Magnesium in PDB 5a4i: 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: 5a4i was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sargent, S.C.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)	32.19 / 1.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.780, 97.580, 182.880, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 14.7

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 5a4i). 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: 5a4i:
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:7.4 occ:1.00 O L:HOH2252 2.1 8.4 1.0 O L:HOH2044 2.1 9.3 1.0 O L:HOH2043 2.1 9.0 1.0 O L:CYS528 2.1 8.4 1.0 OE2 L:GLU57 2.1 8.1 1.0 NE2 L:HIS582 2.2 8.4 1.0 CD L:GLU57 3.1 8.5 1.0 CE1 L:HIS582 3.2 8.4 1.0 CD2 L:HIS582 3.2 8.2 1.0 C L:CYS528 3.3 7.8 1.0 OE1 L:GLU57 3.4 9.1 1.0 N L:CYS528 3.8 8.2 1.0 CA L:CYS528 4.0 8.3 1.0 OE2 L:GLU347 4.1 10.5 1.0 OE1 L:GLU347 4.2 11.0 1.0 OE1 L:GLN527 4.2 12.1 1.0 NZ L:LYS399 4.2 9.8 1.0 O L:HOH2284 4.3 8.8 1.0 ND1 L:HIS582 4.3 8.7 1.0 O L:HOH2258 4.3 9.0 1.0 CB L:CYS528 4.3 8.9 1.0 CG L:HIS582 4.4 8.6 1.0 N L:VAL529 4.4 8.3 1.0 CG L:GLU57 4.4 8.8 1.0 CD L:LYS399 4.5 9.5 1.0 CD L:GLU347 4.6 10.3 1.0 CA L:VAL529 4.6 8.1 1.0 CE L:LYS399 4.7 10.3 1.0 C L:GLN527 4.9 8.4 1.0 CG2 L:VAL529 5.0 9.8 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:7.5 occ:1.00 O M:HOH2048 2.1 9.5 1.0 O M:HOH2257 2.1 9.2 1.0 O M:CYS528 2.1 8.9 1.0 O M:HOH2047 2.1 8.9 1.0 OE2 M:GLU57 2.1 8.5 1.0 NE2 M:HIS582 2.2 8.9 1.0 CD M:GLU57 3.1 9.1 1.0 CE1 M:HIS582 3.1 9.2 1.0 CD2 M:HIS582 3.2 8.5 1.0 C M:CYS528 3.3 8.5 1.0 OE1 M:GLU57 3.4 9.8 1.0 N M:CYS528 3.8 8.3 1.0 CA M:CYS528 4.0 8.2 1.0 OE2 M:GLU347 4.1 10.3 1.0 OE1 M:GLU347 4.2 10.7 1.0 OE1 M:GLN527 4.2 11.9 1.0 NZ M:LYS399 4.3 9.9 1.0 O M:HOH2294 4.3 9.0 1.0 ND1 M:HIS582 4.3 8.8 1.0 O M:HOH2264 4.3 8.9 1.0 CB M:CYS528 4.3 8.7 1.0 CG M:HIS582 4.4 9.0 1.0 N M:VAL529 4.4 7.9 1.0 CG M:GLU57 4.5 9.4 1.0 CD M:LYS399 4.5 9.4 1.0 CD M:GLU347 4.6 10.9 1.0 CE M:LYS399 4.6 9.9 1.0 CA M:VAL529 4.7 8.2 1.0 C M:GLN527 4.9 8.7 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