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Nickel in PDB 3h3x: Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State

Enzymatic activity of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State

All present enzymatic activity of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State:
1.12.2.1;

Protein crystallography data

The structure of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State, PDB code: 3h3x was solved by A.Volbeda, N.Martinez, L.Martin, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.400, 99.200, 182.300, 90.00, 92.80, 90.00
R / Rfree (%) 20.3 / 24.7

Other elements in 3h3x:

The structure of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Iron (Fe) 36 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State (pdb code 3h3x). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State, PDB code: 3h3x:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3h3x

Go back to Nickel Binding Sites List in 3h3x
Nickel binding site 1 out of 3 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ni551

b:39.2
occ:1.00
SG Q:CYS72 2.1 38.8 1.0
SG Q:CYS543 2.3 39.3 1.0
SG Q:CYS75 2.4 36.6 1.0
SG Q:CYS546 2.5 36.7 1.0
FE Q:FCO550 2.7 35.9 1.0
CB Q:CYS72 2.8 36.5 1.0
CB Q:CYS75 3.3 36.0 1.0
CB Q:CYS543 3.3 36.9 1.0
CB Q:CYS546 3.5 35.8 1.0
N Q:CYS75 3.6 36.5 1.0
C1 Q:FCO550 3.7 37.6 1.0
CA Q:CYS75 4.0 36.6 1.0
C2 Q:FCO550 4.1 37.3 1.0
C3 Q:FCO550 4.3 34.3 1.0
CA Q:CYS72 4.3 36.5 1.0
CA Q:CYS546 4.5 36.6 1.0
N Q:CYS546 4.5 36.3 1.0
N1 Q:FCO550 4.6 36.5 1.0
CB Q:MET74 4.6 36.3 1.0
NH1 Q:ARG476 4.7 38.1 1.0
CA Q:CYS543 4.8 37.4 1.0
C Q:MET74 4.8 36.7 1.0
C Q:CYS75 4.8 37.1 1.0
N Q:MET74 4.8 36.8 1.0
C Q:CYS72 4.9 36.6 1.0
CG Q:GLU25 4.9 36.7 1.0
O Q:CYS75 4.9 37.2 1.0
CD Q:ARG476 4.9 36.0 1.0
CA Q:MET74 5.0 37.0 1.0

Nickel binding site 2 out of 3 in 3h3x

Go back to Nickel Binding Sites List in 3h3x
Nickel binding site 2 out of 3 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ni551

b:41.0
occ:1.00
SG R:CYS72 2.2 41.1 1.0
SG R:CYS543 2.2 39.6 1.0
SG R:CYS75 2.3 36.8 1.0
SG R:CYS546 2.4 37.8 1.0
FE R:FCO550 2.7 37.1 1.0
CB R:CYS72 3.0 37.9 1.0
CB R:CYS75 3.2 37.0 1.0
CB R:CYS543 3.2 37.3 1.0
CB R:CYS546 3.5 36.4 1.0
N R:CYS75 3.7 36.9 1.0
C1 R:FCO550 3.7 40.2 1.0
CA R:CYS75 4.0 36.9 1.0
C2 R:FCO550 4.1 37.8 1.0
C3 R:FCO550 4.2 36.5 1.0
CA R:CYS72 4.4 37.7 1.0
CA R:CYS546 4.5 36.5 1.0
NH1 R:ARG476 4.5 37.9 1.0
N1 R:FCO550 4.6 41.6 1.0
N R:CYS546 4.6 37.3 1.0
CB R:MET74 4.7 37.5 1.0
CA R:CYS543 4.7 37.4 1.0
C R:CYS75 4.8 36.8 1.0
C R:MET74 4.8 36.8 1.0
O R:CYS75 4.8 37.4 1.0
CD R:ARG476 4.8 36.8 1.0
CZ R:ARG476 4.9 37.3 1.0
N R:MET74 4.9 36.9 1.0
C R:CYS72 5.0 38.0 1.0

Nickel binding site 3 out of 3 in 3h3x

Go back to Nickel Binding Sites List in 3h3x
Nickel binding site 3 out of 3 in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ni551

b:39.2
occ:1.00
SG S:CYS72 2.0 38.3 1.0
SG S:CYS543 2.2 38.7 1.0
SG S:CYS75 2.5 35.1 1.0
SG S:CYS546 2.6 37.0 1.0
CB S:CYS72 2.8 37.5 1.0
FE S:FCO550 2.9 35.6 1.0
CB S:CYS543 3.3 36.8 1.0
CB S:CYS75 3.3 36.3 1.0
CB S:CYS546 3.6 35.6 1.0
N S:CYS75 3.6 36.6 1.0
CA S:CYS75 4.0 36.4 1.0
C1 S:FCO550 4.1 37.2 1.0
C3 S:FCO550 4.2 37.3 1.0
C2 S:FCO550 4.2 40.0 1.0
CA S:CYS72 4.3 37.2 1.0
CB S:MET74 4.5 36.3 1.0
CA S:CYS546 4.6 35.8 1.0
N S:CYS546 4.6 36.3 1.0
C S:MET74 4.7 36.3 1.0
C S:CYS75 4.7 36.9 1.0
N S:MET74 4.7 36.3 1.0
NH1 S:ARG476 4.7 39.3 1.0
CA S:CYS543 4.7 37.3 1.0
C S:CYS72 4.8 37.4 1.0
O S:CYS75 4.8 37.5 1.0
CG S:GLU25 4.8 36.7 1.0
CA S:MET74 4.9 36.9 1.0
N1 S:FCO550 4.9 40.8 1.0
CD S:ARG476 5.0 35.1 1.0

Reference:

S.Dementin, F.Leroux, L.Cournac, A.L.De Lacey, A.Volbeda, C.Leger, B.Burlat, N.Martinez, S.Champ, L.Martin, O.Sanganas, M.Haumann, V.M.Fernandez, B.Guigliarelli, J.C.Fontecilla-Camps, M.Rousset. Introduction of Methionines in the Gas Channel Makes [Nife] Hydrogenase Aero-Tolerant J.Am.Chem.Soc. V. 131 10156 2009.
ISSN: ISSN 0002-7863
PubMed: 19580279
DOI: 10.1021/JA9018258
Page generated: Wed Oct 9 17:19:30 2024

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