Nickel in PDB 6gam: Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme)

All present enzymatic activity of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme):
1.12.99.6;

The structure of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme), PDB code: 6gam was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.32 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.477, 100.471, 168.656, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 17

The structure of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) (pdb code 6gam). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme), PDB code: 6gam:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:10.5 occ:1.00 O L:HOH1041 1.6 44.0 1.0 SG L:CYS546 2.2 13.0 1.0 SG L:CYS61 2.3 9.9 1.0 SG L:CYS64 2.3 9.7 1.0 SG L:CYS549 2.4 9.4 1.0 FE L:FCO601 2.6 8.8 1.0 CB L:CYS61 3.1 9.0 1.0 CB L:CYS546 3.4 10.8 1.0 CB L:CYS64 3.5 9.7 1.0 CB L:CYS549 3.5 9.0 1.0 C1 L:FCO601 3.6 8.8 1.0 N L:CYS64 3.7 9.4 1.0 C2 L:FCO601 3.8 8.4 1.0 CA L:CYS64 4.1 9.7 1.0 C3 L:FCO601 4.2 8.9 1.0 N L:CYS549 4.5 8.9 1.0 CA L:CYS549 4.5 8.9 1.0 NH1 L:ARG479 4.5 10.3 1.0 N1 L:FCO601 4.6 9.6 1.0 CA L:CYS61 4.6 8.8 1.0 CA L:CYS546 4.7 9.8 1.0 CB L:VAL63 4.7 9.8 1.0 CD L:ARG479 4.7 9.0 1.0 N2 L:FCO601 4.8 8.0 1.0 CZ L:ARG479 4.8 9.4 1.0 C L:VAL63 4.9 10.2 1.0 NE L:ARG479 4.9 8.5 1.0 C L:CYS64 4.9 9.8 1.0 NE2 L:HIS68 5.0 9.6 1.0

Nickel binding site 2 out of 2 in the Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of E14Q Variant of E. Coli Hydrogenase-2 (As-Isolated Enzyme) within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:12.1 occ:1.00 O M:HOH973 1.6 43.3 1.0 SG M:CYS546 2.2 15.0 1.0 SG M:CYS61 2.3 11.5 1.0 SG M:CYS64 2.3 11.1 1.0 SG M:CYS549 2.4 11.0 1.0 FE M:FCO601 2.6 10.4 1.0 CB M:CYS61 3.1 11.1 1.0 CB M:CYS546 3.3 12.0 1.0 CB M:CYS64 3.5 10.4 1.0 CB M:CYS549 3.5 10.9 1.0 C1 M:FCO601 3.7 10.2 1.0 N M:CYS64 3.7 10.2 1.0 C2 M:FCO601 3.8 9.7 1.0 CA M:CYS64 4.1 10.3 1.0 C3 M:FCO601 4.2 11.3 1.0 N M:CYS549 4.5 10.9 1.0 CA M:CYS549 4.5 11.2 1.0 NH1 M:ARG479 4.5 11.4 1.0 CA M:CYS61 4.6 10.1 1.0 N1 M:FCO601 4.6 11.2 1.0 CB M:VAL63 4.7 11.4 1.0 CA M:CYS546 4.7 11.8 1.0 CD M:ARG479 4.7 11.1 1.0 N2 M:FCO601 4.8 9.5 1.0 C M:VAL63 4.8 10.8 1.0 CZ M:ARG479 4.9 10.8 1.0 NE M:ARG479 4.9 10.8 1.0 C M:CYS64 4.9 10.2 1.0

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798