Nickel in PDB 6g7m: Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2

All present enzymatic activity of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2:
1.12.99.6;

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m was solved by S.B.Carr, F.A.Armstrong, L.Zhang, S.E.Beaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.75 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.237, 100.986, 169.425, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	24 atoms

The binding sites of Nickel atom in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 (pdb code 6g7m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:14.8 occ:1.00 O L:HOH997 1.9 12.7 1.0 SG L:CYS546 2.2 15.7 1.0 SG L:CYS61 2.2 13.2 1.0 SG L:CYS64 2.5 12.4 1.0 SG L:CYS549 2.6 11.5 1.0 FE L:FCO601 2.9 11.1 1.0 CB L:CYS61 3.1 12.8 1.0 CB L:CYS546 3.3 13.6 1.0 CB L:CYS64 3.6 13.1 1.0 CB L:CYS549 3.6 11.6 1.0 N L:CYS64 3.7 13.4 1.0 C1 L:FCO601 4.0 11.4 1.0 C2 L:FCO601 4.2 10.6 1.0 CA L:CYS64 4.2 12.9 1.0 CB L:VAL63 4.4 12.2 1.0 N L:CYS549 4.5 11.4 1.0 C3 L:FCO601 4.5 12.1 1.0 CA L:CYS61 4.6 11.9 1.0 CA L:CYS549 4.6 11.0 1.0 NH1 L:ARG479 4.6 12.0 1.0 CA L:CYS546 4.7 11.9 1.0 C L:VAL63 4.8 13.0 1.0 N1 L:FCO601 4.9 11.7 1.0 CZ L:ARG479 4.9 10.7 1.0 N L:VAL63 4.9 12.1 1.0 CD L:ARG479 4.9 11.7 1.0 CG L:GLU14 4.9 13.8 1.0 NE L:ARG479 5.0 10.1 1.0 CA L:VAL63 5.0 12.5 1.0

Nickel binding site 2 out of 2 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:16.5 occ:1.00 O M:HOH959 1.8 15.3 1.0 SG M:CYS546 2.2 16.4 1.0 SG M:CYS61 2.2 16.6 1.0 SG M:CYS64 2.5 13.8 1.0 SG M:CYS549 2.5 13.4 1.0 FE M:FCO601 2.9 12.6 1.0 CB M:CYS61 3.1 15.1 1.0 CB M:CYS546 3.3 14.8 1.0 CB M:CYS549 3.6 12.4 1.0 CB M:CYS64 3.6 14.1 1.0 N M:CYS64 3.8 14.8 1.0 C1 M:FCO601 4.0 11.6 1.0 C2 M:FCO601 4.2 11.7 1.0 CA M:CYS64 4.2 14.1 1.0 N M:CYS549 4.5 12.6 1.0 CB M:VAL63 4.5 15.8 1.0 C3 M:FCO601 4.5 12.2 1.0 CA M:CYS549 4.6 13.0 1.0 CA M:CYS61 4.6 14.2 1.0 NH1 M:ARG479 4.6 13.6 1.0 CA M:CYS546 4.7 13.9 1.0 C M:VAL63 4.8 14.9 1.0 CD M:ARG479 4.9 12.4 1.0 CZ M:ARG479 4.9 12.2 1.0 N1 M:FCO601 4.9 12.4 1.0 NE M:ARG479 4.9 12.0 1.0 CG1 M:VAL63 5.0 17.1 1.0 N M:VAL63 5.0 14.6 1.0 CG M:GLU14 5.0 18.1 1.0

L.Zhang, S.E.Beaton, S.B.Carr, F.A.Armstrong. Direct Visible Light Activation of A Surface Cysteine-Engineered [Nife]-Hydrogenase By Silver Nanoclusters Energy Environ Sci 2019.
ISSN: ISSN 1754-5706
DOI: 10.1039/C8EE02361A