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Magnesium in PDB 6g7m: Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2

Enzymatic activity of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2

All present enzymatic activity of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2:
1.12.99.6;

Protein crystallography data

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m was solved by S.B.Carr, F.A.Armstrong, L.Zhang, S.E.Beaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.75 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.237, 100.986, 169.425, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19

Other elements in 6g7m:

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 24 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 (pdb code 6g7m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6g7m

Go back to Magnesium Binding Sites List in 6g7m
Magnesium binding site 1 out of 4 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg603

b:7.1
occ:1.00
 O L:HOH747 2.0 11.2 1.0
O L:HOH743 2.1 11.0 1.0
O L:HOH722 2.1 12.5 1.0
O L:ALA498 2.1 10.9 1.0
OE2 L:GLU42 2.2 12.7 1.0
NE2 L:HIS552 2.2 11.6 1.0
CE1 L:HIS552 3.1 11.8 1.0
CD L:GLU42 3.2 11.9 1.0
CD2 L:HIS552 3.2 10.8 1.0
C L:ALA498 3.3 12.4 1.0
OE1 L:GLU42 3.5 12.8 1.0
N L:ALA498 3.8 11.7 1.0
OE1 L:GLN497 4.0 16.4 1.0
CA L:ALA498 4.1 11.4 1.0
OE2 L:GLU329 4.2 13.4 1.0
O L:HOH793 4.2 12.7 1.0
OE1 L:GLU329 4.2 15.7 1.0
O L:HOH932 4.3 12.2 1.0
ND1 L:HIS552 4.3 11.3 1.0
NZ L:LYS366 4.3 12.0 1.0
CG L:HIS552 4.4 11.9 1.0
N L:VAL499 4.4 12.5 1.0
CB L:ALA498 4.5 12.3 1.0
CG L:GLU42 4.5 12.8 1.0
CD L:LYS366 4.5 12.3 1.0
CD L:GLU329 4.6 14.6 1.0
CA L:VAL499 4.7 12.5 1.0
C L:GLN497 4.8 12.0 1.0
CE L:LYS366 4.8 12.3 1.0
CA L:GLN497 5.0 12.3 1.0

Magnesium binding site 2 out of 4 in 6g7m

Go back to Magnesium Binding Sites List in 6g7m
Magnesium binding site 2 out of 4 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg604

b:47.1
occ:1.00
 O L:HOH939 2.1 24.7 1.0
O L:HOH985 2.4 23.7 1.0
O L:HOH817 2.5 28.2 1.0
OD1 L:ASN81 4.0 19.4 1.0
ND2 L:ASN294 4.1 17.3 1.0
O L:HOH733 4.3 22.2 1.0
CA L:SER78 4.3 12.6 1.0
CA L:ASN81 4.4 14.5 1.0
O L:GLU77 4.4 14.5 1.0
O L:HOH934 4.5 20.8 1.0
O L:ILE82 4.5 15.0 1.0
O L:HOH899 4.6 16.9 1.0
O L:SER78 4.6 14.2 1.0
OG L:SER319 4.7 21.4 1.0
N L:ILE82 4.9 14.4 1.0
C L:ASN81 4.9 14.6 1.0
OD1 L:ASP83 4.9 22.1 1.0
CG L:ASN81 4.9 17.4 1.0
C L:SER78 5.0 13.2 1.0
N L:SER78 5.0 12.5 1.0
O L:HOH1029 5.0 26.0 1.0

Magnesium binding site 3 out of 4 in 6g7m

Go back to Magnesium Binding Sites List in 6g7m
Magnesium binding site 3 out of 4 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:9.2
occ:1.00
 O M:ALA498 2.1 14.9 1.0
OE2 M:GLU42 2.1 13.5 1.0
O M:HOH710 2.1 14.1 1.0
O M:HOH734 2.1 13.3 1.0
NE2 M:HIS552 2.2 12.6 1.0
O M:HOH742 2.2 13.5 1.0
CE1 M:HIS552 3.1 13.4 1.0
CD M:GLU42 3.2 14.4 1.0
CD2 M:HIS552 3.2 12.3 1.0
C M:ALA498 3.3 13.5 1.0
OE1 M:GLU42 3.5 14.4 1.0
N M:ALA498 3.8 12.7 1.0
OE1 M:GLN497 4.0 17.4 1.0
CA M:ALA498 4.0 12.7 1.0
OE2 M:GLU329 4.2 19.0 1.0
O M:HOH721 4.3 15.7 1.0
OE1 M:GLU329 4.3 16.9 1.0
ND1 M:HIS552 4.3 12.4 1.0
NZ M:LYS366 4.3 15.5 1.0
O M:HOH894 4.3 12.8 1.0
CG M:HIS552 4.3 12.2 1.0
N M:VAL499 4.4 13.4 1.0
CB M:ALA498 4.4 12.7 1.0
CG M:GLU42 4.5 15.3 1.0
CD M:LYS366 4.5 15.0 1.0
CD M:GLU329 4.7 17.0 1.0
CA M:VAL499 4.7 13.2 1.0
C M:GLN497 4.7 13.6 1.0
CE M:LYS366 4.8 14.6 1.0
CA M:GLN497 5.0 12.4 1.0

Magnesium binding site 4 out of 4 in 6g7m

Go back to Magnesium Binding Sites List in 6g7m
Magnesium binding site 4 out of 4 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg604

b:39.5
occ:1.00
 O M:HOH981 2.1 26.8 1.0
O M:HOH995 2.1 31.1 1.0
O M:HOH968 2.2 25.9 1.0
O M:HOH745 3.7 22.0 1.0
N M:LYS460 4.5 15.4 1.0
O T:HOH514 4.7 30.3 1.0
O M:PHE458 4.8 15.1 1.0
CB M:LYS460 5.0 19.6 1.0
CA M:VAL459 5.0 16.7 1.0

Reference:

L.Zhang, S.E.Beaton, S.B.Carr, F.A.Armstrong. Direct Visible Light Activation of A Surface Cysteine-Engineered [Nife]-Hydrogenase By Silver Nanoclusters Energy Environ Sci 2019.
ISSN: ISSN 1754-5706
DOI: 10.1039/C8EE02361A
Page generated: Tue Oct 1 01:01:48 2024

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