Magnesium in PDB 6en9: E. Coli Hydrogenase-2 (Hydrogen Reduced Form)

All present enzymatic activity of E. Coli Hydrogenase-2 (Hydrogen Reduced Form):
1.12.99.6;

The structure of E. Coli Hydrogenase-2 (Hydrogen Reduced Form), PDB code: 6en9 was solved by S.B.Carr, S.E.Beaton, R.M.Evans, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.35 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.602, 100.540, 168.587, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.5

The structure of E. Coli Hydrogenase-2 (Hydrogen Reduced Form) 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 (Hydrogen Reduced Form) (pdb code 6en9). 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 (Hydrogen Reduced Form), PDB code: 6en9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Hydrogenase-2 (Hydrogen Reduced Form)


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 (Hydrogen Reduced Form) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg603 b:9.7 occ:1.00 O L:HOH733 2.1 13.9 1.0 O L:HOH766 2.1 12.6 1.0 O L:HOH727 2.1 12.4 1.0 O L:ALA498 2.1 12.3 1.0 OE2 L:GLU42 2.1 12.2 1.0 NE2 L:HIS552 2.2 12.7 1.0 CE1 L:HIS552 3.1 12.0 1.0 CD L:GLU42 3.2 11.6 1.0 CD2 L:HIS552 3.2 11.6 1.0 C L:ALA498 3.3 12.2 1.0 OE1 L:GLU42 3.5 12.8 1.0 N L:ALA498 3.8 12.7 1.0 OE1 L:GLN497 4.0 16.4 1.0 CA L:ALA498 4.0 12.2 1.0 OE2 L:GLU329 4.1 14.6 1.0 OE1 L:GLU329 4.2 15.6 1.0 O L:HOH958 4.2 11.8 1.0 O L:HOH782 4.2 13.1 1.0 ND1 L:HIS552 4.3 11.2 1.0 CG L:HIS552 4.3 12.3 1.0 NZ L:LYS366 4.3 14.3 1.0 N L:VAL499 4.4 12.4 1.0 CB L:ALA498 4.4 12.2 1.0 CG L:GLU42 4.5 12.6 1.0 CD L:LYS366 4.5 13.8 1.0 CD L:GLU329 4.6 15.1 1.0 CE L:LYS366 4.7 13.0 1.0 CA L:VAL499 4.7 13.2 1.0 C L:GLN497 4.7 12.7 1.0 CA L:GLN497 4.9 13.1 1.0

Magnesium binding site 2 out of 2 in the E. Coli Hydrogenase-2 (Hydrogen Reduced Form)


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 (Hydrogen Reduced Form) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:12.4 occ:1.00 O M:HOH720 2.0 15.2 1.0 OE2 M:GLU42 2.1 15.0 1.0 O M:ALA498 2.1 15.6 1.0 O M:HOH742 2.1 16.2 1.0 O M:HOH769 2.1 14.4 1.0 NE2 M:HIS552 2.2 15.0 1.0 CD M:GLU42 3.1 15.3 1.0 CE1 M:HIS552 3.1 14.6 1.0 CD2 M:HIS552 3.2 14.8 1.0 C M:ALA498 3.3 14.8 1.0 OE1 M:GLU42 3.5 15.0 1.0 N M:ALA498 3.7 14.9 1.0 OE1 M:GLN497 4.0 17.6 1.0 CA M:ALA498 4.0 15.6 1.0 OE2 M:GLU329 4.1 18.0 1.0 OE1 M:GLU329 4.2 17.1 1.0 O M:HOH751 4.2 15.5 1.0 ND1 M:HIS552 4.3 13.6 1.0 O M:HOH884 4.3 14.8 1.0 NZ M:LYS366 4.3 16.2 1.0 CG M:HIS552 4.3 13.2 1.0 N M:VAL499 4.3 14.1 1.0 CB M:ALA498 4.4 15.1 1.0 CG M:GLU42 4.5 16.4 1.0 CD M:LYS366 4.5 16.6 1.0 CD M:GLU329 4.6 17.0 1.0 CA M:VAL499 4.7 14.8 1.0 C M:GLN497 4.7 15.0 1.0 CE M:LYS366 4.7 15.1 1.0 CA M:GLN497 4.9 14.7 1.0 CD M:GLN497 5.0 16.8 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