Nickel in PDB 6en9: E. Coli Hydrogenase-2 (Hydrogen Reduced Form)

All present enzymatic activity of E. Coli Hydrogenase-2 (Hydrogen Reduced Form):
1.12.99.6;

The structure of E. Coli Hydrogenase-2 (Hydrogen Reduced Form), PDB code: 6en9 was solved by S.B.Carr, S.E.Beaton, R.M.Evans, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.35 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.602, 100.540, 168.587, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.5

The structure of E. Coli Hydrogenase-2 (Hydrogen Reduced Form) also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the E. Coli Hydrogenase-2 (Hydrogen Reduced Form) (pdb code 6en9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the E. Coli Hydrogenase-2 (Hydrogen Reduced Form), PDB code: 6en9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-2 (Hydrogen Reduced Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of E. Coli Hydrogenase-2 (Hydrogen Reduced Form) within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:13.4 occ:1.00 SG L:CYS546 2.1 30.0 1.0 SG L:CYS61 2.2 13.6 1.0 SG L:CYS64 2.3 12.7 1.0 SG L:CYS549 2.4 12.5 1.0 FE L:FCO601 2.7 12.1 1.0 CB L:CYS61 3.1 13.3 1.0 CB L:CYS546 3.3 30.0 1.0 CB L:CYS549 3.5 11.4 1.0 CB L:CYS64 3.5 11.8 1.0 C1 L:FCO601 3.7 12.6 1.0 N L:CYS64 3.8 12.2 1.0 C2 L:FCO601 3.8 12.4 1.0 CA L:CYS64 4.2 12.2 1.0 C3 L:FCO601 4.3 12.5 1.0 N L:CYS549 4.4 11.7 1.0 CA L:CYS549 4.5 11.9 1.0 NH1 L:ARG479 4.5 13.0 1.0 CA L:CYS61 4.5 11.7 1.0 N1 L:FCO601 4.6 12.5 1.0 CB L:VAL63 4.7 12.9 1.0 CA L:CYS546 4.7 13.5 1.0 CD L:ARG479 4.7 11.5 1.0 N2 L:FCO601 4.8 11.2 1.0 NE L:ARG479 4.9 11.4 1.0 CZ L:ARG479 4.9 11.7 1.0 C L:VAL63 4.9 13.2 1.0 C L:CYS64 4.9 12.1 1.0 NE2 L:HIS68 5.0 12.7 1.0

Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-2 (Hydrogen Reduced Form)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of E. Coli Hydrogenase-2 (Hydrogen Reduced Form) within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:15.7 occ:1.00 SG M:CYS546 2.2 30.0 1.0 SG M:CYS61 2.2 15.9 1.0 SG M:CYS64 2.3 13.6 1.0 SG M:CYS549 2.3 15.1 1.0 FE M:FCO601 2.7 14.1 1.0 CB M:CYS61 3.1 16.3 1.0 CB M:CYS546 3.4 30.0 1.0 CB M:CYS64 3.4 13.1 1.0 CB M:CYS549 3.5 13.9 1.0 C1 M:FCO601 3.7 13.8 1.0 N M:CYS64 3.7 13.6 1.0 C2 M:FCO601 3.8 12.5 1.0 CA M:CYS64 4.1 13.3 1.0 C3 M:FCO601 4.3 15.0 1.0 N M:CYS549 4.4 13.6 1.0 CA M:CYS549 4.5 14.1 1.0 CA M:CYS61 4.5 14.2 1.0 NH1 M:ARG479 4.5 14.5 1.0 N1 M:FCO601 4.6 15.3 1.0 CB M:VAL63 4.7 14.7 1.0 N2 M:FCO601 4.7 12.1 1.0 CA M:CYS546 4.7 15.9 1.0 CD M:ARG479 4.8 14.5 1.0 C M:VAL63 4.9 14.5 1.0 CZ M:ARG479 4.9 14.3 1.0 NE M:ARG479 4.9 14.3 1.0 C M:CYS64 4.9 13.2 1.0 NE2 M:HIS68 5.0 14.6 1.0

S.E.Beaton, R.M.Evans, A.J.Finney, C.M.Lamont, F.A.Armstrong, F.Sargent, S.B.Carr. The Structure of Hydrogenase-2 Fromescherichia Coli: Implications For H2-Driven Proton Pumping. Biochem. J. V. 475 1353 2018.
ISSN: ESSN 1470-8728
PubMed: 29555844
DOI: 10.1042/BCJ20180053