Nickel in PDB 3use: Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

All present enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form:
1.12.99.6;

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use 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)	29.82 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.930, 97.790, 183.290, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 16.8

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	32 atoms
Chlorine	(Cl)	3 atoms

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

Nickel binding site 1 out of 2 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:11.5 occ:1.00 O L:HOH701 1.9 9.7 1.0 SG L:CYS576 2.2 10.9 1.0 SG L:CYS76 2.2 9.6 1.0 O L:HOH702 2.4 10.3 0.2 SG L:CYS79 2.5 9.2 1.0 SG L:CYS579 2.6 8.6 1.0 FE L:FCO601 2.9 8.7 1.0 CB L:CYS76 3.1 9.4 1.0 CB L:CYS576 3.2 9.6 1.0 CB L:CYS79 3.6 8.0 1.0 CB L:CYS579 3.7 8.1 1.0 N L:CYS79 3.7 8.2 1.0 C1 L:FCO601 4.0 7.8 1.0 C2 L:FCO601 4.1 8.7 1.0 CA L:CYS79 4.2 8.0 1.0 NH1 L:ARG509 4.4 9.5 1.0 C3 L:FCO601 4.4 8.8 1.0 CA L:CYS76 4.5 8.7 1.0 CB L:VAL78 4.5 7.7 1.0 N L:CYS579 4.6 8.7 1.0 CZ L:ARG509 4.6 9.1 1.0 CA L:CYS576 4.6 8.8 1.0 CA L:CYS579 4.6 7.6 1.0 C L:VAL78 4.7 9.2 1.0 NE L:ARG509 4.8 8.9 1.0 CD L:ARG509 4.9 8.0 1.0 N1 L:FCO601 4.9 9.2 1.0 N L:VAL78 4.9 7.9 1.0 CA L:VAL78 4.9 9.1 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:11.7 occ:1.00 O M:HOH701 1.8 9.9 1.0 SG M:CYS576 2.2 10.0 1.0 SG M:CYS76 2.2 12.0 1.0 O M:HOH702 2.4 9.6 0.2 SG M:CYS79 2.4 8.4 1.0 SG M:CYS579 2.7 8.0 1.0 FE M:FCO601 2.9 7.9 1.0 CB M:CYS76 3.1 9.2 1.0 CB M:CYS576 3.2 8.1 1.0 CB M:CYS79 3.6 8.2 1.0 CB M:CYS579 3.7 7.3 1.0 N M:CYS79 3.7 8.2 1.0 C1 M:FCO601 4.0 8.5 1.0 C2 M:FCO601 4.1 7.1 1.0 CA M:CYS79 4.2 9.1 1.0 NH1 M:ARG509 4.3 8.1 1.0 C3 M:FCO601 4.4 8.0 1.0 CA M:CYS76 4.5 6.9 1.0 CZ M:ARG509 4.5 9.0 1.0 CB M:VAL78 4.6 10.5 1.0 CA M:CYS576 4.6 7.7 1.0 N M:CYS579 4.6 6.4 1.0 CA M:CYS579 4.6 6.3 1.0 NE M:ARG509 4.7 6.5 1.0 C M:VAL78 4.7 8.7 1.0 CD M:ARG509 4.8 6.3 1.0 N1 M:FCO601 4.9 8.5 1.0 N M:VAL78 4.9 8.3 1.0 CA M:VAL78 5.0 9.4 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