Nickel in PDB 5jrd: E. Coli Hydrogenase-1 Variant P508A

All present enzymatic activity of E. Coli Hydrogenase-1 Variant P508A:
1.12.99.6;

The structure of E. Coli Hydrogenase-1 Variant P508A, PDB code: 5jrd was solved by S.B.Carr, S.E.V.Phillips, F.A.Armstrong, R.M.Evans, E.J.Brooke, S.T.A.Islam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.69 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.691, 98.589, 185.373, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.1

The structure of E. Coli Hydrogenase-1 Variant P508A also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	26 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Nickel atom in the E. Coli Hydrogenase-1 Variant P508A (pdb code 5jrd). 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-1 Variant P508A, PDB code: 5jrd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the E. Coli Hydrogenase-1 Variant P508A


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-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:19.5 occ:0.80 SG L:CYS576 1.9 20.4 0.8 SG L:CYS76 1.9 19.1 0.8 O L:HOH949 2.0 10.1 1.0 OD L:CSO79 2.0 16.7 1.0 SG L:CYS579 2.5 12.3 1.0 CB L:CYS76 2.8 19.2 0.8 CB L:CYS76 2.8 17.8 0.2 SG L:CSO79 3.1 12.1 1.0 FE L:FCO601 3.2 11.3 1.0 CB L:CYS576 3.3 14.3 0.8 CB L:CYS576 3.4 10.1 0.2 SG L:CYS576 3.4 11.0 0.2 SG L:CYS76 3.4 19.9 0.2 CB L:CYS579 3.6 11.0 1.0 N L:CSO79 4.0 17.4 1.0 CA L:CYS76 4.1 14.0 0.8 C1 L:FCO601 4.2 11.2 1.0 CB L:CSO79 4.2 16.3 1.0 CA L:CYS76 4.2 13.5 0.2 N L:CYS579 4.3 10.1 1.0 CA L:CYS579 4.4 10.9 1.0 CB L:VAL78 4.5 17.7 1.0 C2 L:FCO601 4.5 11.5 1.0 CA L:CYS576 4.6 10.2 0.2 CA L:CYS576 4.6 10.7 0.8 CA L:CSO79 4.7 16.9 1.0 C3 L:FCO601 4.7 11.6 1.0 C L:CYS76 4.7 12.2 1.0 N L:VAL78 4.8 15.8 1.0 CG L:GLU28 4.8 19.1 1.0 OE1 L:GLU28 4.9 20.6 1.0 C L:VAL78 5.0 19.6 1.0 CA L:VAL78 5.0 17.1 1.0

Nickel binding site 2 out of 2 in the E. Coli Hydrogenase-1 Variant P508A


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-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:21.2 occ:0.80 O M:HOH918 1.9 10.2 1.0 SG M:CYS576 1.9 21.9 0.8 SG M:CYS76 2.0 19.5 0.8 OD M:CSO79 2.0 18.3 1.0 SG M:CYS579 2.6 12.5 1.0 CB M:CYS76 2.8 20.4 0.8 CB M:CYS76 2.8 20.0 0.2 SG M:CSO79 3.1 12.4 1.0 FE M:FCO601 3.1 11.5 1.0 CB M:CYS576 3.3 14.9 0.8 SG M:CYS576 3.3 10.9 0.2 SG M:CYS76 3.4 22.8 0.2 CB M:CYS576 3.4 11.0 0.2 CB M:CYS579 3.6 11.2 1.0 N M:CSO79 4.0 16.5 1.0 CB M:CSO79 4.1 15.4 1.0 C1 M:FCO601 4.1 11.7 1.0 CA M:CYS76 4.2 15.0 0.8 CA M:CYS76 4.2 14.8 0.2 N M:CYS579 4.3 11.0 1.0 C2 M:FCO601 4.4 11.7 1.0 CB M:VAL78 4.4 19.0 1.0 CA M:CYS579 4.5 10.9 1.0 CA M:CYS576 4.6 11.0 0.2 CA M:CYS576 4.6 10.8 0.8 CA M:CSO79 4.6 17.0 1.0 C3 M:FCO601 4.7 10.9 1.0 C M:CYS76 4.8 12.2 1.0 N M:VAL78 4.8 16.5 1.0 CG M:GLU28 4.8 18.7 1.0 OE1 M:GLU28 4.9 20.4 1.0 C M:VAL78 4.9 19.4 1.0 CA M:VAL78 4.9 17.8 1.0 NH1 M:ARG509 5.0 17.4 1.0

E.J.Brooke, R.M.Evans, S.T.Islam, G.M.Roberts, S.A.Wehlin, S.B.Carr, S.E.Phillips, F.A.Armstrong. Importance of the Active Site "Canopy" Residues in An O2-Tolerant [Nife]-Hydrogenase. Biochemistry V. 56 132 2017.
ISSN: ISSN 1520-4995
PubMed: 28001048
DOI: 10.1021/ACS.BIOCHEM.6B00868