Zinc in PDB 8iht: RPD3S Bound to the Nucleosome

All present enzymatic activity of RPD3S Bound to the Nucleosome:
3.5.1.98;

The structure of RPD3S Bound to the Nucleosome also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the RPD3S Bound to the Nucleosome (pdb code 8iht). 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 RPD3S Bound to the Nucleosome, PDB code: 8iht:

Zinc binding site 1 out of 1 in the RPD3S Bound to the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RPD3S Bound to the Nucleosome 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