Zinc in PDB 6hoy: Human SIRT6 in Complex with Adp-Ribose and the Inhibitor Trichostatin A

The structure of Human SIRT6 in Complex with Adp-Ribose and the Inhibitor Trichostatin A, PDB code: 6hoy 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)	45.65 / 1.70
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	91.291, 91.291, 143.681, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 18.5

The binding sites of Zinc atom in the Human SIRT6 in Complex with Adp-Ribose and the Inhibitor Trichostatin A (pdb code 6hoy). 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 Inhibitor Trichostatin A, PDB code: 6hoy:
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 Inhibitor Trichostatin A


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 Inhibitor Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:48.0 occ:1.00 SG A:CYS144 1.9 47.0 1.0 SG A:CYS141 2.1 45.8 1.0 SG A:CYS166 2.2 43.7 1.0 SG A:CYS177 2.5 52.1 1.0 CB A:CYS166 3.0 40.8 1.0 CB A:CYS141 3.0 40.4 1.0 CB A:CYS144 3.3 48.8 1.0 CB A:CYS177 3.3 55.5 1.0 N A:CYS144 3.6 53.0 1.0 CA A:CYS144 4.0 46.5 1.0 CB A:LYS143 4.3 66.6 1.0 CA A:CYS166 4.4 37.3 1.0 N A:GLY179 4.5 51.2 1.0 CA A:CYS141 4.5 40.4 1.0 CA A:GLY179 4.6 50.5 1.0 CA A:CYS177 4.7 50.0 1.0 C A:LYS143 4.7 52.5 1.0 CB A:VAL168 4.8 51.6 1.0 C A:CYS144 4.8 48.9 1.0 CA A:LYS143 4.9 62.7 1.0 CG2 A:VAL168 4.9 48.2 1.0 CB A:THR146 4.9 44.8 1.0 OG1 A:THR146 5.0 50.8 1.0 C A:CYS177 5.0 53.2 1.0

Zinc binding site 2 out of 2 in the Human SIRT6 in Complex with Adp-Ribose and the Inhibitor Trichostatin A


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 Inhibitor Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:52.4 occ:1.00 SG B:CYS141 2.1 54.7 1.0 SG B:CYS144 2.1 50.9 1.0 SG B:CYS166 2.3 56.0 1.0 SG B:CYS177 2.5 62.2 1.0 CB B:CYS166 2.9 52.6 1.0 CB B:CYS141 3.0 49.9 1.0 CB B:CYS144 3.4 54.6 1.0 CB B:CYS177 3.4 61.0 1.0 N B:CYS144 3.6 55.1 1.0 CA B:CYS144 4.0 52.6 1.0 CB B:LYS143 4.2 75.9 1.0 CA B:CYS166 4.4 51.6 1.0 CA B:CYS141 4.4 49.6 1.0 N B:GLY179 4.4 52.7 1.0 CA B:GLY179 4.5 48.5 1.0 C B:LYS143 4.6 62.2 1.0 CA B:CYS177 4.8 56.9 1.0 CA B:LYS143 4.8 69.4 1.0 C B:CYS144 4.9 53.6 1.0 C B:CYS177 5.0 57.1 1.0 CB B:THR146 5.0 54.1 1.0 CB B:VAL168 5.0 64.0 1.0 OG1 B:THR146 5.0 65.9 1.0 N B:LYS143 5.0 68.2 1.0

W.You, C.Steegborn. Structural Basis of Sirtuin 6 Inhibition By the Hydroxamate Trichostatin A: Implications For Protein Deacylase Drug Development. J.Med.Chem. V. 61 10922 2018.
ISSN: ISSN 0022-2623
PubMed: 30395713
DOI: 10.1021/ACS.JMEDCHEM.8B01455