Magnesium in PDB 1yq9: Structure of the Unready Oxidized Form of [Nife] Hydrogenase

All present enzymatic activity of Structure of the Unready Oxidized Form of [Nife] Hydrogenase:
1.12.2.1;

The structure of Structure of the Unready Oxidized Form of [Nife] Hydrogenase, PDB code: 1yq9 was solved by A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, 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)	13.00 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.750, 93.440, 69.030, 89.33, 102.41, 90.95
R / Rfree (%)	13.2 / 18.3

The structure of Structure of the Unready Oxidized Form of [Nife] Hydrogenase also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Iron	(Fe)	24 atoms

The binding sites of Magnesium atom in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase (pdb code 1yq9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase, PDB code: 1yq9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Unready Oxidized Form of [Nife] Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg540 b:9.8 occ:1.00 O H:LEU482 2.1 13.4 1.0 O H:HOH5013 2.1 7.6 1.0 O H:HOH5011 2.1 7.9 1.0 OE1 H:GLU46 2.1 10.1 1.0 NE2 H:HIS536 2.1 11.7 1.0 O H:HOH5012 2.1 6.8 1.0 CE1 H:HIS536 3.0 10.0 1.0 CD H:GLU46 3.1 9.8 1.0 CD2 H:HIS536 3.2 9.5 1.0 C H:LEU482 3.2 13.6 1.0 OE2 H:GLU46 3.5 7.6 1.0 N H:LEU482 3.7 13.9 1.0 CA H:LEU482 3.9 13.7 1.0 NE2 H:GLN481 4.1 9.0 1.0 ND1 H:HIS536 4.2 9.9 1.0 OE1 H:GLU321 4.2 13.1 1.0 OE2 H:GLU321 4.2 15.1 1.0 O H:HOH5045 4.3 11.5 1.0 CG H:HIS536 4.3 9.3 1.0 NZ H:LYS358 4.3 8.9 1.0 N H:VAL483 4.3 11.9 1.0 O H:HOH5065 4.3 5.2 1.0 CB H:LEU482 4.4 13.9 1.0 CG H:GLU46 4.5 10.2 1.0 CE H:LYS358 4.6 9.9 1.0 CD H:GLU321 4.6 14.0 1.0 CA H:VAL483 4.7 11.6 1.0 CD H:LYS358 4.7 8.0 1.0 C H:GLN481 4.7 14.3 1.0

Magnesium binding site 2 out of 2 in the Structure of the Unready Oxidized Form of [Nife] Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Unready Oxidized Form of [Nife] Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg540 b:8.8 occ:1.00 O I:LEU482 2.1 12.6 1.0 O I:HOH5024 2.1 8.8 1.0 O I:HOH5025 2.1 5.8 1.0 O I:HOH5026 2.1 7.6 1.0 OE1 I:GLU46 2.2 9.5 1.0 NE2 I:HIS536 2.2 11.4 1.0 CE1 I:HIS536 3.1 10.5 1.0 CD I:GLU46 3.1 9.2 1.0 C I:LEU482 3.2 13.3 1.0 CD2 I:HIS536 3.2 9.8 1.0 OE2 I:GLU46 3.5 8.0 1.0 N I:LEU482 3.7 13.7 1.0 CA I:LEU482 4.0 13.4 1.0 OE1 I:GLU321 4.0 12.2 1.0 OE2 I:GLU321 4.1 15.1 1.0 NE2 I:GLN481 4.1 9.7 1.0 ND1 I:HIS536 4.2 10.0 1.0 O I:HOH5044 4.3 2.0 1.0 N I:VAL483 4.3 11.6 1.0 NZ I:LYS358 4.3 10.0 1.0 CG I:HIS536 4.3 9.0 1.0 O I:HOH5068 4.4 2.6 1.0 CB I:LEU482 4.4 13.8 1.0 CG I:GLU46 4.5 10.8 1.0 CD I:GLU321 4.5 13.6 1.0 CA I:VAL483 4.6 11.3 1.0 C I:GLN481 4.7 14.1 1.0 CE I:LYS358 4.8 10.0 1.0 CD I:LYS358 4.8 8.2 1.0

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X