Magnesium in PDB 6ehs: E. Coli Hydrogenase-2 Chemically Reduced Structure

All present enzymatic activity of E. Coli Hydrogenase-2 Chemically Reduced Structure:
1.12.99.6;

The structure of E. Coli Hydrogenase-2 Chemically Reduced Structure, PDB code: 6ehs was solved by S.B.Carr, R.M.Evans, S.E.Beaton, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.08 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.885, 100.065, 168.801, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 16.3

The structure of E. Coli Hydrogenase-2 Chemically Reduced Structure also contains other interesting chemical elements:

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

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

Magnesium binding site 1 out of 2 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg603 b:9.2 occ:1.00 O L:HOH732 2.1 15.1 1.0 OE2 L:GLU42 2.1 12.5 1.0 O L:HOH720 2.1 12.7 1.0 O L:ALA498 2.1 14.7 1.0 O L:HOH737 2.1 13.0 1.0 NE2 L:HIS552 2.2 12.1 1.0 CD L:GLU42 3.1 13.4 1.0 CE1 L:HIS552 3.1 12.7 1.0 CD2 L:HIS552 3.2 12.0 1.0 C L:ALA498 3.3 12.2 1.0 OE1 L:GLU42 3.5 14.5 1.0 N L:ALA498 3.7 11.5 1.0 CA L:ALA498 4.0 11.5 1.0 OE1 L:GLN497 4.0 17.4 1.0 OE2 L:GLU329 4.1 17.3 1.0 OE1 L:GLU329 4.2 20.7 1.0 O L:HOH788 4.2 14.1 1.0 O L:HOH924 4.3 12.3 1.0 ND1 L:HIS552 4.3 11.8 1.0 NZ L:LYS366 4.3 16.0 1.0 CG L:HIS552 4.3 11.5 1.0 CB L:ALA498 4.4 13.1 1.0 N L:VAL499 4.4 12.5 1.0 CG L:GLU42 4.5 14.1 1.0 CD L:LYS366 4.5 15.5 1.0 CD L:GLU329 4.6 17.2 1.0 C L:GLN497 4.7 12.7 1.0 CA L:VAL499 4.7 12.8 1.0 CE L:LYS366 4.7 14.9 1.0 CA L:GLN497 4.9 13.3 1.0

Magnesium binding site 2 out of 2 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:11.5 occ:1.00 O M:HOH713 2.1 17.0 1.0 O M:HOH758 2.1 16.2 1.0 OE2 M:GLU42 2.1 15.1 1.0 O M:ALA498 2.1 15.0 1.0 O M:HOH733 2.1 16.2 1.0 NE2 M:HIS552 2.2 14.7 1.0 CE1 M:HIS552 3.1 12.9 1.0 CD M:GLU42 3.1 16.3 1.0 CD2 M:HIS552 3.3 15.0 1.0 C M:ALA498 3.3 13.8 1.0 OE1 M:GLU42 3.5 16.6 1.0 N M:ALA498 3.8 14.3 1.0 OE1 M:GLN497 4.0 20.4 1.0 CA M:ALA498 4.0 13.9 1.0 OE2 M:GLU329 4.1 21.1 1.0 OE1 M:GLU329 4.2 21.8 1.0 O M:HOH782 4.2 14.8 1.0 ND1 M:HIS552 4.2 12.9 1.0 O M:HOH894 4.3 14.3 1.0 NZ M:LYS366 4.3 17.5 1.0 CG M:HIS552 4.4 13.6 1.0 N M:VAL499 4.4 14.3 1.0 CB M:ALA498 4.4 14.1 1.0 CG M:GLU42 4.5 15.6 1.0 CD M:LYS366 4.6 18.2 1.0 CD M:GLU329 4.6 20.0 1.0 CA M:VAL499 4.7 14.1 1.0 C M:GLN497 4.7 14.1 1.0 CE M:LYS366 4.7 18.3 1.0 CA M:GLN497 4.9 13.5 1.0

S.E.Beaton, R.M.Evans, A.J.Finney, C.M.Lamont, F.A.Armstrong, F.Sargent, S.B.Carr. The Structure of Hydrogenase-2 Fromescherichia Coli: Implications For H2-Driven Proton Pumping. Biochem. J. V. 475 1353 2018.
ISSN: ESSN 1470-8728
PubMed: 29555844
DOI: 10.1042/BCJ20180053