Magnesium in PDB 3ayz: Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition

All present enzymatic activity of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition:
1.12.5.1;

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition, PDB code: 3ayz was solved by Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.646, 116.664, 113.612, 90.00, 91.34, 90.00
R / Rfree (%)	13.9 / 17.1

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Iron	(Fe)	32 atoms

The binding sites of Magnesium atom in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition (pdb code 3ayz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition, PDB code: 3ayz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:6.2 occ:1.00 O A:HOH912 2.0 7.2 1.0 O A:HOH822 2.1 6.6 1.0 OE2 A:GLU57 2.1 6.1 1.0 NE2 A:HIS596 2.1 6.0 1.0 O A:HOH616 2.1 6.8 1.0 O A:CYS542 2.1 6.2 1.0 CD A:GLU57 3.1 6.0 1.0 CE1 A:HIS596 3.1 5.5 1.0 CD2 A:HIS596 3.2 6.1 1.0 C A:CYS542 3.3 5.8 1.0 OE1 A:GLU57 3.4 7.1 1.0 N A:CYS542 3.8 6.3 1.0 CA A:CYS542 4.0 5.7 1.0 OE1 A:GLN541 4.1 8.8 1.0 OE2 A:GLU346 4.1 7.2 1.0 OE1 A:GLU346 4.1 7.1 1.0 O A:HOH893 4.2 6.6 1.0 NZ A:LYS399 4.2 7.7 1.0 ND1 A:HIS596 4.3 5.6 1.0 CB A:CYS542 4.3 6.3 1.0 O A:HOH901 4.3 6.4 1.0 N A:VAL543 4.4 5.3 1.0 CG A:HIS596 4.4 4.9 1.0 CG A:GLU57 4.4 7.4 1.0 CD A:LYS399 4.5 7.1 1.0 CD A:GLU346 4.6 6.5 1.0 CE A:LYS399 4.7 7.1 1.0 CA A:VAL543 4.7 5.4 1.0 C A:GLN541 4.8 5.7 1.0 CG2 A:VAL543 5.0 7.3 1.0

Magnesium binding site 2 out of 2 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:8.9 occ:1.00 O C:HOH800 2.1 9.7 1.0 O C:HOH765 2.1 9.1 1.0 OE2 C:GLU57 2.1 9.2 1.0 NE2 C:HIS596 2.1 8.4 1.0 O C:HOH785 2.1 9.1 1.0 O C:CYS542 2.1 8.7 1.0 CE1 C:HIS596 3.1 8.7 1.0 CD C:GLU57 3.1 8.7 1.0 CD2 C:HIS596 3.2 8.3 1.0 C C:CYS542 3.3 8.3 1.0 OE1 C:GLU57 3.4 10.0 1.0 N C:CYS542 3.7 9.2 1.0 CA C:CYS542 4.0 8.3 1.0 OE1 C:GLN541 4.1 11.8 1.0 OE2 C:GLU346 4.1 9.7 1.0 OE1 C:GLU346 4.2 10.3 1.0 O C:HOH598 4.2 9.0 1.0 NZ C:LYS399 4.3 10.2 1.0 ND1 C:HIS596 4.3 8.5 1.0 CB C:CYS542 4.3 8.7 1.0 O C:HOH818 4.3 8.9 1.0 CG C:HIS596 4.3 7.9 1.0 N C:VAL543 4.4 8.3 1.0 CG C:GLU57 4.4 9.7 1.0 CD C:GLU346 4.6 9.4 1.0 CD C:LYS399 4.6 10.1 1.0 CE C:LYS399 4.7 10.4 1.0 CA C:VAL543 4.7 8.3 1.0 C C:GLN541 4.8 8.6 1.0 CG2 C:VAL543 5.0 10.2 1.0

Y.Shomura, K.S.Yoon, H.Nishihara, Y.Higuchi. Structural Basis For A [4FE-3S] Cluster in the Oxygen-Tolerant Membrane-Bound [Nife]-Hydrogenase Nature V. 479 253 2011.
ISSN: ISSN 0028-0836
PubMed: 22002607
DOI: 10.1038/NATURE10504