Zinc in PDB 5yqo: Crystal Structure of SIRT2 in Complex with Selective Inhibitor L5C

The structure of Crystal Structure of SIRT2 in Complex with Selective Inhibitor L5C, PDB code: 5yqo was solved by H.Wang, Y.Yu, G.Li, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.33 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.938, 73.918, 55.635, 90.00, 95.24, 90.00
R / Rfree (%)	16.9 / 19.3

The binding sites of Zinc atom in the Crystal Structure of SIRT2 in Complex with Selective Inhibitor L5C (pdb code 5yqo). 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 SIRT2 in Complex with Selective Inhibitor L5C, PDB code: 5yqo:

Zinc binding site 1 out of 1 in the Crystal Structure of SIRT2 in Complex with Selective Inhibitor L5C


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 SIRT2 in Complex with Selective Inhibitor L5C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:11.6 occ:1.00 SG A:CYS224 2.3 11.2 1.0 SG A:CYS200 2.3 12.7 1.0 SG A:CYS221 2.3 11.8 1.0 SG A:CYS195 2.3 10.2 1.0 HB3 A:CYS200 2.8 10.8 1.0 HB3 A:CYS221 3.0 12.3 1.0 CB A:CYS200 3.1 9.0 1.0 HB2 A:CYS195 3.1 9.2 1.0 CB A:CYS221 3.1 10.3 1.0 HB2 A:CYS221 3.1 12.3 1.0 CB A:CYS195 3.2 7.7 1.0 HB2 A:CYS200 3.3 10.8 1.0 HB3 A:CYS195 3.4 9.2 1.0 HB3 A:CYS224 3.4 15.7 1.0 H A:CYS224 3.4 15.3 1.0 CB A:CYS224 3.5 13.1 1.0 HB2 A:ASP223 3.6 20.7 1.0 HB2 A:SER226 3.8 15.8 1.0 H A:HIS202 3.8 14.4 1.0 N A:CYS224 3.9 12.8 1.0 HB2 A:HIS202 4.0 17.2 1.0 HB3 A:HIS202 4.0 17.2 1.0 HB3 A:SER197 4.0 19.2 1.0 H A:SER226 4.2 13.0 1.0 CA A:CYS224 4.2 13.1 1.0 HB2 A:CYS224 4.3 15.7 1.0 H A:ARG201 4.3 13.6 1.0 H A:ASP223 4.4 14.9 1.0 CB A:ASP223 4.4 17.2 1.0 CB A:HIS202 4.4 14.3 1.0 CA A:CYS200 4.5 10.3 1.0 O A:HOH828 4.6 21.2 1.0 CA A:CYS221 4.6 11.5 1.0 HH A:TYR204 4.6 20.7 1.0 H A:GLN225 4.6 14.8 1.0 HB3 A:ASP223 4.6 20.7 1.0 CA A:CYS195 4.6 7.7 1.0 N A:ARG201 4.6 11.3 1.0 N A:HIS202 4.7 12.0 1.0 HG A:SER226 4.7 17.7 1.0 H A:SER197 4.7 12.8 1.0 CB A:SER226 4.7 13.1 1.0 C A:ASP223 4.8 14.7 1.0 HB2 A:SER197 4.8 19.2 1.0 C A:CYS224 4.8 10.4 1.0 C A:CYS200 4.8 13.2 1.0 CB A:SER197 4.8 16.0 1.0 HA A:CYS195 4.8 9.2 1.0 HA A:CYS221 4.9 13.8 1.0 HA A:CYS200 4.9 12.4 1.0 N A:GLN225 4.9 12.3 1.0 N A:SER226 5.0 10.8 1.0 OG A:SER226 5.0 14.8 1.0 CA A:ASP223 5.0 15.2 1.0

L.L.Yang, H.L.Wang, L.Zhong, C.Yuan, S.Y.Liu, Z.J.Yu, S.Liu, Y.H.Yan, C.Wu, Y.Wang, Z.Wang, Y.Yu, Q.Chen, G.B.Li. X-Ray Crystal Structure Guided Discovery of New Selective, Substrate-Mimicking Sirtuin 2 Inhibitors That Exhibit Activities Against Non-Small Cell Lung Cancer Cells. Eur J Med Chem V. 155 806 2018.
ISSN: ISSN 1768-3254
PubMed: 29957526
DOI: 10.1016/J.EJMECH.2018.06.041