Nickel in PDB 5xvd: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition, PDB code: 5xvd was solved by K.Nishikawa, H.Matsuura, N.D.Muhd Noor, H.Tai, S.Hirota, J.Kim, J.Kang, M.Tateno, K.S.Yoon, S.Ogo, Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.72 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.940, 118.980, 96.810, 90.00, 100.57, 90.00
R / Rfree (%)	12.1 / 16.6

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	32 atoms
Sodium	(Na)	2 atoms

The binding sites of Nickel atom in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition (pdb code 5xvd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition, PDB code: 5xvd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:12.2 occ:1.00 NI L:NFV602 0.0 12.2 1.0 O4 L:NFV602 1.8 13.2 1.0 SG L:CSO546 2.4 16.4 1.0 SG L:CYS61 2.4 12.1 1.0 SG L:CYS64 2.4 11.9 1.0 SG L:CYS549 2.6 10.8 1.0 FE L:NFV602 2.8 10.1 1.0 CB L:CYS61 3.2 11.3 1.0 CB L:CSO546 3.3 13.0 1.0 CB L:CYS64 3.4 11.1 1.0 CB L:CYS549 3.6 9.7 1.0 OD L:CSO546 3.6 16.2 0.3 N L:CYS64 3.7 12.1 1.0 C2 L:NFV602 3.9 9.1 1.0 C3 L:NFV602 4.0 8.5 1.0 CA L:CYS64 4.1 11.6 1.0 C1 L:NFV602 4.4 9.0 1.0 CB L:VAL63 4.4 13.6 1.0 NH1 L:ARG479 4.4 11.9 1.0 N L:CYS549 4.6 10.6 1.0 OG L:SER548 4.6 13.1 0.3 CA L:CYS549 4.6 9.8 1.0 CA L:CYS61 4.6 11.1 1.0 CA L:CSO546 4.7 11.8 1.0 C L:VAL63 4.7 13.3 1.0 CZ L:ARG479 4.8 10.4 1.0 CD L:ARG479 4.8 9.6 1.0 N2 L:NFV602 4.9 11.2 1.0 NE L:ARG479 4.9 10.5 1.0 CG1 L:VAL63 4.9 14.4 1.0 CA L:VAL63 4.9 13.2 1.0 N L:VAL63 4.9 12.7 1.0 C L:CYS64 5.0 12.3 1.0

Nickel binding site 2 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An Air- Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:14.9 occ:1.00 NI M:NFV602 0.0 14.9 1.0 O4 M:NFV602 1.8 16.2 1.0 SG M:CYS64 2.4 14.7 1.0 SG M:CSO546 2.4 20.0 1.0 SG M:CYS61 2.4 16.0 1.0 SG M:CYS549 2.6 15.1 1.0 FE M:NFV602 2.9 13.4 1.0 CB M:CYS61 3.2 15.0 1.0 CB M:CSO546 3.3 17.5 1.0 CB M:CYS64 3.4 15.3 1.0 CB M:CYS549 3.6 15.1 1.0 N M:CYS64 3.6 16.2 1.0 OD M:CSO546 3.7 20.9 0.4 C2 M:NFV602 4.0 12.2 1.0 C3 M:NFV602 4.0 12.5 1.0 CA M:CYS64 4.1 14.6 1.0 CB M:VAL63 4.4 15.7 1.0 C1 M:NFV602 4.5 12.4 1.0 NH1 M:ARG479 4.5 15.1 1.0 N M:CYS549 4.6 13.6 1.0 CA M:CYS549 4.6 14.0 1.0 CA M:CYS61 4.7 13.9 1.0 C M:VAL63 4.7 15.7 1.0 CA M:CSO546 4.7 16.4 1.0 CZ M:ARG479 4.8 14.6 1.0 CD M:ARG479 4.8 14.2 1.0 NE M:ARG479 4.9 15.3 1.0 N2 M:NFV602 4.9 13.7 1.0 CG1 M:VAL63 4.9 15.7 1.0 CA M:VAL63 4.9 15.9 1.0 N M:VAL63 5.0 16.2 1.0 C M:CYS64 5.0 15.6 1.0 N3 M:NFV602 5.0 14.3 1.0

N.D.M.Noor, H.Matsuura, K.Nishikawa, H.Tai, S.Hirota, J.Kim, J.Kang, M.Tateno, K.S.Yoon, S.Ogo, S.Kubota, Y.Shomura, Y.Higuchi. Redox-Dependent Conformational Changes of A Proximal [4FE-4S] Cluster in Hyb-Type [Nife]-Hydrogenase to Protect the Active Site From O2. Chem.Commun.(Camb.) V. 54 12385 2018.
ISSN: ESSN 1364-548X
PubMed: 30328414
DOI: 10.1039/C8CC06261G