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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:

Nickel (Ni) 6 atoms
Iron (Fe) 72 atoms

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


Mono view


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

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


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


Mono view


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

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Oxidized Form of Ni-Fe Hydrogenase


Mono view


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


Mono view


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


Mono view


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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