Nickel in PDB 8x9f: Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev

All present enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev:
1.2.7.4;

The structure of Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev, PDB code: 8x9f was solved by H.H.Lee, Y.Heo, H.J.Yoon, S.M.Kim, S.Y.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.05 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.251, 74.783, 71.214, 90, 111.18, 90
R / Rfree (%)	24.5 / 26.7

The structure of Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

The binding sites of Nickel atom in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev (pdb code 8x9f). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev, PDB code: 8x9f:

Nickel binding site 1 out of 1 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Co Dehydrogenase Mutant in Complex with Ev within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni703 b:38.7 occ:0.62 NI A:XCC703 0.0 38.7 0.6 SG A:CYS526 2.0 32.6 1.0 S1 A:XCC703 2.2 37.6 0.6 S4 A:XCC703 2.5 38.8 0.6 FE2 A:XCC703 2.6 39.0 0.6 FE3 A:XCC703 2.9 38.9 0.6 CB A:CYS526 3.0 32.0 1.0 FE4 A:XCC703 3.6 38.0 0.6 FE1 A:XCC703 3.9 39.0 0.6 S3 A:XCC703 3.9 38.5 0.6 CA A:CYS526 4.2 30.3 1.0 NE2 A:HIS261 4.3 37.7 1.0 NZ A:LYS563 4.5 34.7 1.0 SG A:CYS295 4.6 35.1 1.0 CE A:LYS563 4.7 32.9 1.0 SG A:CYS446 4.7 34.8 1.0 CA A:GLY445 4.8 34.6 1.0 CD1 A:ILE567 4.8 28.5 1.0 S2 A:XCC703 4.8 39.0 0.6 C A:GLY445 4.9 35.1 1.0 CB A:LYS563 4.9 30.0 1.0

S.M.Kim, S.H.Kang, J.Lee, Y.Heo, E.G.Poloniataki, J.Kang, H.J.Yoon, S.Y.Kong, Y.Yun, H.Kim, J.Ryu, H.H.Lee, Y.H.Kim. Identifying A Key Spot For Electron Mediator-Interaction to Tailor Co Dehydrogenase'S Affinity Nat Commun V. 15 2732 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-46909-1