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

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

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

Resolution Low / High (Å)	92.78 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.855, 98.979, 185.207, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 14.2

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

Magnesium binding site 1 out of 2 in the 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 The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg603 b:4.5 occ:1.00 O L:HOH2051 2.1 6.5 1.0 O L:HOH2292 2.1 6.1 1.0 O L:HOH2050 2.1 6.2 1.0 O L:CYS528 2.2 5.7 1.0 OE2 L:GLU57 2.2 5.7 1.0 NE2 L:HIS582 2.2 5.3 1.0 CD L:GLU57 3.2 5.8 1.0 CE1 L:HIS582 3.2 5.3 1.0 CD2 L:HIS582 3.3 5.4 1.0 C L:CYS528 3.3 5.3 1.0 OE1 L:GLU57 3.5 5.9 1.0 N L:CYS528 3.8 5.2 1.0 CA L:CYS528 4.1 5.5 1.0 OE2 L:GLU347 4.1 7.7 1.0 OE1 L:GLN527 4.2 8.8 1.0 OE1 L:GLU347 4.2 7.7 1.0 NZ L:LYS399 4.3 6.4 1.0 O L:HOH2331 4.3 5.9 1.0 ND1 L:HIS582 4.3 5.7 1.0 O L:HOH2299 4.3 6.4 1.0 CB L:CYS528 4.4 6.1 1.0 CG L:HIS582 4.4 5.6 1.0 N L:VAL529 4.4 5.4 1.0 CG L:GLU57 4.5 6.0 1.0 CD L:LYS399 4.6 6.7 1.0 CD L:GLU347 4.6 6.8 1.0 CA L:VAL529 4.7 5.4 1.0 CE L:LYS399 4.7 7.1 1.0 C L:GLN527 5.0 5.5 1.0

Magnesium binding site 2 out of 2 in the 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 The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:4.4 occ:1.00 O M:HOH2053 2.1 6.5 1.0 O M:HOH2288 2.1 6.1 1.0 O M:HOH2052 2.1 6.0 1.0 O M:CYS528 2.2 5.7 1.0 OE2 M:GLU57 2.2 5.7 1.0 NE2 M:HIS582 2.2 5.6 1.0 CD M:GLU57 3.2 5.6 1.0 CE1 M:HIS582 3.2 5.6 1.0 CD2 M:HIS582 3.3 5.7 1.0 C M:CYS528 3.3 5.7 1.0 OE1 M:GLU57 3.5 6.5 1.0 N M:CYS528 3.8 5.8 1.0 CA M:CYS528 4.0 5.7 1.0 OE2 M:GLU347 4.1 7.1 1.0 OE1 M:GLU347 4.2 7.2 1.0 OE1 M:GLN527 4.3 8.4 1.0 NZ M:LYS399 4.3 6.4 1.0 ND1 M:HIS582 4.3 5.8 1.0 O M:HOH2333 4.3 5.8 1.0 O M:HOH2295 4.3 6.0 1.0 CB M:CYS528 4.4 6.1 1.0 CG M:HIS582 4.4 5.8 1.0 N M:VAL529 4.4 5.7 1.0 CG M:GLU57 4.5 6.2 1.0 CD M:LYS399 4.6 6.5 1.0 CD M:GLU347 4.6 7.0 1.0 CE M:LYS399 4.7 6.4 1.0 CA M:VAL529 4.7 5.7 1.0 C M:GLN527 4.9 5.5 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: ESSN 1552-4469
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976