Zinc in PDB 8ga8: Structure of the Yeast (Hdac) RPD3L Complex

All present enzymatic activity of Structure of the Yeast (Hdac) RPD3L Complex:
3.5.1.98;

The binding sites of Zinc atom in the Structure of the Yeast (Hdac) RPD3L Complex (pdb code 8ga8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Yeast (Hdac) RPD3L Complex, PDB code: 8ga8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Yeast (Hdac) RPD3L Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Yeast (Hdac) RPD3L Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:51.3 occ:1.00 OD1 B:ASP186 2.0 40.1 1.0 OD2 B:ASP274 2.0 37.0 1.0 OD2 B:ASP186 2.1 40.1 1.0 ND1 B:HIS188 2.3 35.5 1.0 CG B:ASP186 2.3 40.1 1.0 CG B:ASP274 3.0 37.0 1.0 CE1 B:HIS188 3.1 35.5 1.0 CG B:HIS188 3.4 35.5 1.0 OD1 B:ASP274 3.5 37.0 1.0 CB B:ASP186 3.8 40.1 1.0 CB B:HIS188 3.9 35.5 1.0 N B:HIS188 4.1 35.5 1.0 CB B:ASP274 4.2 37.0 1.0 NE2 B:HIS188 4.3 35.5 1.0 CA B:GLY311 4.3 38.0 1.0 OH B:TYR313 4.3 41.5 1.0 NE2 B:HIS151 4.4 34.9 1.0 CD2 B:HIS188 4.5 35.5 1.0 N B:VAL187 4.5 36.8 1.0 CE1 B:TYR313 4.5 41.5 1.0 CA B:HIS188 4.6 35.5 1.0 CA B:ASP186 4.7 40.1 1.0 CZ B:TYR313 4.7 41.5 1.0 CE1 B:HIS150 4.8 36.2 1.0 C B:ASP186 4.9 40.1 1.0 N B:GLY312 4.9 42.1 1.0 N B:GLY311 5.0 38.0 1.0

Zinc binding site 2 out of 2 in the Structure of the Yeast (Hdac) RPD3L Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Yeast (Hdac) RPD3L Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:44.9 occ:1.00 OD1 E:ASP186 2.0 36.8 1.0 OD2 E:ASP274 2.0 32.4 1.0 OD2 E:ASP186 2.2 36.8 1.0 ND1 E:HIS188 2.3 37.9 1.0 CG E:ASP186 2.4 36.8 1.0 CE1 E:HIS188 2.9 37.9 1.0 CG E:ASP274 3.0 32.4 1.0 OD1 E:ASP274 3.4 32.4 1.0 CG E:HIS188 3.5 37.9 1.0 CB E:ASP186 3.9 36.8 1.0 CB E:HIS188 4.1 37.9 1.0 CG1 E:VAL187 4.1 39.1 1.0 OH E:TYR313 4.1 36.1 1.0 NE2 E:HIS188 4.2 37.9 1.0 N E:HIS188 4.2 37.9 1.0 CE1 E:HIS151 4.4 45.7 1.0 CB E:ASP274 4.4 32.4 1.0 CA E:GLY311 4.4 31.6 1.0 N E:VAL187 4.4 39.1 1.0 CD2 E:HIS188 4.5 37.9 1.0 CE2 E:TYR313 4.6 36.1 1.0 CA E:ASP186 4.7 36.8 1.0 CE1 E:HIS150 4.8 45.2 1.0 CA E:HIS188 4.8 37.9 1.0 CZ E:TYR313 4.9 36.1 1.0 C E:ASP186 4.9 36.8 1.0

A.B.Patel, J.Qing, K.H.Tam, S.Zaman, M.Luiso, I.Radhakrishnan, Y.He. Cryo-Em Structure of the Saccharomyces Cerevisiae RPD3L Histone Deacetylase Complex. Nat Commun V. 14 3061 2023.
ISSN: ESSN 2041-1723
PubMed: 37244892
DOI: 10.1038/S41467-023-38687-Z