Magnesium in PDB 5jrd: E. Coli Hydrogenase-1 Variant P508A

All present enzymatic activity of E. Coli Hydrogenase-1 Variant P508A:
1.12.99.6;

The structure of E. Coli Hydrogenase-1 Variant P508A, PDB code: 5jrd was solved by S.B.Carr, S.E.V.Phillips, F.A.Armstrong, R.M.Evans, E.J.Brooke, S.T.A.Islam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.69 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.691, 98.589, 185.373, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.1

The structure of E. Coli Hydrogenase-1 Variant P508A also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Iron	(Fe)	26 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the E. Coli Hydrogenase-1 Variant P508A (pdb code 5jrd). 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-1 Variant P508A, PDB code: 5jrd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Hydrogenase-1 Variant P508A


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-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg603 b:9.4 occ:1.00 O L:HOH730 2.1 10.6 1.0 O L:HOH727 2.1 10.8 1.0 O L:CYS528 2.1 10.2 1.0 O L:HOH726 2.1 10.4 1.0 OE1 L:GLU57 2.2 9.4 1.0 NE2 L:HIS582 2.2 9.2 1.0 CE1 L:HIS582 3.1 9.6 1.0 CD L:GLU57 3.1 9.4 1.0 CD2 L:HIS582 3.3 9.5 1.0 C L:CYS528 3.3 9.1 1.0 OE2 L:GLU57 3.5 10.6 1.0 N L:CYS528 3.8 9.4 1.0 CA L:CYS528 4.0 9.5 1.0 OE2 L:GLU347 4.2 11.6 1.0 OE1 L:GLN527 4.2 12.4 1.0 OE1 L:GLU347 4.2 11.6 1.0 NZ L:LYS399 4.3 11.1 1.0 O L:HOH1012 4.3 10.4 1.0 ND1 L:HIS582 4.3 10.4 1.0 O L:HOH771 4.3 10.7 1.0 CB L:CYS528 4.4 10.6 1.0 N L:VAL529 4.4 9.8 1.0 CG L:HIS582 4.4 9.4 1.0 CG L:GLU57 4.5 10.2 1.0 CD L:LYS399 4.6 10.5 1.0 CD L:GLU347 4.6 10.9 1.0 CA L:VAL529 4.7 10.1 1.0 CE L:LYS399 4.7 10.9 1.0 C L:GLN527 4.9 9.8 1.0

Magnesium binding site 2 out of 2 in the E. Coli Hydrogenase-1 Variant P508A


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-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:9.6 occ:1.00 O M:HOH718 2.1 10.8 1.0 O M:HOH733 2.1 10.4 1.0 O M:CYS528 2.1 10.1 1.0 O M:HOH715 2.1 10.3 1.0 OE1 M:GLU57 2.2 9.7 1.0 NE2 M:HIS582 2.2 10.0 1.0 CD M:GLU57 3.1 10.4 1.0 CE1 M:HIS582 3.2 9.6 1.0 CD2 M:HIS582 3.3 10.4 1.0 C M:CYS528 3.3 9.8 1.0 OE2 M:GLU57 3.5 11.2 1.0 N M:CYS528 3.8 10.0 1.0 CA M:CYS528 4.0 9.8 1.0 OE2 M:GLU347 4.2 11.2 1.0 OE1 M:GLN527 4.2 12.6 1.0 OE1 M:GLU347 4.2 11.9 1.0 NZ M:LYS399 4.3 10.9 1.0 ND1 M:HIS582 4.3 10.1 1.0 O M:HOH1000 4.3 10.4 1.0 O M:HOH787 4.3 11.2 1.0 CB M:CYS528 4.4 10.7 1.0 N M:VAL529 4.4 10.2 1.0 CG M:HIS582 4.4 10.2 1.0 CG M:GLU57 4.5 10.7 1.0 CD M:LYS399 4.6 10.7 1.0 CD M:GLU347 4.6 11.6 1.0 CE M:LYS399 4.7 10.9 1.0 CA M:VAL529 4.7 10.0 1.0 C M:GLN527 4.9 9.9 1.0

E.J.Brooke, R.M.Evans, S.T.Islam, G.M.Roberts, S.A.Wehlin, S.B.Carr, S.E.Phillips, F.A.Armstrong. Importance of the Active Site "Canopy" Residues in An O2-Tolerant [Nife]-Hydrogenase. Biochemistry V. 56 132 2017.
ISSN: ISSN 1520-4995
PubMed: 28001048
DOI: 10.1021/ACS.BIOCHEM.6B00868