Zinc in PDB 6qch: Human SIRT6 in Complex with Adp-Ribose and the Activator Cyanidin

The structure of Human SIRT6 in Complex with Adp-Ribose and the Activator Cyanidin, PDB code: 6qch 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)	45.69 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	91.387, 91.387, 143.806, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20

The binding sites of Zinc atom in the Human SIRT6 in Complex with Adp-Ribose and the Activator Cyanidin (pdb code 6qch). 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 Cyanidin, PDB code: 6qch:
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 Cyanidin


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 Cyanidin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:70.6 occ:1.00 SG A:CYS144 1.9 73.8 1.0 SG A:CYS166 2.2 63.7 1.0 SG A:CYS141 2.2 68.4 1.0 SG A:CYS177 2.5 78.9 1.0 CB A:CYS166 2.8 58.8 1.0 CB A:CYS141 3.0 68.3 1.0 CB A:CYS144 3.5 78.5 1.0 N A:CYS144 3.7 77.6 1.0 CB A:CYS177 3.8 74.1 1.0 CA A:CYS144 4.2 72.5 1.0 N A:GLY179 4.2 65.6 1.0 CA A:CYS166 4.2 62.9 1.0 CA A:GLY179 4.3 69.6 1.0 CA A:CYS141 4.5 70.7 1.0 CB A:LYS143 4.5 67.3 1.0 CG2 A:VAL168 4.7 76.2 1.0 C A:LYS143 4.8 80.0 1.0 CB A:VAL168 4.9 75.7 1.0 CB A:THR146 4.9 68.0 1.0 C A:CYS166 4.9 70.3 1.0 N A:ARG178 5.0 82.6 1.0 C A:CYS177 5.0 76.7 1.0 C A:CYS144 5.0 68.7 1.0

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


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 Cyanidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:84.8 occ:1.00 SG B:CYS144 2.1 77.0 1.0 SG B:CYS141 2.2 74.9 1.0 SG B:CYS166 2.6 75.7 1.0 SG B:CYS177 2.6 95.1 1.0 CB B:CYS141 3.0 81.0 1.0 CB B:CYS166 3.1 72.4 1.0 CB B:CYS144 3.3 85.7 1.0 N B:CYS144 3.5 89.8 1.0 CA B:CYS144 3.9 73.7 1.0 CB B:CYS177 3.9 84.9 1.0 CA B:CYS141 4.4 84.4 1.0 CG2 B:VAL168 4.5 76.4 1.0 CA B:GLY179 4.5 92.4 1.0 CB B:LYS143 4.5 85.6 1.0 N B:GLY179 4.5 88.0 1.0 CA B:CYS166 4.6 66.7 1.0 C B:CYS144 4.6 75.1 1.0 C B:LYS143 4.6 83.8 1.0 N B:LYS145 4.6 81.1 1.0 N B:LYS143 4.8 93.2 1.0 CB B:VAL168 4.8 86.6 1.0 CB B:THR146 4.9 78.8 1.0 CA B:LYS143 4.9 87.9 1.0 OG1 B:THR146 4.9 66.0 1.0 C B:CYS141 4.9 82.8 1.0 O B:GLY179 5.0 97.9 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