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Magnesium 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:

Nickel (Ni) 3 atoms
Iron (Fe) 36 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the V74M Large Subunit Mutant of Ni-Fe Hydrogenase in An Oxidized State, PDB code: 3h3x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3h3x

Go back to Magnesium Binding Sites List in 3h3x
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg553

b:35.2
occ:1.00
O Q:HOH556 2.0 34.9 1.0
O Q:HOH555 2.0 35.5 1.0
O Q:HOH554 2.0 34.4 1.0
O Q:LEU495 2.1 34.3 1.0
OE2 Q:GLU53 2.1 35.3 1.0
NE2 Q:HIS549 2.2 34.5 1.0
CD Q:GLU53 3.1 35.3 1.0
CE1 Q:HIS549 3.1 34.2 1.0
C Q:LEU495 3.2 35.2 1.0
CD2 Q:HIS549 3.3 34.5 1.0
OE1 Q:GLU53 3.4 33.9 1.0
N Q:LEU495 3.7 35.8 1.0
CA Q:LEU495 3.9 35.7 1.0
O Q:HOH659 4.1 34.5 1.0
OE1 Q:GLU334 4.1 38.0 1.0
OE2 Q:GLU334 4.1 38.4 1.0
OE1 Q:GLN494 4.1 37.5 1.0
CB Q:LEU495 4.2 35.6 1.0
ND1 Q:HIS549 4.3 33.7 1.0
NZ Q:LYS372 4.3 35.5 1.0
N Q:VAL496 4.3 35.3 1.0
O Q:HOH577 4.3 34.6 1.0
CG Q:HIS549 4.4 35.1 1.0
CD Q:LYS372 4.4 35.8 1.0
CG Q:GLU53 4.4 34.8 1.0
CD Q:GLU334 4.6 38.1 1.0
C Q:GLN494 4.7 35.5 1.0
CE Q:LYS372 4.7 36.7 1.0
CA Q:VAL496 4.7 35.4 1.0
CA Q:GLN494 5.0 35.7 1.0
CB Q:GLN494 5.0 36.1 1.0

Magnesium binding site 2 out of 3 in 3h3x

Go back to Magnesium Binding Sites List in 3h3x
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg553

b:34.4
occ:1.00
O R:HOH556 2.0 35.6 1.0
O R:HOH555 2.0 33.4 1.0
O R:HOH554 2.1 33.9 1.0
OE2 R:GLU53 2.1 35.0 1.0
O R:LEU495 2.2 35.5 1.0
NE2 R:HIS549 2.2 33.9 1.0
CD R:GLU53 3.1 35.4 1.0
CE1 R:HIS549 3.1 34.4 1.0
CD2 R:HIS549 3.2 35.0 1.0
C R:LEU495 3.3 36.0 1.0
OE1 R:GLU53 3.3 35.6 1.0
N R:LEU495 3.7 36.0 1.0
OE1 R:GLU334 3.8 37.4 1.0
CA R:LEU495 4.0 35.8 1.0
OE2 R:GLU334 4.0 37.8 1.0
OE1 R:GLN494 4.1 35.6 1.0
O R:HOH655 4.2 33.6 1.0
ND1 R:HIS549 4.3 34.0 1.0
CB R:LEU495 4.3 35.5 1.0
CD R:GLU334 4.4 36.9 1.0
CG R:HIS549 4.4 35.0 1.0
CD R:LYS372 4.4 36.1 1.0
NZ R:LYS372 4.4 37.9 1.0
CG R:GLU53 4.4 35.3 1.0
O R:HOH653 4.4 36.5 1.0
N R:VAL496 4.4 35.7 1.0
CE R:LYS372 4.7 37.1 1.0
C R:GLN494 4.7 36.8 1.0
CA R:VAL496 4.8 36.0 1.0

Magnesium binding site 3 out of 3 in 3h3x

Go back to Magnesium Binding Sites List in 3h3x
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg553

b:33.8
occ:1.00
O S:HOH556 2.0 30.1 1.0
O S:HOH555 2.0 34.9 1.0
O S:HOH554 2.0 30.1 1.0
OE2 S:GLU53 2.1 35.5 1.0
O S:LEU495 2.1 34.4 1.0
NE2 S:HIS549 2.2 34.7 1.0
CD S:GLU53 3.0 35.5 1.0
CE1 S:HIS549 3.1 34.6 1.0
CD2 S:HIS549 3.3 33.7 1.0
C S:LEU495 3.3 34.9 1.0
OE1 S:GLU53 3.4 33.3 1.0
N S:LEU495 3.6 35.2 1.0
CA S:LEU495 3.9 35.1 1.0
OE1 S:GLU334 4.0 40.3 1.0
OE1 S:GLN494 4.1 33.8 1.0
O S:HOH626 4.2 24.5 1.0
CB S:LEU495 4.2 35.0 1.0
ND1 S:HIS549 4.3 35.1 1.0
O S:HOH592 4.3 35.6 1.0
NZ S:LYS372 4.3 36.8 1.0
OE2 S:GLU334 4.3 39.7 1.0
CG S:HIS549 4.4 35.5 1.0
N S:VAL496 4.4 34.9 1.0
CG S:GLU53 4.4 35.3 1.0
CD S:LYS372 4.5 36.6 1.0
CD S:GLU334 4.6 38.4 1.0
C S:GLN494 4.7 35.6 1.0
CA S:VAL496 4.7 35.3 1.0
CE S:LYS372 4.8 37.0 1.0
CA S:GLN494 5.0 35.7 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 Aug 14 15:03:46 2024

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