Nickel in PDB 6rp2: Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1

All present enzymatic activity of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1:
1.12.99.6;

The structure of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1, PDB code: 6rp2 was solved by S.B.Carr, F.A.Armstrong, L.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.07 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.720, 97.520, 183.060, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 15.9

The structure of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 (pdb code 6rp2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1, PDB code: 6rp2:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni603 b:16.8 occ:1.00 O L:HOH1097 1.8 16.4 1.0 OD L:CSO79 1.8 19.1 0.8 SG L:CYS576 2.0 21.9 1.0 SG L:CYS76 2.2 15.0 1.0 SG L:CYS579 2.5 11.5 1.0 SG L:CSO79 2.6 11.7 1.0 FE L:FCO602 2.9 10.9 1.0 CB L:CYS76 3.0 12.3 1.0 CB L:CYS576 3.2 14.9 1.0 CB L:CYS579 3.6 9.9 1.0 CB L:CSO79 3.8 12.0 1.0 N L:CSO79 3.8 12.0 1.0 C1 L:FCO602 3.9 11.2 1.0 C2 L:FCO602 4.1 11.2 1.0 CA L:CSO79 4.4 11.7 1.0 NH1 L:ARG509 4.4 13.2 1.0 CB L:VAL78 4.4 11.9 1.0 CA L:CYS76 4.4 11.6 1.0 N L:CYS579 4.5 9.8 1.0 C3 L:FCO602 4.5 11.3 1.0 CA L:CYS579 4.5 10.2 1.0 CA L:CYS576 4.5 11.7 1.0 CZ L:ARG509 4.8 12.0 1.0 N1 L:FCO602 4.8 11.6 1.0 C L:VAL78 4.8 11.8 1.0 NE L:ARG509 4.8 10.6 1.0 CD L:ARG509 4.8 11.1 1.0 N L:VAL78 4.9 11.2 1.0 CA L:VAL78 4.9 11.1 1.0 C L:CYS76 5.0 11.5 1.0

Nickel binding site 2 out of 2 in the Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Threonine to Cysteine (T225C) Variant of E Coli Hydrogenase-1 within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:16.9 occ:1.00 O M:HOH1022 1.8 15.7 1.0 OD M:CSO79 1.8 15.5 0.6 SG M:CYS576 2.0 20.3 1.0 SG M:CYS76 2.2 15.3 1.0 SG M:CYS579 2.6 11.6 1.0 SG M:CSO79 2.6 12.1 1.0 FE M:FCO601 2.9 11.1 1.0 CB M:CYS76 3.0 13.2 1.0 CB M:CYS576 3.2 14.7 1.0 CB M:CYS579 3.6 9.7 1.0 CB M:CSO79 3.8 10.6 1.0 N M:CSO79 3.8 11.3 1.0 C1 M:FCO601 3.9 12.1 1.0 C2 M:FCO601 4.1 11.5 1.0 NH1 M:ARG509 4.3 13.3 1.0 CA M:CSO79 4.4 11.1 1.0 CB M:VAL78 4.4 12.1 1.0 CA M:CYS76 4.4 11.8 1.0 C3 M:FCO601 4.5 11.2 1.0 N M:CYS579 4.5 10.3 1.0 CA M:CYS576 4.5 11.7 1.0 CA M:CYS579 4.5 10.5 1.0 CZ M:ARG509 4.7 12.4 1.0 N1 M:FCO601 4.8 12.4 1.0 C M:VAL78 4.8 11.3 1.0 NE M:ARG509 4.8 11.6 1.0 CD M:ARG509 4.8 11.3 1.0 N M:VAL78 4.9 11.5 1.0 CA M:VAL78 4.9 11.7 1.0 C M:CYS76 5.0 11.2 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 2018.
ISSN: ESSN 1754-5706
DOI: 10.1039/C8EE02361A