Magnesium in PDB 7nem: Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form

Enzymatic activity of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form

All present enzymatic activity of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form:
1.12.99.6;

Protein crystallography data

The structure of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form, PDB code: 7nem was solved by S.B.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.80 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.402, 100.252, 168.536, 90, 90, 90
R / Rfree (%) 15 / 16.7

Other elements in 7nem:

The structure of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 24 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form (pdb code 7nem). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form, PDB code: 7nem:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7nem

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Magnesium binding site 1 out of 4 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg603

b:7.0
occ:1.00
 O L:HOH725 2.1 9.5 1.0
O L:HOH720 2.1 11.5 1.0
O L:HOH755 2.1 9.7 1.0
OE2 L:GLU42 2.1 9.8 1.0
NE2 L:HIS552 2.2 9.6 1.0
O L:ALA498 2.2 10.0 1.0
CE1 L:HIS552 3.1 9.8 1.0
CD L:GLU42 3.2 9.8 1.0
CD2 L:HIS552 3.2 8.5 1.0
C L:ALA498 3.3 9.8 1.0
OE1 L:GLU42 3.5 10.6 1.0
N L:ALA498 3.7 9.9 1.0
OE1 L:GLN497 4.0 13.2 1.0
CA L:ALA498 4.0 9.8 1.0
OE2 L:GLU329 4.1 11.6 1.0
OE1 L:GLU329 4.2 11.8 1.0
O L:HOH800 4.2 10.3 1.0
ND1 L:HIS552 4.2 9.8 1.0
O L:HOH967 4.3 9.5 1.0
CG L:HIS552 4.3 9.6 1.0
NZ L:LYS366 4.3 11.5 1.0
N L:VAL499 4.4 9.7 1.0
CB L:ALA498 4.4 10.1 1.0
CG L:GLU42 4.5 10.8 1.0
CD L:LYS366 4.5 10.8 1.0
CD L:GLU329 4.6 11.3 1.0
C L:GLN497 4.7 10.0 1.0
CA L:VAL499 4.7 10.5 1.0
CE L:LYS366 4.7 9.7 1.0
CA L:GLN497 4.9 10.3 1.0

Magnesium binding site 2 out of 4 in 7nem

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Magnesium binding site 2 out of 4 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg604

b:29.5
occ:1.00
 O L:HOH1106 1.9 29.8 1.0
O L:HOH1050 2.0 22.1 1.0
O L:HOH1059 2.2 23.3 1.0
O L:HOH826 2.2 23.9 1.0
O L:HOH1119 2.3 33.7 1.0
O L:HOH832 2.3 30.8 1.0
ND2 L:ASN294 3.9 14.9 1.0
OD1 L:ASN81 3.9 16.5 1.0
O L:HOH947 4.0 31.6 1.0
O L:HOH917 4.1 33.0 1.0
O L:ILE82 4.3 13.2 1.0
O L:GLU77 4.4 11.9 1.0
O L:HOH1003 4.4 16.1 1.0
CA L:SER78 4.4 11.5 1.0
CA L:ASN81 4.4 11.6 1.0
O L:HOH728 4.5 18.3 1.0
O L:HOH1024 4.5 12.1 1.0
OD1 L:ASP83 4.6 20.6 1.0
O L:SER78 4.6 12.7 1.0
N L:ILE82 4.7 12.1 1.0
C L:ASN81 4.8 12.0 1.0
OG L:SER319 4.8 20.4 1.0
CG L:ASN81 4.9 14.3 1.0
C L:ILE82 5.0 12.8 1.0
C L:GLU77 5.0 11.4 1.0
N L:SER78 5.0 10.5 1.0

Magnesium binding site 3 out of 4 in 7nem

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Magnesium binding site 3 out of 4 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:8.2
occ:1.00
 OE2 M:GLU42 2.1 11.3 1.0
O M:HOH722 2.1 12.2 1.0
O M:HOH728 2.1 11.4 1.0
O M:ALA498 2.1 11.0 1.0
O M:HOH751 2.2 11.5 1.0
NE2 M:HIS552 2.2 11.5 1.0
CE1 M:HIS552 3.1 11.3 1.0
CD M:GLU42 3.1 11.6 1.0
CD2 M:HIS552 3.2 11.2 1.0
C M:ALA498 3.3 11.7 1.0
OE1 M:GLU42 3.5 12.2 1.0
N M:ALA498 3.7 11.3 1.0
OE1 M:GLN497 3.9 13.7 1.0
CA M:ALA498 4.0 11.3 1.0
OE2 M:GLU329 4.1 12.9 1.0
OE1 M:GLU329 4.2 12.5 1.0
O M:HOH752 4.2 11.7 1.0
ND1 M:HIS552 4.3 10.9 1.0
O M:HOH961 4.3 11.5 1.0
CG M:HIS552 4.3 10.1 1.0
NZ M:LYS366 4.3 13.1 1.0
N M:VAL499 4.4 10.8 1.0
CB M:ALA498 4.4 11.5 1.0
CG M:GLU42 4.4 12.0 1.0
CD M:LYS366 4.5 12.9 1.0
CD M:GLU329 4.6 12.0 1.0
C M:GLN497 4.6 11.9 1.0
CA M:VAL499 4.7 10.9 1.0
CE M:LYS366 4.8 12.9 1.0
CA M:GLN497 4.9 11.1 1.0

Magnesium binding site 4 out of 4 in 7nem

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Magnesium binding site 4 out of 4 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg604

b:23.7
occ:1.00
 O T:HOH549 2.0 25.3 1.0
O M:HOH1084 2.0 22.4 1.0
O T:HOH591 2.2 20.6 1.0
O M:HOH739 3.7 17.5 1.0
O T:HOH515 4.0 28.7 1.0
OE1 T:GLU209 4.1 20.6 0.5
OE2 T:GLU209 4.3 19.0 0.5
N M:LYS460 4.4 13.1 1.0
O T:HOH546 4.6 26.4 1.0
CD T:GLU209 4.6 17.1 0.5
O M:PHE458 4.7 14.8 1.0
CB M:LYS460 4.9 14.4 1.0
CA M:VAL459 4.9 13.7 1.0

Reference:

R.M.Evans, S.E.Beaton, L.Kertiss, W.K.Myers, S.B.Carr, F.A.Armstrong. A Comprehensive Structural and Kinetic Investigation of the Role of the Active-Site Argininein Bidirectional Hydrogen Activation By the [Nife]-Hydrogenase "Hyd-2) From Escherichia Coli To Be Published.
Page generated: Thu Oct 3 01:36:13 2024

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