Nickel in PDB 5xvc: [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized Condition, PDB code: 5xvc 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)	37.86 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.970, 121.830, 99.170, 90.00, 102.93, 90.00
R / Rfree (%)	16.6 / 21.7

The structure of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-Oxidized 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 A Ferricyanide-Oxidized Condition (pdb code 5xvc). 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 A Ferricyanide-Oxidized Condition, PDB code: 5xvc:
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 A Ferricyanide-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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:11.7 occ:1.00 NI L:NFV602 0.0 11.7 1.0 O4 L:NFV602 1.9 12.9 1.0 SG L:CSO546 2.3 11.8 1.0 SG L:CYS61 2.3 11.7 1.0 SG L:CYS64 2.7 6.1 1.0 SG L:CYS549 2.7 9.3 1.0 FE L:NFV602 3.0 7.7 1.0 CB L:CYS61 3.1 7.7 1.0 CB L:CSO546 3.2 6.4 1.0 OD L:CSO546 3.5 10.1 0.4 CB L:CYS549 3.6 8.6 1.0 CB L:CYS64 3.7 7.4 1.0 N L:CYS64 3.7 9.0 1.0 C2 L:NFV602 4.0 8.0 1.0 CB L:VAL63 4.2 9.2 1.0 C3 L:NFV602 4.2 4.7 1.0 CA L:CYS64 4.3 7.0 1.0 CA L:CYS61 4.6 7.1 1.0 C1 L:NFV602 4.6 7.7 1.0 N L:CYS549 4.6 6.8 1.0 CA L:CSO546 4.6 8.7 1.0 CA L:CYS549 4.6 8.4 1.0 NH1 L:ARG479 4.6 4.3 1.0 CD L:ARG479 4.7 6.1 1.0 C L:VAL63 4.7 8.5 1.0 N L:VAL63 4.8 7.8 1.0 CZ L:ARG479 4.8 7.1 1.0 NE L:ARG479 4.8 5.6 1.0 CG2 L:VAL63 4.8 6.4 1.0 N2 L:NFV602 4.8 4.5 1.0 CA L:VAL63 4.9 7.9 1.0 CG L:GLU14 5.0 15.5 1.0 CG1 L:VAL63 5.0 7.9 1.0

Nickel binding site 2 out of 2 in the [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 in A Ferricyanide-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 A Ferricyanide-Oxidized Condition within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni701 b:14.4 occ:1.00 NI M:NFV701 0.0 14.4 1.0 O4 M:NFV701 2.0 11.9 1.0 SG M:CSO546 2.3 13.9 1.0 SG M:CYS61 2.3 14.8 1.0 SG M:CYS549 2.7 8.8 1.0 SG M:CYS64 2.8 9.3 1.0 FE M:NFV701 3.1 9.3 1.0 CB M:CYS61 3.1 12.6 1.0 CB M:CSO546 3.2 10.8 1.0 CB M:CYS64 3.6 9.7 1.0 CB M:CYS549 3.6 8.6 1.0 N M:CYS64 3.7 16.0 1.0 OD M:CSO546 3.7 13.4 0.3 C2 M:NFV701 4.1 7.7 1.0 CA M:CYS64 4.2 12.3 1.0 C3 M:NFV701 4.3 6.7 1.0 CB M:VAL63 4.5 11.3 1.0 CA M:CYS61 4.6 13.8 1.0 N M:CYS549 4.6 9.2 1.0 C1 M:NFV701 4.6 9.6 1.0 CA M:CYS549 4.6 8.0 1.0 NH1 M:ARG479 4.6 9.1 1.0 CA M:CSO546 4.6 9.2 1.0 C M:VAL63 4.7 13.6 1.0 CZ M:ARG479 4.8 9.3 1.0 CD M:ARG479 4.8 7.5 1.0 NE M:ARG479 4.8 7.0 1.0 N M:VAL63 4.9 15.0 1.0 CA M:VAL63 5.0 10.2 1.0 N2 M:NFV701 5.0 7.7 1.0 C M:CYS64 5.0 13.9 1.0 CG M:GLU14 5.0 16.4 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