Nickel in PDB 3uqy: H2-Reduced Structure of E. Coli Hydrogenase-1

All present enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1:
1.12.99.6;

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.710, 97.400, 183.730, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 16

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Nickel atom in the H2-Reduced Structure of E. Coli Hydrogenase-1 (pdb code 3uqy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the H2-Reduced Structure 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 H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:9.0 occ:1.00 SG L:CYS576 2.2 10.2 1.0 SG L:CYS76 2.3 8.3 1.0 SG L:CYS79 2.3 6.7 1.0 SG L:CYS579 2.5 8.1 1.0 FE L:FCO601 2.6 6.8 1.0 CB L:CYS76 3.1 7.4 1.0 CB L:CYS576 3.3 7.8 1.0 CB L:CYS79 3.4 7.5 1.0 CB L:CYS579 3.5 7.4 1.0 C1 L:FCO601 3.7 5.8 1.0 C2 L:FCO601 3.7 6.4 1.0 N L:CYS79 3.7 6.7 1.0 CA L:CYS79 4.1 6.3 1.0 C3 L:FCO601 4.2 8.0 1.0 NH1 L:ARG509 4.2 7.9 1.0 CA L:CYS76 4.5 6.8 1.0 CA L:CYS579 4.6 5.7 1.0 N L:CYS579 4.6 5.7 1.0 N1 L:FCO601 4.6 6.8 1.0 N2 L:FCO601 4.6 8.9 1.0 CB L:VAL78 4.6 6.0 1.0 CZ L:ARG509 4.7 7.1 1.0 CA L:CYS576 4.7 6.3 1.0 CD L:ARG509 4.7 7.0 1.0 C L:VAL78 4.8 8.2 1.0 NE L:ARG509 4.8 7.1 1.0

Nickel binding site 2 out of 2 in the H2-Reduced Structure 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 H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:9.3 occ:1.00 SG M:CYS576 2.1 10.5 1.0 SG M:CYS79 2.3 7.3 1.0 SG M:CYS76 2.3 8.3 1.0 SG M:CYS579 2.5 7.5 1.0 FE M:FCO601 2.6 7.0 1.0 CB M:CYS76 3.1 7.4 1.0 CB M:CYS576 3.3 7.8 1.0 CB M:CYS79 3.4 6.6 1.0 CB M:CYS579 3.5 5.6 1.0 C1 M:FCO601 3.7 6.1 1.0 C2 M:FCO601 3.7 5.1 1.0 N M:CYS79 3.7 6.9 1.0 C3 M:FCO601 4.2 7.3 1.0 CA M:CYS79 4.2 7.5 1.0 NH1 M:ARG509 4.2 7.5 1.0 CA M:CYS76 4.5 6.1 1.0 CA M:CYS579 4.6 6.5 1.0 N1 M:FCO601 4.6 7.8 1.0 N M:CYS579 4.6 6.1 1.0 N2 M:FCO601 4.6 6.7 1.0 CD M:ARG509 4.6 6.6 1.0 CA M:CYS576 4.7 7.9 1.0 CZ M:ARG509 4.7 6.9 1.0 CB M:VAL78 4.7 7.0 1.0 NE M:ARG509 4.8 6.9 1.0 C M:VAL78 4.8 7.8 1.0

A.Volbeda, P.Amara, C.Darnault, J.M.Mouesca, A.Parkin, M.M.Roessler, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Crystallographic and Computational Studies of the O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli. Proc.Natl.Acad.Sci.Usa V. 109 5305 2012.
ISSN: ISSN 0027-8424
PubMed: 22431599
DOI: 10.1073/PNAS.1119806109