Nickel in PDB 6fpw: Structure of Fully Reduced Hydrogenase (Hyd-1)

All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1):
1.12.99.6;

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1), PDB code: 6fpw 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)	91.46 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.835, 97.729, 182.911, 90.00, 90.00, 90.00
R / Rfree (%)	11.4 / 14.4

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	6 atoms

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

Nickel binding site 1 out of 2 in the Structure of Fully Reduced 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 Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni601 b:10.2 occ:1.00 NI L:EJ2601 0.0 10.2 1.0 H L:EJ2601 1.6 9.8 1.0 SG L:CYS576 2.2 12.6 1.0 SG L:CYS76 2.2 10.4 1.0 SG L:CYS79 2.3 9.4 1.0 SG L:CYS579 2.5 9.6 1.0 FE L:EJ2601 2.6 9.3 1.0 H L:CYS79 2.8 9.7 1.0 HB2 L:CYS76 3.1 10.3 1.0 CB L:CYS76 3.1 10.8 1.0 HB3 L:CYS76 3.1 11.0 1.0 HB2 L:CYS579 3.3 8.6 1.0 CB L:CYS576 3.3 11.1 1.0 HB3 L:CYS576 3.3 11.4 1.0 HB3 L:CYS79 3.4 9.4 1.0 CB L:CYS79 3.4 9.6 1.0 HB2 L:CYS576 3.5 11.2 1.0 CB L:CYS579 3.5 8.2 1.0 C1 L:EJ2601 3.6 9.7 1.0 C2 L:EJ2601 3.7 9.9 1.0 N L:CYS79 3.7 9.7 1.0 HB L:VAL78 3.7 10.6 1.0 H L:CYS579 3.9 8.9 1.0 HD2 L:ARG509 4.0 12.1 1.0 HH11 L:ARG509 4.0 12.6 1.0 CA L:CYS79 4.1 9.8 1.0 C3 L:EJ2601 4.1 9.3 1.0 HB3 L:CYS579 4.2 8.1 1.0 NH1 L:ARG509 4.2 13.0 1.0 HB2 L:CYS79 4.2 9.9 1.0 H L:VAL78 4.4 8.9 1.0 HE2 L:HIS83 4.4 10.8 0.0 HH12 L:ARG509 4.4 12.6 1.0 CA L:CYS76 4.5 9.6 1.0 CA L:CYS579 4.5 9.0 1.0 N1 L:EJ2601 4.5 9.7 1.0 N L:CYS579 4.6 9.2 1.0 N2 L:EJ2601 4.6 9.8 1.0 CA L:CYS576 4.7 9.6 1.0 CB L:VAL78 4.7 10.6 1.0 HA L:CYS579 4.7 8.8 1.0 CZ L:ARG509 4.7 12.2 1.0 CD L:ARG509 4.7 11.9 1.0 HA L:CYS76 4.7 9.5 1.0 HG11 L:VAL78 4.8 12.5 1.0 C L:VAL78 4.8 10.1 1.0 HA L:CYS576 4.8 9.6 1.0 NE L:ARG509 4.8 11.2 1.0 HA L:CYS79 4.9 10.0 1.0 C L:CYS79 5.0 9.8 1.0

Nickel binding site 2 out of 2 in the Structure of Fully Reduced 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 Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni601 b:10.3 occ:1.00 NI M:EJ2601 0.0 10.3 1.0 H M:EJ2601 1.6 9.8 1.0 SG M:CYS576 2.2 13.0 1.0 SG M:CYS76 2.2 10.4 1.0 SG M:CYS79 2.2 9.5 1.0 SG M:CYS579 2.5 9.7 1.0 FE M:EJ2601 2.6 9.4 1.0 H M:CYS79 2.8 9.3 1.0 CB M:CYS76 3.1 9.5 1.0 HB2 M:CYS76 3.1 9.6 1.0 HB3 M:CYS76 3.1 9.3 1.0 HB3 M:CYS79 3.3 8.9 1.0 HB2 M:CYS579 3.3 8.9 1.0 CB M:CYS576 3.3 10.9 1.0 CB M:CYS79 3.4 8.8 1.0 HB3 M:CYS576 3.4 11.2 1.0 HB2 M:CYS576 3.5 11.3 1.0 CB M:CYS579 3.6 8.8 1.0 C1 M:EJ2601 3.7 9.5 1.0 C2 M:EJ2601 3.7 10.0 1.0 N M:CYS79 3.7 9.0 1.0 HB M:VAL78 3.7 11.1 1.0 HD2 M:ARG509 3.9 11.5 1.0 H M:CYS579 3.9 9.5 1.0 HH11 M:ARG509 3.9 12.6 1.0 CA M:CYS79 4.1 9.4 1.0 C3 M:EJ2601 4.1 8.8 1.0 HB2 M:CYS79 4.2 9.1 1.0 HB3 M:CYS579 4.2 9.1 1.0 NH1 M:ARG509 4.2 13.1 1.0 H M:VAL78 4.4 9.7 1.0 HH12 M:ARG509 4.4 12.4 1.0 HE2 M:HIS83 4.4 10.5 0.0 CA M:CYS76 4.5 9.0 1.0 N1 M:EJ2601 4.6 10.6 1.0 CA M:CYS579 4.6 9.8 1.0 N2 M:EJ2601 4.6 10.6 1.0 N M:CYS579 4.6 9.3 1.0 CB M:VAL78 4.7 11.0 1.0 CA M:CYS576 4.7 10.2 1.0 CZ M:ARG509 4.7 11.6 1.0 CD M:ARG509 4.7 11.2 1.0 HA M:CYS579 4.7 9.6 1.0 HA M:CYS76 4.8 9.0 1.0 HG11 M:VAL78 4.8 12.7 1.0 C M:VAL78 4.8 9.7 1.0 NE M:ARG509 4.8 11.9 1.0 HA M:CYS79 4.8 9.6 1.0 HA M:CYS576 4.9 10.5 1.0 HD3 M:ARG509 5.0 11.4 1.0 C M:CYS79 5.0 10.6 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