Nickel in PDB 5a4m: Mechanism of Hydrogen Activation By Nife-Hydrogenases

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

The structure of Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4m was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sergent, S.B.Carr, S.E.V.Philips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.62 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.671, 97.162, 182.911, 90.00, 90.00, 90.00
R / Rfree (%)	13.425 / 16.235

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

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Nickel atom in the Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5a4m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni601 b:26.7 occ:1.00 NI L:NFV601 0.0 26.7 1.0 O4 L:NFV601 2.0 19.4 1.0 O L:HOH2106 2.2 28.6 1.0 SG L:CYS576 2.2 26.7 1.0 SG L:CYS76 2.3 28.3 1.0 SG L:CYS579 2.5 15.9 1.0 SG L:CYS79 2.6 18.6 1.0 FE L:NFV601 2.9 15.5 1.0 CB L:CYS76 3.0 23.2 1.0 CB L:CYS576 3.2 18.6 1.0 CB L:CYS579 3.6 15.5 1.0 CB L:CYS79 3.8 20.1 1.0 N L:CYS79 3.8 21.0 1.0 C2 L:NFV601 3.9 16.9 1.0 C3 L:NFV601 4.0 15.9 1.0 CA L:CYS76 4.3 20.7 1.0 CA L:CYS79 4.4 21.0 1.0 CB L:VAL78 4.4 22.9 1.0 N L:CYS579 4.4 15.3 1.0 NH1 L:ARG509 4.5 18.4 1.0 CA L:CYS576 4.5 15.9 1.0 CA L:CYS579 4.5 14.5 1.0 C1 L:NFV601 4.6 14.4 1.0 CZ L:ARG509 4.8 18.9 1.0 C L:VAL78 4.8 22.1 1.0 N L:VAL78 4.8 22.3 1.0 N2 L:NFV601 4.8 16.1 1.0 C L:CYS76 4.8 19.2 1.0 CA L:VAL78 4.9 21.7 1.0 NE L:ARG509 4.9 17.1 1.0 CD L:ARG509 4.9 17.5 1.0 N3 L:NFV601 5.0 15.7 1.0

Nickel binding site 2 out of 2 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni603 b:26.9 occ:1.00 NI M:NFV603 0.0 26.9 1.0 O4 M:NFV603 2.0 19.9 1.0 SG M:CYS576 2.2 26.8 1.0 SG M:CYS76 2.3 28.6 1.0 SG M:CYS579 2.5 16.2 1.0 SG M:CYS79 2.6 18.5 1.0 FE M:NFV603 2.8 16.3 1.0 CB M:CYS76 3.0 21.9 1.0 CB M:CYS576 3.1 19.6 1.0 CB M:CYS579 3.6 16.6 1.0 CB M:CYS79 3.7 19.7 1.0 N M:CYS79 3.8 19.9 1.0 C2 M:NFV603 3.9 17.8 1.0 C3 M:NFV603 4.0 15.9 1.0 CB M:VAL78 4.3 24.4 1.0 CA M:CYS79 4.4 20.2 1.0 NH1 M:ARG509 4.4 19.3 1.0 CA M:CYS76 4.4 19.8 1.0 C1 M:NFV603 4.4 17.7 1.0 N M:CYS579 4.5 15.2 1.0 CA M:CYS576 4.5 18.0 1.0 CA M:CYS579 4.6 15.3 1.0 CZ M:ARG509 4.7 19.3 1.0 C M:VAL78 4.8 22.2 1.0 N M:VAL78 4.8 21.8 1.0 N2 M:NFV603 4.8 17.3 1.0 CD M:ARG509 4.8 17.1 1.0 NE M:ARG509 4.9 17.7 1.0 CA M:VAL78 4.9 23.2 1.0 C M:CYS76 4.9 19.1 1.0 N3 M:NFV603 5.0 14.5 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: ISSN 1552-4450
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976