Zinc in PDB 8py3: Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor

The structure of Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor, PDB code: 8py3 was solved by F.Friedrich, A.Colcerasa, O.Einsle, M.Jung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.77 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.123, 73.43, 55.038, 90, 95.64, 90
R / Rfree (%)	16.6 / 18.5

The structure of Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor (pdb code 8py3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor, PDB code: 8py3:

Zinc binding site 1 out of 1 in the Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human SIRT2 in Complex with A 1,2,4-Oxadiazole Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.5 occ:1.00 SG A:CYS224 2.3 19.7 1.0 SG A:CYS200 2.3 24.1 1.0 SG A:CYS195 2.3 18.6 1.0 SG A:CYS221 2.3 21.4 1.0 CB A:CYS221 3.1 20.8 1.0 CB A:CYS200 3.1 19.7 1.0 CB A:CYS195 3.2 16.7 1.0 CB A:CYS224 3.5 20.6 1.0 N A:CYS224 3.9 23.6 1.0 CA A:CYS224 4.2 24.4 1.0 CB A:HIS202 4.5 22.4 1.0 CB A:ASP223 4.5 26.5 1.0 CA A:CYS200 4.5 23.6 1.0 CA A:CYS221 4.6 24.1 1.0 N A:ARG201 4.6 22.3 1.0 CA A:CYS195 4.6 18.1 1.0 N A:HIS202 4.6 22.3 1.0 C A:CYS224 4.8 23.4 1.0 CB A:SER197 4.8 20.6 1.0 CB A:SER226 4.8 19.2 1.0 C A:ASP223 4.8 26.2 1.0 C A:CYS200 4.8 26.4 1.0 N A:GLN225 4.9 20.2 1.0 N A:SER226 4.9 19.7 1.0 N A:ASP223 5.0 22.8 1.0

A.Colcerasa, F.Friedrich, J.Melesina, P.Moser, A.Vogelmann, P.Tzortzoglou, E.Neuwirt, M.Sum, D.Robaa, L.Zhang, E.Ramos-Morales, C.Romier, O.Einsle, E.Metzger, R.Schule, O.Gross, W.Sippl, M.Jung. Structure-Activity Studies of 1,2,4-Oxadiazoles For the Inhibition of the Nad + -Dependent Lysine Deacylase Sirtuin 2. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38847803
DOI: 10.1021/ACS.JMEDCHEM.4C00229