Nickel in PDB 6ehs: E. Coli Hydrogenase-2 Chemically Reduced Structure

All present enzymatic activity of E. Coli Hydrogenase-2 Chemically Reduced Structure:
1.12.99.6;

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

Resolution Low / High (Å)	86.08 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.885, 100.065, 168.801, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 16.3

The structure of E. Coli Hydrogenase-2 Chemically Reduced Structure 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 Chemically Reduced Structure (pdb code 6ehs). 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 Chemically Reduced Structure, PDB code: 6ehs:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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 Chemically Reduced Structure within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:17.8 occ:1.00 O L:HOH1014 1.8 23.3 1.0 SG L:CSO546 2.1 23.0 1.0 SG L:CYS61 2.2 16.8 1.0 SG L:CYS549 2.4 13.0 1.0 SG L:CYS64 2.5 14.3 1.0 FE L:FCO601 2.8 12.2 1.0 CB L:CYS61 3.0 14.7 1.0 CB L:CSO546 3.2 17.4 1.0 OD L:CSO546 3.3 25.6 0.5 CB L:CYS549 3.5 10.8 1.0 CB L:CYS64 3.6 14.8 1.0 C1 L:FCO601 3.8 10.9 1.0 N L:CYS64 3.8 19.4 1.0 C2 L:FCO601 4.0 12.5 1.0 CA L:CYS64 4.3 15.2 1.0 N L:CYS549 4.4 12.3 1.0 C3 L:FCO601 4.4 12.8 1.0 CA L:CYS549 4.5 12.1 1.0 CA L:CYS61 4.5 12.6 1.0 CB L:VAL63 4.5 15.0 1.0 CA L:CSO546 4.6 12.2 1.0 NH1 L:ARG479 4.6 13.7 1.0 N1 L:FCO601 4.7 12.1 1.0 C L:VAL63 4.9 16.8 1.0 CD L:ARG479 4.9 12.6 1.0 CZ L:ARG479 4.9 12.8 1.0 NE L:ARG479 4.9 12.2 1.0 CG L:GLU14 5.0 21.9 1.0 N L:VAL63 5.0 15.3 1.0 OE1 L:GLU14 5.0 25.3 1.0

Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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 Chemically Reduced Structure within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:19.9 occ:1.00 O M:HOH976 1.8 24.5 1.0 SG M:CSO546 2.1 26.1 1.0 SG M:CYS61 2.2 18.3 1.0 SG M:CYS549 2.4 14.4 1.0 SG M:CYS64 2.5 15.6 1.0 FE M:FCO601 2.8 13.8 1.0 CB M:CYS61 3.0 17.3 1.0 CB M:CSO546 3.3 19.4 1.0 OD M:CSO546 3.3 25.0 0.5 CB M:CYS549 3.5 12.9 1.0 CB M:CYS64 3.6 19.3 1.0 C1 M:FCO601 3.8 12.4 1.0 N M:CYS64 3.8 17.8 1.0 C2 M:FCO601 4.1 13.2 1.0 CA M:CYS64 4.3 16.4 1.0 N M:CYS549 4.3 13.5 1.0 C3 M:FCO601 4.4 13.8 1.0 CA M:CYS549 4.4 13.7 1.0 CA M:CYS61 4.5 15.6 1.0 CB M:VAL63 4.5 18.4 1.0 CA M:CSO546 4.6 15.1 1.0 NH1 M:ARG479 4.6 14.4 1.0 N1 M:FCO601 4.7 14.1 1.0 C M:VAL63 4.9 18.0 1.0 CD M:ARG479 4.9 14.8 1.0 CG M:GLU14 4.9 24.1 1.0 CZ M:ARG479 4.9 13.6 1.0 NE M:ARG479 5.0 14.3 1.0 N M:VAL63 5.0 15.7 1.0 OE1 M:GLU14 5.0 32.4 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