Nickel 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:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	32 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Membrane-Bound Respiratory [Nife] Hydrogenase From Hydrogenovibrio Marinus in An Air-Oxidized Condition, PDB code: 3ayz:
Jump to Nickel binding site number: 1; 2;

Nickel 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 Nickel with other atoms in the Ni 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:Ni602 b:12.9 occ:1.00 O A:O610 1.4 8.4 0.4 O A:O609 1.7 8.0 0.7 O A:O606 1.7 12.7 1.0 SG A:CYS590 2.1 15.8 1.0 SG A:CYS76 2.1 12.4 1.0 O A:O607 2.3 8.1 0.7 SG A:CYS79 2.5 8.4 1.0 SG A:CYS593 2.6 7.7 1.0 FE A:FE2601 2.8 6.7 1.0 CB A:CYS76 3.1 14.2 1.0 O A:O608 3.2 9.2 0.7 CB A:CYS590 3.2 14.0 1.0 CB A:CYS79 3.5 9.1 1.0 CB A:CYS593 3.7 9.6 1.0 N A:CYS79 3.7 8.8 1.0 C A:CYN605 4.0 6.5 1.0 C A:CYN604 4.1 6.7 1.0 CA A:CYS79 4.2 8.4 1.0 NH1 A:ARG523 4.3 8.2 1.0 C A:CMO603 4.4 6.8 1.0 CA A:CYS76 4.4 7.6 1.0 CB A:VAL78 4.5 10.0 1.0 CA A:CYS590 4.5 8.2 1.0 CZ A:ARG523 4.5 7.2 1.0 N A:CYS593 4.6 6.7 1.0 CA A:CYS593 4.7 6.7 1.0 NE A:ARG523 4.7 7.4 1.0 C A:VAL78 4.8 8.2 1.0 CD A:ARG523 4.8 7.8 1.0 N A:VAL78 4.9 9.6 1.0 N A:CYN605 4.9 6.2 1.0 CA A:VAL78 4.9 9.1 1.0 C A:CYS76 4.9 6.5 1.0 CG A:GLU28 5.0 24.4 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni602 b:15.3 occ:1.00 O C:O610 1.5 7.9 0.4 O C:O609 1.7 8.6 0.7 O C:O606 1.8 14.4 1.0 SG C:CYS590 2.0 18.8 1.0 SG C:CYS76 2.1 14.7 1.0 O C:O607 2.3 8.1 0.6 SG C:CYS79 2.5 10.6 1.0 SG C:CYS593 2.6 10.0 1.0 FE C:FE2601 2.9 9.0 1.0 CB C:CYS76 3.1 15.2 1.0 O C:O608 3.1 9.1 0.5 CB C:CYS590 3.2 18.4 1.0 CB C:CYS79 3.5 11.1 1.0 CB C:CYS593 3.6 12.7 1.0 N C:CYS79 3.8 9.9 1.0 C C:CYN605 4.0 8.6 1.0 C C:CYN604 4.1 9.4 1.0 CA C:CYS79 4.2 9.9 1.0 NH1 C:ARG523 4.3 11.5 1.0 CB C:VAL78 4.4 11.8 1.0 CA C:CYS76 4.4 9.5 1.0 C C:CMO603 4.4 8.2 1.0 CA C:CYS590 4.5 10.4 1.0 CZ C:ARG523 4.5 9.8 1.0 N C:CYS593 4.6 8.6 1.0 CA C:CYS593 4.7 9.2 1.0 NE C:ARG523 4.7 10.4 1.0 C C:VAL78 4.8 10.2 1.0 CD C:ARG523 4.8 10.6 1.0 N C:VAL78 4.9 10.6 1.0 N C:CYN605 4.9 8.5 1.0 CA C:VAL78 4.9 10.6 1.0 CG C:GLU28 4.9 25.3 1.0 C C:CYS76 5.0 8.0 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