Zinc in PDB 8hpo: Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast

All present enzymatic activity of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast:
3.5.1.98;

The structure of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast (pdb code 8hpo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast, PDB code: 8hpo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:38.7 occ:1.00 OD1 F:ASP186 1.8 19.2 1.0 OD2 F:ASP274 2.0 20.1 1.0 ND1 F:HIS188 2.4 19.0 1.0 CG F:ASP186 2.9 19.2 1.0 CG F:ASP274 3.0 20.1 1.0 CE1 F:HIS188 3.2 19.0 1.0 CG F:HIS188 3.2 19.0 1.0 OD1 F:ASP274 3.4 20.1 1.0 OD2 F:ASP186 3.5 19.2 1.0 CB F:HIS188 3.6 19.0 1.0 N F:HIS188 3.8 19.0 1.0 CB F:ASP186 4.0 19.2 1.0 NE2 F:HIS151 4.1 20.4 1.0 NE2 F:HIS188 4.2 19.0 1.0 CB F:ASP274 4.3 20.1 1.0 CD2 F:HIS188 4.3 19.0 1.0 CA F:HIS188 4.3 19.0 1.0 N F:VAL187 4.3 18.1 1.0 NE2 F:HIS150 4.4 18.9 1.0 CG1 F:VAL187 4.5 18.1 1.0 OH F:TYR313 4.5 18.5 1.0 CE2 F:TYR313 4.7 18.5 1.0 CA F:GLY311 4.8 18.7 1.0 C F:VAL187 4.8 18.1 1.0 CD2 F:HIS151 4.9 20.4 1.0 CE1 F:HIS150 4.9 18.9 1.0 CA F:ASP186 5.0 19.2 1.0 CA F:VAL187 5.0 18.1 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of A SIN3/Hdac Complex From Budding Yeast within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn501 b:45.3 occ:1.00 OD1 G:ASP186 2.0 32.5 1.0 OD2 G:ASP274 2.1 29.1 1.0 ND1 G:HIS188 2.3 31.8 1.0 CG G:ASP186 3.0 32.5 1.0 CG G:ASP274 3.1 29.1 1.0 CE1 G:HIS188 3.2 31.8 1.0 CG G:HIS188 3.3 31.8 1.0 OD2 G:ASP186 3.4 32.5 1.0 OD1 G:ASP274 3.6 29.1 1.0 CB G:HIS188 3.7 31.8 1.0 OH G:TYR313 4.0 34.0 1.0 N G:HIS188 4.1 31.8 1.0 CG1 G:VAL187 4.3 31.3 1.0 NE2 G:HIS188 4.3 31.8 1.0 CB G:ASP186 4.3 32.5 1.0 CB G:ASP274 4.3 29.1 1.0 CD2 G:HIS188 4.4 31.8 1.0 CE2 G:TYR313 4.5 34.0 1.0 CA G:GLY311 4.5 27.1 1.0 CA G:HIS188 4.5 31.8 1.0 NE2 G:HIS150 4.6 39.4 1.0 NE2 G:HIS151 4.7 42.4 1.0 N G:VAL187 4.7 31.3 1.0 CZ G:TYR313 4.7 34.0 1.0

Z.Guo, C.Chu, Y.Lu, X.Zhang, Y.Xiao, M.Wu, S.Gao, C.C.L.Wong, X.Zhan, C.Wang. Structure of A SIN3-Hdac Complex From Budding Yeast. Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
PubMed: 37081318
DOI: 10.1038/S41594-023-00975-Z