Zinc in PDB 8ihn: Cryo-Em Structure of the RPD3S Core Complex

All present enzymatic activity of Cryo-Em Structure of the RPD3S Core Complex:
3.5.1.98;

The structure of Cryo-Em Structure of the RPD3S Core Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of the RPD3S Core Complex (pdb code 8ihn). 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 Cryo-Em Structure of the RPD3S Core Complex, PDB code: 8ihn:

Zinc binding site 1 out of 1 in the Cryo-Em Structure of the RPD3S Core Complex


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 the RPD3S Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn501 b:78.8 occ:1.00 OD2 L:ASP186 2.0 61.4 1.0 OD2 L:ASP274 2.0 63.9 1.0 OD1 L:ASP186 2.2 61.4 1.0 ND1 L:HIS188 2.3 58.1 1.0 CG L:ASP186 2.4 61.4 1.0 CG L:ASP274 3.1 63.9 1.0 CE1 L:HIS188 3.2 58.1 1.0 CG L:HIS188 3.3 58.1 1.0 CB L:HIS188 3.7 58.1 1.0 CB L:ASP274 3.7 63.9 1.0 CB L:ASP186 3.9 61.4 1.0 N L:HIS188 4.0 58.1 1.0 OH L:TYR313 4.0 62.5 1.0 NE2 L:HIS151 4.2 55.7 1.0 OD1 L:ASP274 4.2 63.9 1.0 NE2 L:HIS150 4.2 55.8 1.0 NE2 L:HIS188 4.3 58.1 1.0 CD2 L:HIS188 4.4 58.1 1.0 CE1 L:HIS150 4.4 55.8 1.0 CA L:HIS188 4.5 58.1 1.0 N L:VAL187 4.5 59.2 1.0 CZ L:TYR313 4.5 62.5 1.0 CG1 L:VAL187 4.5 59.2 1.0 CE2 L:TYR313 4.6 62.5 1.0 CD2 L:HIS151 4.8 55.7 1.0 CA L:ASP186 4.8 61.4 1.0 C L:ASP186 4.8 61.4 1.0 CA L:GLY311 5.0 60.5 1.0

Y.Zhang, M.Xu, P.Wang, J.Zhou, G.Wang, S.Han, G.Cai, X.Wang. Structural Basis For Nucleosome Binding and Catalysis By the Yeast RPD3S/Hdac Holoenzyme. Cell Res. V. 33 971 2023.
ISSN: ISSN 1001-0602
PubMed: 37845487
DOI: 10.1038/S41422-023-00884-2