Zinc in PDB 5y2f: Human SIRT6 in Complex with Allosteric Activator Mdl-801

The structure of Human SIRT6 in Complex with Allosteric Activator Mdl-801, PDB code: 5y2f was solved by J.Zhang, Z.Huang, K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.85 / 2.53
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	162.422, 162.422, 162.422, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.7

The structure of Human SIRT6 in Complex with Allosteric Activator Mdl-801 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Bromine	(Br)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Human SIRT6 in Complex with Allosteric Activator Mdl-801 (pdb code 5y2f). 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 Human SIRT6 in Complex with Allosteric Activator Mdl-801, PDB code: 5y2f:

Zinc binding site 1 out of 1 in the Human SIRT6 in Complex with Allosteric Activator Mdl-801


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 Allosteric Activator Mdl-801 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:63.1 occ:1.00 SG A:CYS142 2.3 62.2 1.0 SG A:CYS164 2.3 51.7 1.0 SG A:CYS175 2.3 83.9 1.0 SG A:CYS139 2.4 66.7 1.0 CB A:CYS164 3.2 54.6 1.0 CB A:CYS139 3.3 65.3 1.0 CB A:CYS175 3.3 87.6 1.0 CB A:CYS142 3.3 66.5 1.0 N A:CYS142 3.7 72.8 1.0 CA A:CYS142 4.1 71.3 1.0 CB A:LYS141 4.6 91.7 1.0 CA A:CYS164 4.6 56.5 1.0 N A:GLY177 4.7 74.0 1.0 CA A:CYS175 4.7 87.3 1.0 CA A:CYS139 4.7 59.6 1.0 C A:CYS142 4.8 68.2 1.0 C A:LYS141 4.8 71.0 1.0 CB A:THR144 4.9 57.9 1.0 CB A:VAL166 4.9 66.7 1.0 CA A:GLY177 4.9 71.8 1.0 OG1 A:THR144 4.9 54.6 1.0 CG2 A:VAL166 4.9 67.8 1.0 N A:LYS143 5.0 67.0 1.0

Z.Huang, J.Zhao, W.Deng, Y.Chen, J.Shang, K.Song, L.Zhang, C.Wang, S.Lu, X.Yang, B.He, J.Min, H.Hu, M.Tan, J.Xu, Q.Zhang, J.Zhong, X.Sun, Z.Mao, H.Lin, M.Xiao, Y.E.Chin, H.Jiang, Y.Xu, G.Chen, J.Zhang. Identification of A Cellularly Active SIRT6 Allosteric Activator. Nat. Chem. Biol. V. 14 1118 2018.
ISSN: ESSN 1552-4469
PubMed: 30374165
DOI: 10.1038/S41589-018-0150-0