Magnesium in PDB 4uqp: High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air

All present enzymatic activity of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air:
1.12.2.1;

The structure of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air, PDB code: 4uqp 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 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.700, 100.900, 116.700, 90.00, 105.90, 90.00
R / Rfree (%)	11.983 / 15.633

The structure of High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Iron	(Fe)	24 atoms

The binding sites of Magnesium atom in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air (pdb code 4uqp). 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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air, PDB code: 4uqp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg1554 b:6.9 occ:1.00 O Q:HOH2704 2.0 7.6 1.0 O Q:HOH2703 2.1 7.9 1.0 O Q:HOH2702 2.1 7.6 1.0 O Q:LEU495 2.1 6.9 1.0 OE2 Q:GLU53 2.2 7.7 1.0 NE2 Q:HIS549 2.2 7.0 1.0 CE1 Q:HIS549 3.1 6.7 1.0 CD Q:GLU53 3.1 7.2 1.0 CD2 Q:HIS549 3.2 6.8 1.0 C Q:LEU495 3.3 6.5 1.0 OE1 Q:GLU53 3.4 7.9 1.0 N Q:LEU495 3.7 6.1 1.0 CA Q:LEU495 4.0 6.6 1.0 OE2 Q:GLU334 4.0 9.2 1.0 OE1 Q:GLN494 4.1 8.0 1.0 OE1 Q:GLU334 4.2 7.8 1.0 O Q:HOH2725 4.2 7.2 1.0 CB Q:LEU495 4.2 7.0 1.0 ND1 Q:HIS549 4.3 7.0 1.0 NZ Q:LYS372 4.3 8.6 1.0 O Q:HOH2718 4.3 8.1 1.0 CG Q:HIS549 4.4 6.4 1.0 N Q:VAL496 4.4 7.6 1.0 CG Q:GLU53 4.5 6.6 1.0 CD Q:GLU334 4.6 7.8 1.0 CD Q:LYS372 4.6 8.1 1.0 CA Q:VAL496 4.7 7.6 1.0 CE Q:LYS372 4.7 7.5 1.0 C Q:GLN494 4.7 7.1 1.0 CA Q:GLN494 5.0 6.9 1.0

Magnesium binding site 2 out of 2 in the High-Resolution Structure of the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air


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 the D. Fructosovorans Nife-Hydrogenase L122A Mutant After Exposure to Air within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1557 b:6.8 occ:1.00 O R:HOH2703 2.0 8.1 1.0 O R:HOH2704 2.0 7.7 1.0 O R:HOH2702 2.1 7.8 1.0 O R:LEU495 2.1 6.5 1.0 OE2 R:GLU53 2.2 7.2 1.0 NE2 R:HIS549 2.2 6.4 1.0 CE1 R:HIS549 3.1 6.6 1.0 CD R:GLU53 3.1 7.5 1.0 CD2 R:HIS549 3.2 6.5 1.0 C R:LEU495 3.3 6.8 1.0 OE1 R:GLU53 3.4 8.0 1.0 N R:LEU495 3.7 7.2 1.0 CA R:LEU495 4.0 6.4 1.0 OE1 R:GLN494 4.1 9.1 1.0 OE2 R:GLU334 4.1 8.5 1.0 OE1 R:GLU334 4.2 8.6 1.0 O R:HOH2718 4.2 7.0 1.0 O R:HOH2720 4.2 7.9 1.0 NZ R:LYS372 4.2 7.9 1.0 ND1 R:HIS549 4.3 6.4 1.0 CB R:LEU495 4.3 6.8 1.0 CG R:HIS549 4.4 6.3 1.0 N R:VAL496 4.4 6.9 1.0 CG R:GLU53 4.5 7.0 1.0 CD R:LYS372 4.5 7.1 1.0 CD R:GLU334 4.6 7.2 1.0 CA R:VAL496 4.6 6.8 1.0 CE R:LYS372 4.7 8.1 1.0 C R:GLN494 4.7 7.4 1.0 CA R:GLN494 5.0 7.2 1.0 CG2 R:VAL496 5.0 8.1 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