Nickel in PDB 5xvb: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition, PDB code: 5xvb 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)	38.02 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.730, 121.610, 98.880, 90.00, 102.65, 90.00
R / Rfree (%)	18.1 / 21.9

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced Condition (pdb code 5xvb). 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 H2- Reduced Condition, PDB code: 5xvb:
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 H2- Reduced 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 H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:23.0 occ:1.00 NI L:NFU602 0.0 23.0 1.0 SG L:CYS546 2.4 24.5 1.0 SG L:CYS64 2.5 16.9 1.0 SG L:CYS549 2.5 17.6 1.0 SG L:CYS61 2.6 23.5 1.0 FE L:NFU602 2.7 17.3 1.0 CB L:CYS61 3.2 18.9 1.0 CB L:CYS546 3.3 15.0 1.0 CB L:CYS549 3.4 19.1 1.0 CB L:CYS64 3.5 16.7 1.0 N L:CYS64 3.7 20.4 1.0 C1 L:NFU602 3.8 14.6 1.0 C2 L:NFU602 3.9 13.4 1.0 CA L:CYS64 4.2 17.3 1.0 C3 L:NFU602 4.3 17.6 1.0 NH1 L:ARG479 4.5 12.7 1.0 CB L:VAL63 4.5 16.1 1.0 CA L:CYS549 4.5 16.4 1.0 N1 L:NFU602 4.5 16.2 1.0 N L:CYS549 4.6 16.6 1.0 CD L:ARG479 4.6 12.8 1.0 CA L:CYS546 4.6 14.8 1.0 CA L:CYS61 4.7 17.9 1.0 CZ L:ARG479 4.7 15.2 1.0 NE L:ARG479 4.7 13.7 1.0 C L:VAL63 4.8 18.9 1.0 N2 L:NFU602 4.8 13.6 1.0 C L:CYS64 4.9 20.6 1.0 CG1 L:VAL63 5.0 16.4 1.0 CG L:GLU14 5.0 20.9 1.0

Nickel binding site 2 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in An H2- Reduced 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 H2- Reduced Condition within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:25.9 occ:1.00 NI M:NFU602 0.0 25.9 1.0 SG M:CYS546 2.5 29.5 1.0 SG M:CYS549 2.6 18.0 1.0 SG M:CYS64 2.6 20.1 1.0 SG M:CYS61 2.6 29.7 1.0 FE M:NFU602 2.7 19.5 1.0 CB M:CYS61 3.2 20.7 1.0 CB M:CYS546 3.3 21.9 1.0 CB M:CYS549 3.4 19.8 1.0 CB M:CYS64 3.5 20.1 1.0 N M:CYS64 3.7 25.3 1.0 C2 M:NFU602 3.9 15.4 1.0 C1 M:NFU602 3.9 17.2 1.0 CA M:CYS64 4.2 22.3 1.0 NH1 M:ARG479 4.4 20.2 1.0 C3 M:NFU602 4.4 22.3 1.0 CA M:CYS549 4.6 19.3 1.0 CD M:ARG479 4.6 13.8 1.0 CB M:VAL63 4.6 20.0 1.0 N M:CYS549 4.7 19.0 1.0 CZ M:ARG479 4.7 19.6 1.0 CA M:CYS546 4.7 19.7 1.0 N1 M:NFU602 4.7 20.4 1.0 CA M:CYS61 4.7 19.9 1.0 OG M:SER548 4.7 21.0 0.4 NE M:ARG479 4.7 18.2 1.0 C M:VAL63 4.8 25.0 1.0 N2 M:NFU602 4.9 15.1 1.0 C M:CYS64 4.9 22.8 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