Zinc in PDB 8hn9: Human SIRT3 Recognizing CCNE2K348LA Peptide

The structure of Human SIRT3 Recognizing CCNE2K348LA Peptide, PDB code: 8hn9 was solved by Y.Wang, W.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.23 / 3.70
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	235.676, 235.676, 235.676, 90, 90, 90
R / Rfree (%)	19.7 / 21.8

The binding sites of Zinc atom in the Human SIRT3 Recognizing CCNE2K348LA Peptide (pdb code 8hn9). 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 SIRT3 Recognizing CCNE2K348LA Peptide, PDB code: 8hn9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT3 Recognizing CCNE2K348LA Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT3 Recognizing CCNE2K348LA Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:32.8 occ:1.00 CB A:CYS280 2.3 30.5 1.0 CB A:CYS259 2.4 32.8 1.0 SG A:CYS280 2.5 30.5 1.0 CB A:CYS283 2.5 32.8 1.0 SG A:CYS283 2.5 32.8 1.0 N A:CYS259 3.1 63.1 1.0 CA A:CYS259 3.2 64.1 1.0 CB A:CYS256 3.3 32.8 1.0 SG A:CYS259 3.4 32.8 1.0 SG A:CYS256 3.6 32.8 1.0 CA A:CYS283 3.6 38.8 1.0 CA A:CYS280 3.8 37.8 1.0 N A:GLY285 3.8 37.0 1.0 N A:CYS283 3.8 42.6 1.0 C A:CYS283 4.1 37.0 1.0 N A:THR284 4.1 37.5 1.0 C A:VAL258 4.3 60.9 1.0 O A:GLY285 4.3 43.3 1.0 CA A:GLY285 4.3 36.5 1.0 N A:CYS280 4.4 39.6 1.0 C A:CYS280 4.4 42.9 1.0 C A:CYS259 4.5 54.2 1.0 CB A:VAL258 4.6 40.0 1.0 C A:GLY285 4.7 37.8 1.0 CA A:CYS256 4.7 42.7 1.0 O A:CYS280 4.7 38.6 1.0 CA A:VAL258 4.8 54.8 1.0 N A:VAL258 4.8 56.0 1.0 C A:THR284 4.9 44.7 1.0 O A:CYS283 5.0 37.6 1.0 N A:GLN260 5.0 52.6 1.0

Zinc binding site 2 out of 2 in the Human SIRT3 Recognizing CCNE2K348LA Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT3 Recognizing CCNE2K348LA Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:32.8 occ:1.00 CB B:CYS283 2.5 60.5 1.0 CB B:CYS280 2.6 30.5 1.0 SG B:CYS280 2.8 30.5 1.0 CB B:CYS256 2.9 32.8 1.0 SG B:CYS283 3.3 96.6 1.0 CA B:CYS283 3.6 43.7 1.0 CA B:CYS280 3.6 52.8 1.0 O B:GLY285 3.7 55.1 1.0 N B:CYS280 3.7 51.6 1.0 N B:GLY285 3.8 41.7 1.0 N B:CYS283 3.9 44.4 1.0 SG B:CYS256 3.9 32.8 1.0 N B:THR284 4.0 53.9 1.0 C B:CYS283 4.1 52.0 1.0 CA B:CYS256 4.1 52.1 1.0 C B:CYS280 4.2 58.5 1.0 CA B:GLY285 4.2 40.8 1.0 C B:GLY285 4.3 46.5 1.0 O B:CYS280 4.4 48.8 1.0 CG2 B:VAL287 4.6 46.2 1.0 SG B:CYS259 4.8 32.8 1.0 C B:THR284 4.8 51.4 1.0 CA B:THR284 4.9 52.7 1.0 CB B:CYS259 4.9 32.8 1.0 N B:PRO281 4.9 62.5 1.0 C B:CYS256 4.9 45.1 1.0 N B:CYS259 5.0 61.5 1.0 O B:CYS283 5.0 44.3 1.0 CE2 B:PHE263 5.0 64.2 1.0

J.Jin, L.Bai, D.Wang, W.Ding, Z.Cao, P.Yan, Y.Li, L.Xi, Y.Wang, X.Zheng, H.Wei, C.Ding, Y.Wang. SIRT3-Dependent Delactylation of Cyclin E2 Prevents Hepatocellular Carcinoma Growth. Embo Rep. 56052 2023.
ISSN: ESSN 1469-3178
PubMed: 36896611
DOI: 10.15252/EMBR.202256052