Nickel in PDB 6ehq: E. Coli Hydrogenase-2 (As Isolated Form).

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

The structure of E. Coli Hydrogenase-2 (As Isolated Form)., PDB code: 6ehq 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)	86.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.064, 100.090, 168.135, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19

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

Magnesium	(Mg)	2 atoms
Iron	(Fe)	26 atoms

The binding sites of Nickel atom in the E. Coli Hydrogenase-2 (As Isolated Form). (pdb code 6ehq). 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 (As Isolated Form)., PDB code: 6ehq:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-2 (As Isolated 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 (As Isolated Form). within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:26.6 occ:1.00 O L:HOH868 1.8 23.6 1.0 SG L:CYS61 2.2 26.6 1.0 SG L:CYS546 2.2 26.5 1.0 SG L:CYS549 2.5 18.2 1.0 SG L:CYS64 2.5 24.0 1.0 FE L:FCO601 2.9 22.0 1.0 CB L:CYS61 3.0 26.5 1.0 CB L:CYS546 3.3 24.0 1.0 CB L:CYS549 3.5 19.7 1.0 CB L:CYS64 3.6 25.4 1.0 N L:CYS64 3.8 27.4 1.0 C1 L:FCO601 3.9 22.6 1.0 C2 L:FCO601 4.2 20.7 1.0 CA L:CYS64 4.3 26.2 1.0 N L:CYS549 4.4 20.5 1.0 CA L:CYS61 4.4 25.8 1.0 CB L:VAL63 4.5 28.4 1.0 C3 L:FCO601 4.5 22.1 1.0 CA L:CYS549 4.5 19.9 1.0 NH1 L:ARG479 4.6 24.3 1.0 CA L:CYS546 4.7 23.7 1.0 N1 L:FCO601 4.8 22.8 1.0 C L:VAL63 4.8 27.8 1.0 CG L:GLU14 4.9 33.4 1.0 N L:VAL63 4.9 27.7 1.0 CZ L:ARG479 4.9 23.2 1.0 CD L:ARG479 5.0 21.8 1.0 CA L:VAL63 5.0 28.3 1.0 CG1 L:VAL63 5.0 29.0 1.0

Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-2 (As Isolated 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 (As Isolated Form). within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:29.0 occ:1.00 O M:HOH831 1.9 23.1 1.0 SG M:CYS546 2.2 31.2 1.0 SG M:CYS61 2.2 29.8 1.0 SG M:CYS549 2.5 23.0 1.0 SG M:CYS64 2.5 25.0 1.0 FE M:FCO601 2.9 23.0 1.0 CB M:CYS61 3.0 29.5 1.0 CB M:CYS546 3.2 28.3 1.0 CB M:CYS549 3.5 22.7 1.0 CB M:CYS64 3.7 27.1 1.0 N M:CYS64 3.8 28.6 1.0 C1 M:FCO601 3.9 23.9 1.0 C2 M:FCO601 4.1 21.4 1.0 CA M:CYS64 4.3 28.5 1.0 N M:CYS549 4.4 22.6 1.0 C3 M:FCO601 4.4 22.5 1.0 CA M:CYS549 4.5 22.8 1.0 CA M:CYS61 4.5 29.2 1.0 CB M:VAL63 4.5 29.9 1.0 NH1 M:ARG479 4.5 23.3 1.0 CA M:CYS546 4.6 27.0 1.0 N1 M:FCO601 4.8 23.6 1.0 C M:VAL63 4.9 29.3 1.0 CG M:GLU14 4.9 36.3 1.0 CZ M:ARG479 4.9 23.8 1.0 CD M:ARG479 5.0 24.7 1.0 N M:VAL63 5.0 29.5 1.0 CG1 M:VAL63 5.0 29.9 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