Nickel in PDB 7nem: Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form

All present enzymatic activity of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form:
1.12.99.6;

The structure of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form, PDB code: 7nem was solved by S.B.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.80 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.402, 100.252, 168.536, 90, 90, 90
R / Rfree (%)	15 / 16.7

The structure of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	1 atom

The binding sites of Nickel atom in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form (pdb code 7nem). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form, PDB code: 7nem:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:10.0 occ:1.00 O2 L:OXY605 1.8 18.6 0.9 SG L:CYS546 2.2 11.2 1.0 SG L:CYS64 2.3 9.7 1.0 SG L:CYS549 2.3 9.4 1.0 SG L:CYS61 2.3 9.6 1.0 FE L:FCO601 2.6 9.6 1.0 O1 L:OXY605 3.0 16.7 0.9 CB L:CYS61 3.2 10.0 1.0 CB L:CYS546 3.3 10.0 1.0 CB L:CYS64 3.4 9.4 1.0 CB L:CYS549 3.4 8.7 1.0 C1 L:FCO601 3.6 8.3 1.0 N L:CYS64 3.8 10.8 1.0 C2 L:FCO601 3.8 10.4 1.0 CA L:CYS64 4.2 10.4 1.0 C3 L:FCO601 4.2 9.7 1.0 CA L:CYS549 4.5 9.5 1.0 N L:CYS549 4.5 9.3 1.0 N1 L:FCO601 4.5 9.2 1.0 CA L:CYS546 4.6 9.8 1.0 CA L:CYS61 4.6 9.1 1.0 CB L:VAL63 4.7 9.8 1.0 N2 L:FCO601 4.9 10.4 1.0 C L:VAL63 4.9 11.1 1.0 C L:CYS64 4.9 11.7 1.0 CD L:LYS479 5.0 12.1 1.0 NE2 L:HIS68 5.0 9.8 1.0

Nickel binding site 2 out of 2 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:11.1 occ:1.00 O1 M:OXY606 1.7 23.2 1.0 SG M:CYS546 2.2 12.5 1.0 SG M:CYS64 2.3 10.6 1.0 SG M:CYS549 2.3 10.5 1.0 SG M:CYS61 2.4 10.6 1.0 FE M:FCO601 2.6 10.6 1.0 O2 M:OXY606 2.9 20.1 1.0 CB M:CYS61 3.2 10.5 1.0 CB M:CYS546 3.3 11.7 1.0 CB M:CYS64 3.4 9.8 1.0 CB M:CYS549 3.5 9.7 1.0 C1 M:FCO601 3.6 10.9 1.0 N M:CYS64 3.8 11.0 1.0 C2 M:FCO601 3.8 10.6 1.0 CA M:CYS64 4.2 10.6 1.0 C3 M:FCO601 4.2 9.9 1.0 CA M:CYS549 4.5 10.6 1.0 N M:CYS549 4.5 10.3 1.0 N1 M:FCO601 4.5 11.4 1.0 CA M:CYS61 4.6 9.8 1.0 CA M:CYS546 4.7 11.2 1.0 CB M:VAL63 4.7 11.8 1.0 N2 M:FCO601 4.8 10.9 1.0 C M:VAL63 4.9 11.4 1.0 CD M:LYS479 4.9 13.9 1.0 C M:CYS64 5.0 11.4 1.0

R.M.Evans, S.E.Beaton, L.Kertiss, W.K.Myers, S.B.Carr, F.A.Armstrong. A Comprehensive Structural and Kinetic Investigation of the Role of the Active-Site Argininein Bidirectional Hydrogen Activation By the [Nife]-Hydrogenase "Hyd-2) From Escherichia Coli To Be Published.