Potassium in PDB 8w9d: Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1

The structure of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1 also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Potassium atom in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1 (pdb code 8w9d). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1, PDB code: 8w9d:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K1001 b:30.0 occ:1.00 OD2 B:ASP184 1.9 23.3 1.0 O B:HIS188 2.3 29.6 1.0 O B:PHE208 2.9 19.9 1.0 O B:ASP186 3.0 28.4 1.0 CG B:ASP184 3.1 23.3 1.0 O B:ASP184 3.2 23.3 1.0 C B:HIS188 3.6 29.6 1.0 C B:PHE208 3.6 19.9 1.0 C B:ASP186 3.7 28.4 1.0 N B:ASP186 3.7 28.4 1.0 CB B:HIS209 3.8 21.9 1.0 C B:ASP184 3.8 23.3 1.0 N B:PHE208 3.9 19.9 1.0 OD1 B:ASP184 3.9 23.3 1.0 CB B:SER207 4.0 22.4 1.0 CA B:ASP186 4.0 28.4 1.0 CB B:ASP186 4.0 28.4 1.0 OG B:SER207 4.0 22.4 1.0 CA B:HIS209 4.1 21.9 1.0 CB B:ASP184 4.1 23.3 1.0 N B:HIS209 4.2 21.9 1.0 CA B:HIS189 4.3 25.4 1.0 N B:HIS188 4.3 29.6 1.0 C B:ILE185 4.3 24.4 1.0 N B:HIS189 4.4 25.4 1.0 C B:SER207 4.4 22.4 1.0 CA B:PHE208 4.4 19.9 1.0 N B:ILE185 4.4 24.4 1.0 CA B:SER207 4.4 22.4 1.0 CA B:ILE185 4.5 24.4 1.0 N B:GLY190 4.6 30.3 1.0 CA B:HIS188 4.6 29.6 1.0 CA B:ASP184 4.6 23.3 1.0 N B:VAL187 4.7 27.5 1.0 C B:VAL187 4.7 27.5 1.0 ND1 B:HIS209 4.7 21.9 1.0 CG B:HIS209 4.7 21.9 1.0 C B:HIS189 4.8 25.4 1.0

Potassium binding site 2 out of 2 in the Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cryo-Em Structure of the RPD3S-Nucleosome Complex From Budding Yeast in State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K1002 b:30.0 occ:1.00 O B:PHE197 2.5 24.6 1.0 O B:VAL203 2.7 23.5 1.0 O B:TYR232 3.0 25.8 1.0 O B:THR200 3.0 20.6 1.0 C B:PHE197 3.8 24.6 1.0 C B:VAL203 3.9 23.5 1.0 CB B:TYR232 3.9 25.8 1.0 C B:TYR232 3.9 25.8 1.0 C B:THR200 4.2 20.6 1.0 CG2 B:THR200 4.3 20.6 1.0 CB B:PHE197 4.4 24.6 1.0 CA B:MET204 4.5 29.2 1.0 N B:THR200 4.5 20.6 1.0 CA B:TYR198 4.5 25.8 1.0 C B:TYR198 4.5 25.8 1.0 CA B:TYR232 4.6 25.8 1.0 O B:GLY229 4.6 25.0 1.0 N B:TYR198 4.6 25.8 1.0 O B:TYR198 4.6 25.8 1.0 N B:MET204 4.6 29.2 1.0 N B:THR205 4.6 46.5 1.0 CA B:PHE197 4.7 24.6 1.0 CG2 B:THR205 4.8 46.5 1.0 CA B:THR200 4.9 20.6 1.0 CB B:ALA233 4.9 23.6 1.0 N B:ALA233 4.9 23.6 1.0 CA B:VAL203 4.9 23.5 1.0

C.Wang, C.Chu, Z.Guo, X.Zhan. Structures and Dynamics of RPD3S Complex Bound to Nucleosome. Sci Adv V. 10 K7678 2024.
ISSN: ESSN 2375-2548
PubMed: 38598631
DOI: 10.1126/SCIADV.ADK7678