Nickel in PDB 5a4f: 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: 5a4f was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sargent, S.B.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)	91.64 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.757, 97.770, 183.288, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 15.7

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 5a4f). 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: 5a4f:
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:15.7 occ:1.00 OD L:CSO79 1.7 21.5 1.0 O L:HOH2071 1.7 21.4 1.0 SG L:CYS576 2.1 16.6 1.0 SG L:CYS76 2.2 15.5 1.0 SG L:CYS579 2.5 9.5 1.0 SG L:CSO79 2.6 11.8 1.0 FE L:FCO601 2.9 9.2 1.0 CB L:CYS76 3.1 12.8 1.0 CB L:CYS576 3.2 12.0 1.0 CB L:CYS579 3.5 8.8 1.0 CB L:CSO79 3.8 12.8 1.0 N L:CSO79 3.8 11.8 1.0 C1 L:FCO601 3.9 9.3 1.0 C2 L:FCO601 4.0 9.6 1.0 NH1 L:ARG509 4.2 22.1 1.0 CA L:CSO79 4.4 11.6 1.0 N L:CYS579 4.4 7.4 1.0 C3 L:FCO601 4.4 8.8 1.0 CA L:CYS579 4.5 7.8 1.0 CA L:CYS76 4.5 10.5 1.0 CA L:CYS576 4.5 8.7 1.0 CB L:VAL78 4.6 14.1 1.0 CZ L:ARG509 4.6 18.0 1.0 N1 L:FCO601 4.7 10.1 1.0 C L:VAL78 4.8 14.1 1.0 CD L:ARG509 4.8 19.0 1.0 NE L:ARG509 4.8 17.7 1.0 N L:VAL78 4.9 11.0 1.0 CA L:VAL78 5.0 12.6 1.0 N2 L:FCO601 5.0 9.5 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:15.7 occ:1.00 O M:HOH2074 1.7 20.1 1.0 OD M:CSO79 1.8 21.1 1.0 SG M:CYS576 2.1 16.5 1.0 SG M:CYS76 2.2 13.5 0.8 SG M:CYS579 2.5 9.4 1.0 SG M:CSO79 2.6 11.7 1.0 FE M:FCO601 2.8 9.2 1.0 CB M:CYS76 3.1 11.5 1.0 CB M:CYS576 3.2 12.8 1.0 CB M:CYS579 3.5 8.7 1.0 CB M:CSO79 3.7 11.6 1.0 N M:CSO79 3.8 11.4 1.0 C1 M:FCO601 3.9 9.4 1.0 C2 M:FCO601 4.0 9.8 1.0 NH1 M:ARG509 4.1 22.9 1.0 CA M:CSO79 4.4 11.7 1.0 C3 M:FCO601 4.4 9.2 1.0 N M:CYS579 4.4 7.5 1.0 CA M:CYS76 4.5 10.6 1.0 CA M:CYS579 4.5 8.4 1.0 CA M:CYS576 4.5 9.7 1.0 CZ M:ARG509 4.6 19.3 1.0 CB M:VAL78 4.6 14.4 1.0 N1 M:FCO601 4.8 9.7 1.0 CD M:ARG509 4.8 19.6 1.0 C M:VAL78 4.8 14.6 1.0 NE M:ARG509 4.8 17.5 1.0 N M:VAL78 4.9 12.2 1.0 N2 M:FCO601 4.9 10.0 1.0 CA M:VAL78 5.0 13.1 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