Nickel in PDB 6fpo: High Resolution Structure of Native Hydrogenase (Hyd-1)

All present enzymatic activity of High Resolution Structure of Native Hydrogenase (Hyd-1):
1.12.99.6;

The structure of High Resolution Structure of Native Hydrogenase (Hyd-1), PDB code: 6fpo was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.55 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.786, 97.733, 183.102, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 13.4

The structure of High Resolution Structure of Native Hydrogenase (Hyd-1) 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 High Resolution Structure of Native Hydrogenase (Hyd-1) (pdb code 6fpo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the High Resolution Structure of Native Hydrogenase (Hyd-1), PDB code: 6fpo:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:14.3 occ:0.80 O L:HOH1040 1.8 10.7 1.0 OD L:CSO79 1.8 14.0 0.8 SG L:CYS576 2.0 16.8 1.0 SG L:CYS76 2.1 14.1 1.0 SG L:CYS579 2.5 8.5 1.0 SG L:CSO79 2.8 8.8 1.0 CB L:CYS76 2.9 13.1 1.0 FE L:FCO601 3.0 8.1 1.0 CB L:CYS576 3.2 11.9 1.0 CB L:CYS579 3.6 7.7 1.0 N L:CSO79 3.8 10.2 1.0 CB L:CSO79 3.9 10.3 1.0 C1 L:FCO601 4.0 8.2 1.0 C2 L:FCO601 4.2 8.0 1.0 CA L:CYS76 4.3 9.8 1.0 N L:CYS579 4.4 7.3 1.0 CB L:VAL78 4.4 11.7 1.0 CA L:CSO79 4.5 9.7 1.0 CA L:CYS579 4.5 7.2 1.0 C3 L:FCO601 4.5 8.1 1.0 CA L:CYS576 4.5 8.6 1.0 NH1 L:ARG509 4.7 11.3 1.0 N L:VAL78 4.8 10.4 1.0 C L:VAL78 4.8 10.7 1.0 C L:CYS76 4.8 8.5 1.0 CA L:VAL78 4.9 10.4 1.0 CZ L:ARG509 4.9 9.6 1.0 N1 L:FCO601 4.9 8.4 1.0 CG L:GLU28 4.9 13.9 1.0 NE L:ARG509 5.0 9.1 1.0

Nickel binding site 2 out of 2 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:14.2 occ:0.80 O M:HOH1177 1.8 10.5 1.0 SG M:CYS576 2.0 16.6 1.0 SG M:CYS76 2.1 14.7 1.0 OD M:CSO79 2.2 12.6 0.6 SG M:CYS579 2.6 8.5 1.0 CB M:CYS76 2.9 12.9 1.0 FE M:FCO601 3.0 8.0 1.0 SG M:CSO79 3.1 9.0 1.0 CB M:CYS576 3.2 12.5 1.0 CB M:CYS579 3.6 8.0 1.0 N M:CSO79 3.8 9.9 1.0 CB M:CSO79 4.0 10.1 1.0 C1 M:FCO601 4.0 8.2 1.0 C2 M:FCO601 4.2 8.0 1.0 CA M:CYS76 4.3 9.8 1.0 N M:CYS579 4.4 7.4 1.0 CB M:VAL78 4.4 12.1 1.0 CA M:CYS579 4.5 7.2 1.0 C3 M:FCO601 4.5 7.7 1.0 CA M:CYS576 4.5 8.6 1.0 CA M:CSO79 4.6 9.7 1.0 NH1 M:ARG509 4.7 11.0 1.0 N M:VAL78 4.8 10.8 1.0 C M:VAL78 4.8 10.6 1.0 CZ M:ARG509 4.8 9.9 1.0 CA M:VAL78 4.8 10.6 1.0 C M:CYS76 4.9 9.1 1.0 N1 M:FCO601 4.9 8.5 1.0 CG M:GLU28 4.9 13.8 1.0 NE M:ARG509 5.0 9.3 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