Zinc in PDB 5y0z: Human SIRT2 in Complex with A Specific Inhibitor, NPD11033

The structure of Human SIRT2 in Complex with A Specific Inhibitor, NPD11033, PDB code: 5y0z was solved by N.Kudo, A.Ito, M.Yoshida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.987, 115.685, 71.055, 90.00, 89.99, 90.00
R / Rfree (%)	21 / 24.2

The binding sites of Zinc atom in the Human SIRT2 in Complex with A Specific Inhibitor, NPD11033 (pdb code 5y0z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SIRT2 in Complex with A Specific Inhibitor, NPD11033, PDB code: 5y0z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT2 in Complex with A Specific Inhibitor, NPD11033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT2 in Complex with A Specific Inhibitor, NPD11033 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:20.6 occ:1.00 SG A:CYS221 2.3 20.6 1.0 SG A:CYS195 2.3 21.3 1.0 SG A:CYS200 2.3 19.3 1.0 SG A:CYS224 2.4 21.6 1.0 CB A:CYS221 3.1 21.0 1.0 CB A:CYS200 3.2 19.5 1.0 CB A:CYS195 3.2 19.4 1.0 CB A:CYS224 3.5 21.5 1.0 N A:CYS224 3.9 22.2 1.0 CA A:CYS224 4.2 22.3 1.0 CB A:HIS202 4.4 22.8 1.0 CB A:ASP223 4.5 24.6 1.0 CA A:CYS221 4.5 21.3 1.0 N A:HIS202 4.6 21.1 1.0 CA A:CYS200 4.6 20.3 1.0 N A:ARG201 4.6 20.4 1.0 CA A:CYS195 4.7 18.5 1.0 CB A:SER226 4.7 19.2 1.0 OG A:SER226 4.7 18.8 1.0 CB A:SER197 4.7 20.0 1.0 C A:CYS224 4.8 22.2 1.0 C A:CYS200 4.8 20.5 1.0 N A:GLN225 4.9 22.3 1.0 C A:ASP223 4.9 23.1 1.0 N A:SER226 4.9 21.2 1.0

Zinc binding site 2 out of 2 in the Human SIRT2 in Complex with A Specific Inhibitor, NPD11033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT2 in Complex with A Specific Inhibitor, NPD11033 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:20.9 occ:1.00 SG B:CYS195 2.3 21.4 1.0 SG B:CYS200 2.3 20.1 1.0 SG B:CYS221 2.3 20.3 1.0 SG B:CYS224 2.4 20.6 1.0 CB B:CYS221 3.1 20.4 1.0 CB B:CYS200 3.2 20.3 1.0 CB B:CYS195 3.2 18.8 1.0 CB B:CYS224 3.5 21.0 1.0 N B:CYS224 3.9 21.9 1.0 CA B:CYS224 4.3 21.9 1.0 CB B:HIS202 4.4 22.9 1.0 CA B:CYS200 4.5 21.4 1.0 N B:HIS202 4.5 21.1 1.0 CB B:ASP223 4.6 24.6 1.0 N B:ARG201 4.6 20.7 1.0 CA B:CYS221 4.6 21.1 1.0 CA B:CYS195 4.6 18.1 1.0 CB B:SER226 4.7 20.2 1.0 OG B:SER226 4.7 20.0 1.0 CB B:SER197 4.7 20.5 1.0 C B:CYS200 4.8 21.6 1.0 C B:CYS224 4.8 21.9 1.0 N B:SER226 4.9 21.6 1.0 C B:ASP223 5.0 23.2 1.0 N B:GLN225 5.0 21.5 1.0

N.Kudo, A.Ito, M.Arata, A.Nakata, M.Yoshida. Identification of A Novel Small Molecule That Inhibits Deacetylase But Not Defatty-Acylase Reaction Catalysed By SIRT2. Philos. Trans. R. Soc. V. 373 2018LOND., B, Biol. Sci..
ISSN: ESSN 1471-2970
PubMed: 29685974
DOI: 10.1098/RSTB.2017.0070