Nickel in PDB 7vxq: The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77

All present enzymatic activity of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77:
1.12.99.6;

The structure of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77, PDB code: 7vxq was solved by K.Nishikawa, K.Higuchi, T.Imanishi, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.49 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.39, 122.32, 99.91, 90, 103.12, 90
R / Rfree (%)	16.1 / 19.3

The structure of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 (pdb code 7vxq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77, PDB code: 7vxq:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:27.5 occ:1.00 NI A:NFU702 0.0 27.5 1.0 C A:CMO703 1.8 25.9 0.3 SG A:CYS546 2.3 30.3 1.0 SG A:CYS64 2.3 22.7 1.0 SG A:CYS61 2.3 28.4 1.0 SG A:CYS549 2.4 24.4 1.0 FE A:NFU702 2.6 25.3 1.0 O A:CMO703 2.9 26.4 0.3 CB A:CYS61 3.1 28.6 1.0 CB A:CYS546 3.3 26.2 1.0 CB A:CYS64 3.4 21.1 1.0 CB A:CYS549 3.5 23.6 1.0 C1 A:NFU702 3.7 23.8 1.0 N A:CYS64 3.8 26.7 1.0 C2 A:NFU702 3.8 21.5 1.0 CA A:CYS64 4.2 24.6 1.0 C3 A:NFU702 4.4 25.0 1.0 N A:CYS549 4.5 23.8 1.0 CA A:CYS549 4.5 24.2 1.0 CA A:CYS61 4.6 26.2 1.0 NH1 A:ARG479 4.6 24.6 1.0 N1 A:NFU702 4.6 24.7 1.0 CA A:CYS546 4.7 26.0 1.0 CD A:ARG479 4.7 23.1 1.0 CB A:VAL63 4.7 28.3 1.0 N2 A:NFU702 4.8 21.2 1.0 CZ A:ARG479 4.9 25.2 1.0 NE A:ARG479 4.9 25.0 1.0 C A:VAL63 4.9 27.1 1.0 C A:CYS64 4.9 27.9 1.0 OE2 A:GLU14 4.9 38.0 1.0 CG A:GLU14 5.0 31.3 1.0

Nickel binding site 2 out of 2 in the The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Carbon Monoxide Complex of [Nife]-Hydrogenase (Hyb-Type) From Citrobacter Sp. S-77 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni702 b:28.7 occ:1.00 NI C:NFU702 0.0 28.7 1.0 C C:CMO703 1.8 28.4 0.3 SG C:CYS61 2.2 32.9 1.0 SG C:CYS546 2.3 32.2 1.0 SG C:CYS64 2.3 26.4 1.0 SG C:CYS549 2.4 25.3 1.0 FE C:NFU702 2.7 25.3 1.0 O C:CMO703 2.9 26.9 0.3 CB C:CYS61 3.1 29.8 1.0 CB C:CYS546 3.3 27.8 1.0 CB C:CYS64 3.4 26.9 1.0 CB C:CYS549 3.4 25.2 1.0 C1 C:NFU702 3.7 24.4 1.0 N C:CYS64 3.8 29.6 1.0 C2 C:NFU702 3.9 25.0 1.0 CA C:CYS64 4.2 29.2 1.0 C3 C:NFU702 4.3 28.9 1.0 CA C:CYS549 4.5 25.3 1.0 NH1 C:ARG479 4.5 25.3 1.0 CA C:CYS61 4.5 25.3 1.0 N C:CYS549 4.5 24.4 1.0 N1 C:NFU702 4.6 27.1 1.0 CA C:CYS546 4.6 25.4 1.0 CD C:ARG479 4.7 23.1 1.0 CB C:VAL63 4.7 26.8 1.0 N2 C:NFU702 4.8 24.8 1.0 NE C:ARG479 4.9 25.2 1.0 CZ C:ARG479 4.9 27.5 1.0 C C:VAL63 4.9 26.8 1.0 C C:CYS64 4.9 25.7 1.0 OE2 C:GLU14 5.0 37.7 1.0

T.Imanishi, K.Nishikawa, M.Taketa, K.Higuchi, H.Tai, S.Hirota, H.Hojo, T.Kawakami, K.Hataguchi, K.Matsumoto, H.Ogata, Y.Higuchi. Structural and Spectroscopic Characterization of Co Inhibition of [Nife]-Hydrogenase From Citrobacter Sp. S-77. Acta Crystallogr.,Sect.F V. 78 66 2022.
ISSN: ESSN 2053-230X
PubMed: 35102895
DOI: 10.1107/S2053230X22000188