2
|
J:GLN481
|
4.3
|
2.7
|
1.0
|
CG
|
J:GLU46
|
4.4
|
2.3
|
1.0
|
ND1
|
J:HIS536
|
4.4
|
2.0
|
1.0
|
CG
|
J:HIS536
|
4.4
|
2.0
|
1.0
|
CD
|
J:GLU321
|
4.5
|
13.2
|
1.0
|
N
|
J:VAL483
|
4.5
|
2.0
|
1.0
|
CB
|
J:LEU482
|
4.5
|
2.0
|
1.0
|
NZ
|
J:LYS358
|
4.5
|
2.0
|
1.0
|
CA
|
J:VAL483
|
4.8
|
2.0
|
1.0
|
CD
|
J:LYS358
|
4.9
|
2.0
|
1.0
|
C
|
J:GLN481
|
4.9
|
2.0
|
1.0
|
CE
|
J:LYS358
|
5.0
|
2.0
|
1.0
|
CG
|
J:LEU482
|
5.0
|
2.6
|
1.0
|
CG2
|
J:VAL483
|
5.0
|
2.0
|
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: Tue Aug 13 23:17:31 2024
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