Zinc in PDB 6qcd: Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin

The structure of Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin, PDB code: 6qcd was solved by W.You, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.68 / 1.84
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	91.366, 91.366, 143.925, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 20.2

The binding sites of Zinc atom in the Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin (pdb code 6qcd). 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 SIRT6 in Complex with Adp-Ribose and the Activator Quercetin, PDB code: 6qcd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:50.4 occ:1.00 SG A:CYS144 2.2 49.9 1.0 SG A:CYS141 2.2 47.8 1.0 SG A:CYS166 2.3 46.5 1.0 SG A:CYS177 2.4 53.6 1.0 CB A:CYS141 3.0 43.8 1.0 CB A:CYS166 3.0 43.8 1.0 CB A:CYS177 3.3 59.2 1.0 CB A:CYS144 3.3 53.8 1.0 N A:CYS144 3.7 51.5 1.0 CA A:CYS144 4.1 47.1 1.0 N A:GLY179 4.4 60.9 1.0 CA A:GLY179 4.4 56.0 1.0 CA A:CYS166 4.5 39.6 1.0 CA A:CYS141 4.5 43.9 1.0 CB A:LYS143 4.5 64.8 1.0 CG2 A:VAL168 4.5 52.4 1.0 CA A:CYS177 4.7 50.7 1.0 C A:LYS143 4.8 57.1 1.0 C A:CYS144 4.8 45.2 1.0 CB A:VAL168 4.9 53.0 1.0 CB A:THR146 4.9 48.3 1.0 N A:LYS145 4.9 50.6 1.0 OG1 A:THR146 4.9 49.7 1.0

Zinc binding site 2 out of 2 in the Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT6 in Complex with Adp-Ribose and the Activator Quercetin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:57.2 occ:1.00 SG B:CYS141 2.2 54.1 1.0 SG B:CYS144 2.2 53.5 1.0 SG B:CYS166 2.3 55.4 1.0 SG B:CYS177 2.4 56.6 1.0 CB B:CYS166 2.9 51.3 1.0 CB B:CYS141 3.0 48.2 1.0 CB B:CYS144 3.3 63.8 1.0 CB B:CYS177 3.4 62.4 1.0 N B:CYS144 3.5 66.8 1.0 CA B:CYS144 3.9 58.3 1.0 CB B:LYS143 4.4 77.3 1.0 CA B:CYS166 4.4 49.9 1.0 N B:GLY179 4.5 57.5 1.0 CA B:GLY179 4.5 57.0 1.0 CA B:CYS141 4.5 53.7 1.0 C B:LYS143 4.6 66.8 1.0 C B:CYS144 4.6 59.0 1.0 CG2 B:VAL168 4.7 60.8 1.0 N B:LYS145 4.7 60.8 1.0 CA B:CYS177 4.8 62.5 1.0 CB B:VAL168 4.8 63.3 1.0 CA B:LYS143 4.9 73.0 1.0

W.You, W.Zheng, S.Weiss, K.F.Chua, C.Steegborn. Structural Basis For the Activation and Inhibition of Sirtuin 6 By Quercetin and Its Derivatives. Sci Rep V. 9 19176 2019.
ISSN: ESSN 2045-2322
PubMed: 31844103
DOI: 10.1038/S41598-019-55654-1