Zinc in PDB 5mgn: Human SIRT6 in Complex with Activator UBCS38

The structure of Human SIRT6 in Complex with Activator UBCS38, PDB code: 5mgn was solved by C.Steegborn, W.You, C.Kambach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 2.07
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	91.868, 91.868, 145.353, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 19.2

The structure of Human SIRT6 in Complex with Activator UBCS38 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Human SIRT6 in Complex with Activator UBCS38 (pdb code 5mgn). 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 Activator UBCS38, PDB code: 5mgn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT6 in Complex with Activator UBCS38


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 Activator UBCS38 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:43.1 occ:1.00 SG A:CYS144 2.2 39.9 1.0 SG A:CYS141 2.2 38.2 1.0 SG A:CYS166 2.3 39.6 1.0 SG A:CYS177 2.3 47.5 1.0 CB A:CYS141 3.1 43.5 1.0 CB A:CYS166 3.2 33.3 1.0 CB A:CYS144 3.3 43.1 1.0 CB A:CYS177 3.6 53.0 1.0 N A:CYS144 3.7 51.5 1.0 CA A:CYS144 4.0 42.1 1.0 N A:GLY179 4.6 44.4 1.0 CA A:CYS166 4.6 36.6 1.0 CA A:CYS141 4.6 41.9 1.0 CA A:GLY179 4.7 44.6 1.0 C A:LYS143 4.8 55.4 1.0 C A:CYS144 4.8 43.7 1.0 CB A:LYS143 4.8 57.0 1.0 CG2 A:VAL168 4.8 43.7 1.0 CB A:VAL168 4.9 48.2 1.0 OG1 A:THR146 5.0 43.1 1.0 CA A:CYS177 5.0 51.4 1.0

Zinc binding site 2 out of 2 in the Human SIRT6 in Complex with Activator UBCS38


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 Activator UBCS38 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:55.2 occ:1.00 SG B:CYS141 2.3 53.1 1.0 SG B:CYS144 2.3 53.8 1.0 SG B:CYS166 2.4 59.3 1.0 SG B:CYS177 2.4 57.3 1.0 CB B:CYS141 3.1 55.4 1.0 CB B:CYS144 3.2 59.8 1.0 CB B:CYS166 3.3 45.8 1.0 N B:CYS144 3.4 58.2 1.0 CB B:CYS177 3.6 54.0 1.0 CA B:CYS144 3.8 56.8 1.0 CB B:LYS143 4.4 51.8 1.0 CA B:CYS141 4.5 57.5 1.0 C B:LYS143 4.5 52.7 1.0 C B:CYS144 4.6 62.2 1.0 OG1 B:THR146 4.7 47.6 1.0 N B:LYS145 4.7 63.5 1.0 CA B:CYS166 4.7 46.2 1.0 CB B:THR146 4.7 45.5 1.0 N B:GLY179 4.8 52.9 1.0 CB B:VAL168 4.8 49.1 1.0 CA B:LYS143 4.9 55.1 1.0 CG2 B:VAL168 4.9 45.7 1.0 N B:LYS143 4.9 61.5 1.0 CA B:CYS177 5.0 54.9 1.0

W.You, D.Rotili, T.M.Li, C.Kambach, M.Meleshin, M.Schutkowski, K.F.Chua, A.Mai, C.Steegborn. Structural Basis of Sirtuin 6 Activation By Synthetic Small Molecules. Angew. Chem. Int. Ed. Engl. V. 56 1007 2017.
ISSN: ESSN 1521-3773
PubMed: 27990725
DOI: 10.1002/ANIE.201610082