Magnesium in PDB 5lry: E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D

All present enzymatic activity of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D:
1.12.99.6;

The structure of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D, PDB code: 5lry was solved by S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.79 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.756, 98.746, 185.243, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 16.3

The structure of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D (pdb code 5lry). 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 [Nife] Hydrogenase Hyd-1 Mutant E28D, PDB code: 5lry:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg604 b:3.2 occ:1.00 O L:HOH719 2.1 8.0 1.0 O L:CYS528 2.1 8.2 1.0 O L:HOH743 2.2 7.3 1.0 OE2 L:GLU57 2.2 7.4 1.0 O L:HOH748 2.2 7.6 1.0 NE2 L:HIS582 2.2 7.1 1.0 CD L:GLU57 3.1 7.6 1.0 CE1 L:HIS582 3.2 7.2 1.0 CD2 L:HIS582 3.3 7.3 1.0 C L:CYS528 3.3 7.8 1.0 OE1 L:GLU57 3.4 7.7 1.0 N L:CYS528 3.8 7.7 1.0 CA L:CYS528 4.0 8.0 1.0 OE2 L:GLU347 4.2 9.5 1.0 OE1 L:GLU347 4.2 9.7 1.0 OE1 L:GLN527 4.2 10.0 1.0 NZ L:LYS399 4.3 7.9 1.0 O L:HOH1004 4.3 8.1 1.0 ND1 L:HIS582 4.3 7.3 1.0 CB L:CYS528 4.4 7.9 1.0 O L:HOH795 4.4 7.0 1.0 N L:VAL529 4.4 7.8 1.0 CG L:HIS582 4.4 7.2 1.0 CG L:GLU57 4.5 7.7 1.0 CD L:LYS399 4.6 7.9 1.0 CD L:GLU347 4.6 9.3 1.0 CA L:VAL529 4.7 7.7 1.0 CE L:LYS399 4.7 8.0 1.0 C L:GLN527 4.9 7.8 1.0

Magnesium binding site 2 out of 2 in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:3.3 occ:1.00 O M:HOH747 2.1 7.4 1.0 O M:CYS528 2.1 7.1 1.0 O M:HOH737 2.2 7.7 1.0 O M:HOH742 2.2 6.8 1.0 OE2 M:GLU57 2.2 7.2 1.0 NE2 M:HIS582 2.3 7.2 1.0 CD M:GLU57 3.2 7.5 1.0 CE1 M:HIS582 3.2 7.0 1.0 CD2 M:HIS582 3.3 7.0 1.0 C M:CYS528 3.3 7.2 1.0 OE1 M:GLU57 3.4 7.6 1.0 N M:CYS528 3.8 7.4 1.0 CA M:CYS528 4.0 7.4 1.0 OE2 M:GLU347 4.2 8.5 1.0 OE1 M:GLU347 4.3 8.5 1.0 OE1 M:GLN527 4.3 9.4 1.0 NZ M:LYS399 4.3 7.4 1.0 O M:HOH814 4.3 7.4 1.0 ND1 M:HIS582 4.3 7.2 1.0 O M:HOH988 4.3 7.1 1.0 CB M:CYS528 4.4 7.4 1.0 N M:VAL529 4.4 7.2 1.0 CG M:HIS582 4.4 7.2 1.0 CG M:GLU57 4.5 7.9 1.0 CD M:LYS399 4.6 7.1 1.0 CD M:GLU347 4.6 8.3 1.0 CE M:LYS399 4.7 7.2 1.0 CA M:VAL529 4.7 7.3 1.0 C M:GLN527 4.9 7.6 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