Nickel in PDB 5lry: E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D

All present enzymatic activity of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D:
1.12.99.6;

The structure of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D, PDB code: 5lry was solved by S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.79 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.756, 98.746, 185.243, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 16.3

The structure of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D (pdb code 5lry). 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 [Nife] Hydrogenase Hyd-1 Mutant E28D, PDB code: 5lry:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni603 b:11.3 occ:1.00 O L:HOH1102 1.8 12.1 1.0 SG L:CSD576 2.1 11.2 1.0 SG L:CYS76 2.2 10.5 1.0 SG L:CYS79 2.5 8.8 1.0 SG L:CYS579 2.7 8.2 1.0 FE L:FCO602 2.9 7.8 1.0 OD1 L:CSD576 3.0 10.3 0.6 CB L:CYS76 3.1 9.5 1.0 OD2 L:CSD576 3.2 10.3 0.7 CB L:CSD576 3.2 9.8 1.0 CB L:CYS79 3.6 8.8 1.0 N L:CYS79 3.7 9.3 1.0 CB L:CYS579 3.8 7.5 1.0 C1 L:FCO602 4.0 7.9 1.0 C2 L:FCO602 4.1 7.9 1.0 CA L:CYS79 4.2 9.1 1.0 CB L:VAL78 4.4 9.9 1.0 C3 L:FCO602 4.5 7.8 1.0 NH1 L:ARG509 4.5 10.8 1.0 CA L:CYS76 4.6 9.0 1.0 CA L:CSD576 4.6 9.3 1.0 N L:CYS579 4.7 7.5 1.0 CZ L:ARG509 4.7 10.4 1.0 C L:VAL78 4.7 9.8 1.0 CA L:CYS579 4.7 7.5 1.0 O S:HOH525 4.8 14.8 0.9 NE L:ARG509 4.9 9.5 1.0 CA L:VAL78 4.9 9.7 1.0 N L:VAL78 4.9 8.9 1.0 N1 L:FCO602 4.9 8.2 1.0 CD L:ARG509 5.0 9.1 1.0

Nickel binding site 2 out of 2 in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:11.4 occ:1.00 O M:HOH1127 1.8 9.8 0.9 SG M:CSD576 2.1 11.1 1.0 SG M:CYS76 2.2 10.3 0.9 SG M:CYS79 2.5 9.0 1.0 SG M:CYS579 2.7 8.2 1.0 FE M:FCO601 2.9 7.7 1.0 OD1 M:CSD576 3.0 10.0 0.5 OD2 M:CSD576 3.1 10.6 0.7 CB M:CYS76 3.2 9.4 1.0 CB M:CSD576 3.2 9.8 1.0 CB M:CYS79 3.6 8.7 1.0 N M:CYS79 3.7 8.9 1.0 CB M:CYS579 3.8 7.4 1.0 C1 M:FCO601 4.0 7.6 1.0 C2 M:FCO601 4.0 8.1 1.0 CA M:CYS79 4.2 9.0 1.0 CB M:VAL78 4.3 10.5 1.0 NH1 M:ARG509 4.4 10.5 1.0 C3 M:FCO601 4.5 7.7 1.0 CA M:CYS76 4.6 9.1 1.0 CZ M:ARG509 4.6 10.1 1.0 CA M:CSD576 4.6 9.1 1.0 N M:CYS579 4.7 7.4 1.0 C M:VAL78 4.7 9.7 1.0 O T:HOH621 4.7 12.9 0.9 CA M:CYS579 4.8 7.4 1.0 NE M:ARG509 4.8 9.3 1.0 N M:VAL78 4.9 9.5 1.0 CA M:VAL78 4.9 9.8 1.0 CD M:ARG509 4.9 9.0 1.0 N1 M:FCO601 4.9 7.9 1.0 N2 M:FCO601 5.0 7.7 1.0

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J.Am.Chem.Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798