Magnesium in PDB 4uql: High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant

All present enzymatic activity of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant:
1.12.2.1;

The structure of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4uql was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.690, 100.850, 116.700, 90.00, 105.96, 90.00
R / Rfree (%)	12.043 / 15.2

The structure of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant (pdb code 4uql). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4uql:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg1552 b:4.0 occ:1.00 O Q:HOH2004 2.1 5.4 1.0 O Q:HOH2003 2.1 5.2 1.0 O Q:LEU495 2.1 4.8 1.0 O Q:HOH2002 2.1 5.2 1.0 OE2 Q:GLU53 2.1 5.1 1.0 NE2 Q:HIS549 2.2 4.4 1.0 CE1 Q:HIS549 3.1 4.4 1.0 CD Q:GLU53 3.1 5.0 1.0 CD2 Q:HIS549 3.2 5.0 1.0 C Q:LEU495 3.3 5.2 1.0 OE1 Q:GLU53 3.4 5.0 1.0 N Q:LEU495 3.7 4.7 1.0 CA Q:LEU495 4.0 4.8 1.0 OE2 Q:GLU334 4.1 6.7 1.0 OE1 Q:GLN494 4.1 6.3 1.0 OE1 Q:GLU334 4.2 5.8 1.0 CB Q:LEU495 4.2 5.3 1.0 ND1 Q:HIS549 4.2 4.4 1.0 O Q:HOH2026 4.3 4.3 1.0 O Q:HOH2019 4.3 5.4 1.0 NZ Q:LYS372 4.3 5.1 1.0 CG Q:HIS549 4.3 4.4 1.0 N Q:VAL496 4.3 4.5 1.0 CG Q:GLU53 4.5 4.8 1.0 CD Q:GLU334 4.6 5.9 1.0 CD Q:LYS372 4.6 5.9 1.0 CA Q:VAL496 4.7 4.7 1.0 CE Q:LYS372 4.7 5.0 1.0 C Q:GLN494 4.7 4.5 1.0 CA Q:GLN494 5.0 5.0 1.0

Magnesium binding site 2 out of 2 in the High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1552 b:4.2 occ:1.00 O R:HOH2003 2.0 5.6 1.0 O R:HOH2004 2.1 5.1 1.0 O R:HOH2002 2.1 5.4 1.0 O R:LEU495 2.1 4.6 1.0 OE2 R:GLU53 2.2 4.5 1.0 NE2 R:HIS549 2.2 4.8 1.0 CE1 R:HIS549 3.1 4.7 1.0 CD R:GLU53 3.1 4.8 1.0 CD2 R:HIS549 3.2 4.3 1.0 C R:LEU495 3.3 4.2 1.0 OE1 R:GLU53 3.4 5.5 1.0 N R:LEU495 3.7 4.8 1.0 CA R:LEU495 4.0 4.4 1.0 OE1 R:GLN494 4.1 6.7 1.0 OE2 R:GLU334 4.1 5.6 1.0 OE1 R:GLU334 4.2 7.1 1.0 NZ R:LYS372 4.2 5.1 1.0 O R:HOH2018 4.2 4.7 1.0 O R:HOH2020 4.2 4.8 1.0 ND1 R:HIS549 4.3 4.4 1.0 CB R:LEU495 4.3 4.1 1.0 CG R:HIS549 4.4 4.2 1.0 N R:VAL496 4.4 4.5 1.0 CG R:GLU53 4.5 5.1 1.0 CD R:LYS372 4.5 5.3 1.0 CD R:GLU334 4.6 5.5 1.0 CA R:VAL496 4.6 4.3 1.0 CE R:LYS372 4.7 5.4 1.0 C R:GLN494 4.7 4.7 1.0 CG2 R:VAL496 5.0 5.7 1.0 CA R:GLN494 5.0 4.9 1.0

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9