Nickel in PDB 5a4i: The Mechanism of Hydrogen Activation By Nife-Hydrogenases

All present enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases:
1.12.99.6;

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4i was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sargent, S.C.Carr, S.E.V.Phillips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.19 / 1.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.780, 97.580, 182.880, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 14.7

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	26 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Nickel atom in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5a4i). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4i:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:13.3 occ:1.00 OD L:CSO79 1.8 21.4 1.0 O L:HOH2065 1.8 13.3 1.0 SG L:CYS76 2.2 14.1 1.0 SG L:CYS576 2.2 15.7 1.0 SG L:CYS579 2.5 9.3 1.0 SG L:CSO79 2.6 11.1 1.0 FE L:FCO601 2.9 8.8 1.0 CB L:CYS76 3.0 12.8 1.0 CB L:CYS576 3.2 12.1 1.0 CB L:CYS579 3.6 9.0 1.0 CB L:CSO79 3.7 11.0 1.0 N L:CSO79 3.8 10.9 1.0 C1 L:FCO601 3.9 9.7 1.0 C2 L:FCO601 4.1 9.2 1.0 CA L:CSO79 4.3 10.3 1.0 N L:CYS579 4.4 8.3 1.0 CA L:CYS76 4.4 9.8 1.0 NH1 L:ARG509 4.5 12.6 1.0 CB L:VAL78 4.5 11.3 1.0 C3 L:FCO601 4.5 8.6 1.0 CA L:CYS579 4.5 8.9 1.0 CA L:CYS576 4.6 9.1 1.0 CZ L:ARG509 4.7 10.2 1.0 C L:VAL78 4.8 11.5 1.0 N1 L:FCO601 4.8 9.7 1.0 NE L:ARG509 4.8 9.5 1.0 N L:VAL78 4.9 10.5 1.0 CA L:VAL78 4.9 11.0 1.0 CD L:ARG509 5.0 9.4 1.0

Nickel binding site 2 out of 2 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:13.5 occ:1.00 O M:HOH2069 1.8 12.3 1.0 OD M:CSO79 1.8 20.0 1.0 SG M:CYS76 2.2 11.9 0.8 SG M:CYS576 2.2 15.8 1.0 SG M:CYS579 2.5 9.2 1.0 SG M:CSO79 2.6 10.9 1.0 FE M:FCO601 2.9 8.8 1.0 CB M:CYS76 3.0 11.4 1.0 CB M:CYS576 3.2 12.2 1.0 CB M:CYS579 3.6 8.7 1.0 CB M:CSO79 3.6 10.5 1.0 N M:CSO79 3.8 10.6 1.0 C1 M:FCO601 3.9 9.1 1.0 C2 M:FCO601 4.1 9.2 1.0 CA M:CSO79 4.3 10.5 1.0 N M:CYS579 4.4 8.2 1.0 CA M:CYS76 4.5 10.1 1.0 NH1 M:ARG509 4.5 11.4 1.0 CB M:VAL78 4.5 12.3 1.0 C3 M:FCO601 4.5 8.6 1.0 CA M:CYS579 4.5 8.4 1.0 CA M:CYS576 4.6 9.3 1.0 CZ M:ARG509 4.6 9.9 1.0 C M:VAL78 4.8 12.1 1.0 N1 M:FCO601 4.8 9.8 1.0 NE M:ARG509 4.8 9.5 1.0 N M:VAL78 4.9 10.9 1.0 CD M:ARG509 4.9 9.7 1.0 CA M:VAL78 4.9 12.1 1.0

R.M.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.Phillips, F.A.Armstrong. Mechanism of Hydrogen Activation By [Nife] Hydrogenases. Nat. Chem. Biol. V. 12 46 2016.
ISSN: ESSN 1552-4469
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976