Magnesium in PDB 5a4m: Mechanism of Hydrogen Activation By Nife-Hydrogenases

All present enzymatic activity of Mechanism of Hydrogen Activation By Nife-Hydrogenases:
1.12.99.6;

The structure of Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4m was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sergent, S.B.Carr, S.E.V.Philips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.62 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.671, 97.162, 182.911, 90.00, 90.00, 90.00
R / Rfree (%)	13.425 / 16.235

The structure of Mechanism of Hydrogen Activation By Nife-Hydrogenases 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5a4m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg602 b:13.8 occ:1.00 O L:HOH2396 2.0 13.9 1.0 O L:HOH2076 2.1 14.5 1.0 O L:HOH2075 2.1 13.3 1.0 O L:CYS528 2.1 15.5 1.0 OE2 L:GLU57 2.2 14.8 1.0 NE2 L:HIS582 2.3 14.4 1.0 CD L:GLU57 3.1 14.7 1.0 CE1 L:HIS582 3.2 15.0 1.0 CD2 L:HIS582 3.3 14.4 1.0 C L:CYS528 3.3 15.1 1.0 OE1 L:GLU57 3.4 15.1 1.0 N L:CYS528 3.8 14.6 1.0 CA L:CYS528 4.0 14.5 1.0 OE2 L:GLU347 4.1 14.8 1.0 OE1 L:GLN527 4.2 17.6 1.0 NZ L:LYS399 4.2 15.0 1.0 OE1 L:GLU347 4.2 16.1 1.0 O L:HOH2457 4.2 13.7 1.0 O L:HOH2404 4.3 14.3 1.0 ND1 L:HIS582 4.3 14.4 1.0 CB L:CYS528 4.3 14.5 1.0 N L:VAL529 4.4 15.0 1.0 CG L:HIS582 4.4 13.7 1.0 CG L:GLU57 4.4 14.8 1.0 CD L:LYS399 4.5 14.8 1.0 CD L:GLU347 4.5 15.2 1.0 CE L:LYS399 4.6 14.5 1.0 CA L:VAL529 4.6 14.5 1.0 C L:GLN527 4.9 14.7 1.0

Magnesium binding site 2 out of 2 in the Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg604 b:13.4 occ:1.00 O M:HOH2069 2.0 12.8 1.0 O M:HOH2390 2.1 14.6 1.0 O M:CYS528 2.1 15.5 1.0 O M:HOH2068 2.1 13.3 1.0 OE2 M:GLU57 2.2 14.2 1.0 NE2 M:HIS582 2.3 15.2 1.0 CD M:GLU57 3.1 15.2 1.0 CE1 M:HIS582 3.2 15.3 1.0 CD2 M:HIS582 3.3 15.1 1.0 C M:CYS528 3.3 16.2 1.0 OE1 M:GLU57 3.4 15.9 1.0 N M:CYS528 3.8 16.1 1.0 CA M:CYS528 4.0 16.0 1.0 OE2 M:GLU347 4.1 15.8 1.0 OE1 M:GLN527 4.2 17.4 1.0 NZ M:LYS399 4.2 14.6 1.0 O M:HOH2445 4.2 14.6 1.0 OE1 M:GLU347 4.2 16.3 1.0 O M:HOH2397 4.3 14.4 1.0 ND1 M:HIS582 4.3 14.9 1.0 CB M:CYS528 4.3 16.1 1.0 N M:VAL529 4.4 15.2 1.0 CG M:HIS582 4.4 14.5 1.0 CG M:GLU57 4.5 14.7 1.0 CD M:LYS399 4.5 14.4 1.0 CD M:GLU347 4.6 15.6 1.0 CE M:LYS399 4.6 14.6 1.0 CA M:VAL529 4.6 15.5 1.0 C M:GLN527 4.9 15.8 1.0

R.M.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.Phillips, F.A.Armstrong. Mechanism of Hydrogen Activation By [Nife] Hydrogenases. Nat.Chem.Biol. V. 12 46 2016.
ISSN: ISSN 1552-4450
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976