Magnesium in PDB 6gam: Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme)

All present enzymatic activity of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme):
1.12.99.6;

The structure of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme), PDB code: 6gam was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.32 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.477, 100.471, 168.656, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 17

The structure of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) (pdb code 6gam). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme), PDB code: 6gam:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg603 b:7.8 occ:1.00 O L:HOH726 2.1 11.0 1.0 O L:HOH739 2.1 9.8 1.0 O L:HOH732 2.1 10.1 1.0 O L:ALA498 2.1 9.4 1.0 OE2 L:GLU42 2.1 9.3 1.0 NE2 L:HIS552 2.2 9.1 1.0 CE1 L:HIS552 3.1 8.5 1.0 CD L:GLU42 3.2 9.7 1.0 CD2 L:HIS552 3.2 9.1 1.0 C L:ALA498 3.3 9.9 1.0 OE1 L:GLU42 3.5 10.2 1.0 N L:ALA498 3.7 10.1 1.0 OE1 L:GLN497 4.0 13.9 1.0 CA L:ALA498 4.0 9.7 1.0 OE2 L:GLU329 4.1 12.6 1.0 OE1 L:GLU329 4.2 13.4 1.0 O L:HOH766 4.2 10.4 1.0 ND1 L:HIS552 4.2 8.9 1.0 O L:HOH922 4.3 9.3 1.0 CG L:HIS552 4.3 9.4 1.0 NZ L:LYS366 4.3 10.8 1.0 N L:VAL499 4.4 10.0 1.0 CB L:ALA498 4.4 9.5 1.0 CG L:GLU42 4.5 10.2 1.0 CD L:LYS366 4.5 10.6 1.0 CD L:GLU329 4.6 12.5 1.0 C L:GLN497 4.7 10.2 1.0 CE L:LYS366 4.7 10.0 1.0 CA L:VAL499 4.7 10.4 1.0 CA L:GLN497 4.9 10.3 1.0

Magnesium binding site 2 out of 2 in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:9.8 occ:1.00 OE2 M:GLU42 2.1 11.3 1.0 O M:HOH726 2.1 11.6 1.0 O M:HOH753 2.1 11.7 1.0 O M:HOH750 2.1 12.0 1.0 O M:ALA498 2.1 12.0 1.0 NE2 M:HIS552 2.2 10.9 1.0 CE1 M:HIS552 3.1 10.8 1.0 CD M:GLU42 3.1 12.2 1.0 CD2 M:HIS552 3.2 10.4 1.0 C M:ALA498 3.3 11.8 1.0 OE1 M:GLU42 3.5 12.4 1.0 N M:ALA498 3.7 11.2 1.0 OE1 M:GLN497 4.0 14.2 1.0 CA M:ALA498 4.0 11.1 1.0 OE2 M:GLU329 4.1 14.2 1.0 O M:HOH743 4.2 11.6 1.0 OE1 M:GLU329 4.2 14.9 1.0 ND1 M:HIS552 4.2 10.0 1.0 O M:HOH898 4.3 10.9 1.0 CG M:HIS552 4.3 9.9 1.0 NZ M:LYS366 4.3 12.5 1.0 N M:VAL499 4.4 10.7 1.0 CB M:ALA498 4.4 11.3 1.0 CG M:GLU42 4.5 13.0 1.0 CD M:LYS366 4.5 13.2 1.0 CD M:GLU329 4.6 14.7 1.0 CA M:VAL499 4.7 11.5 1.0 C M:GLN497 4.7 11.3 1.0 CE M:LYS366 4.7 12.6 1.0 CA M:GLN497 4.9 10.9 1.0

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798