Magnesium in PDB 3ayx: Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition

All present enzymatic activity of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition:
1.12.5.1;

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition, PDB code: 3ayx 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 / 1.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.735, 116.327, 113.629, 90.00, 91.40, 90.00
R / Rfree (%)	13.9 / 16.9

The structure of Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced Condition (pdb code 3ayx). 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 H2-Reduced Condition, PDB code: 3ayx:
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 H2-Reduced 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 H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:8.0 occ:1.00 O A:HOH626 2.0 8.4 1.0 O A:HOH907 2.1 8.5 1.0 NE2 A:HIS596 2.1 8.2 1.0 OE2 A:GLU57 2.1 8.3 1.0 O A:HOH614 2.1 8.5 1.0 O A:CYS542 2.1 8.1 1.0 CD A:GLU57 3.1 8.1 1.0 CE1 A:HIS596 3.1 8.0 1.0 CD2 A:HIS596 3.2 8.0 1.0 C A:CYS542 3.3 7.6 1.0 OE1 A:GLU57 3.4 8.6 1.0 N A:CYS542 3.8 8.0 1.0 CA A:CYS542 4.0 8.1 1.0 OE1 A:GLN541 4.1 10.3 1.0 OE2 A:GLU346 4.1 9.0 1.0 OE1 A:GLU346 4.2 9.2 1.0 O A:HOH893 4.2 8.7 1.0 NZ A:LYS399 4.2 9.5 1.0 ND1 A:HIS596 4.3 7.6 1.0 CB A:CYS542 4.3 7.7 1.0 O A:HOH783 4.3 8.0 1.0 CG A:HIS596 4.3 6.9 1.0 N A:VAL543 4.3 7.5 1.0 CG A:GLU57 4.4 8.8 1.0 CD A:LYS399 4.5 8.7 1.0 CD A:GLU346 4.6 8.7 1.0 CE A:LYS399 4.7 8.6 1.0 CA A:VAL543 4.7 7.5 1.0 C A:GLN541 4.8 7.6 1.0 CG2 A:VAL543 5.0 9.2 1.0

Magnesium binding site 2 out of 2 in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An H2-Reduced 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 H2-Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:10.4 occ:1.00 O C:HOH825 2.1 11.4 1.0 O C:HOH750 2.1 10.6 1.0 O C:HOH600 2.1 10.5 1.0 NE2 C:HIS596 2.1 10.2 1.0 OE2 C:GLU57 2.1 10.4 1.0 O C:CYS542 2.1 10.2 1.0 CE1 C:HIS596 3.1 10.5 1.0 CD C:GLU57 3.1 9.8 1.0 CD2 C:HIS596 3.2 10.3 1.0 C C:CYS542 3.3 9.9 1.0 OE1 C:GLU57 3.4 11.1 1.0 N C:CYS542 3.8 10.9 1.0 CA C:CYS542 4.0 9.6 1.0 OE1 C:GLN541 4.1 13.4 1.0 OE2 C:GLU346 4.1 11.6 1.0 OE1 C:GLU346 4.2 12.0 1.0 O C:HOH787 4.2 11.1 1.0 NZ C:LYS399 4.2 11.6 1.0 ND1 C:HIS596 4.3 9.8 1.0 CB C:CYS542 4.3 10.3 1.0 CG C:HIS596 4.3 9.6 1.0 O C:HOH812 4.3 10.5 1.0 N C:VAL543 4.4 10.0 1.0 CG C:GLU57 4.4 10.9 1.0 CD C:LYS399 4.5 11.7 1.0 CD C:GLU346 4.6 12.5 1.0 CE C:LYS399 4.7 11.1 1.0 CA C:VAL543 4.7 10.2 1.0 C C:GLN541 4.8 10.3 1.0 CG2 C:VAL543 5.0 11.8 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