Calcium in PDB 8bpb: Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom:
3.5.1.98;

The structure of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom (pdb code 8bpb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom, PDB code: 8bpb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:0.0 occ:1.00 OD1 B:ASP175 2.3 19.6 1.0 O B:ASP177 2.4 24.1 1.0 O B:HIS179 2.5 20.1 1.0 O B:PHE199 2.6 26.0 1.0 OG B:SER198 3.1 12.5 1.0 CG B:ASP175 3.3 17.4 1.0 O B:ASP175 3.4 26.4 1.0 C B:PHE199 3.5 10.5 1.0 C B:ASP177 3.5 6.2 1.0 C B:HIS179 3.6 8.0 1.0 N B:PHE199 3.7 5.3 1.0 N B:ASP177 3.8 9.0 1.0 C B:ASP175 3.8 13.8 1.0 CB B:HIS200 3.8 8.7 1.0 CB B:ASP175 3.9 0.0 1.0 CA B:ASP177 4.1 6.5 1.0 CA B:HIS180 4.2 0.0 1.0 CA B:PHE199 4.2 0.0 1.0 CA B:HIS200 4.3 1.2 1.0 C B:ILE176 4.3 10.1 1.0 N B:HIS200 4.3 9.5 1.0 CB B:SER198 4.3 4.3 1.0 N B:ILE176 4.3 8.6 1.0 N B:HIS180 4.3 12.7 1.0 CB B:ASP177 4.4 10.1 1.0 OD2 B:ASP175 4.4 26.1 1.0 C B:SER198 4.4 8.3 1.0 CA B:SER198 4.4 13.3 1.0 CA B:ILE176 4.4 9.1 1.0 N B:HIS179 4.5 4.7 1.0 C B:ILE178 4.5 1.8 1.0 CA B:ASP175 4.5 0.0 1.0 N B:GLY181 4.5 8.3 1.0 ND1 B:HIS200 4.6 0.2 1.0 N B:ILE178 4.6 2.2 1.0 CG B:HIS200 4.7 1.4 1.0 CA B:HIS179 4.7 0.0 1.0 O B:ILE178 4.7 8.8 1.0 C B:HIS180 4.8 9.9 1.0 CA B:ILE178 4.9 8.8 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:20.8 occ:1.00 O B:VAL194 2.3 4.5 1.0 O B:PHE188 2.8 20.8 1.0 O B:TYR223 2.8 21.4 1.0 O B:THR191 3.0 23.0 1.0 C B:VAL194 3.5 7.9 1.0 CB B:TYR223 3.6 6.9 1.0 C B:TYR223 3.7 9.6 1.0 C B:PHE188 4.0 10.1 1.0 CA B:MET195 4.1 8.8 1.0 C B:THR191 4.2 8.2 1.0 N B:MET195 4.3 3.9 1.0 CA B:TYR223 4.3 9.4 1.0 CB B:PHE188 4.5 8.0 1.0 CG2 B:THR191 4.5 21.5 1.0 O B:TYR189 4.6 24.4 1.0 O B:GLY220 4.6 24.9 1.0 CA B:VAL194 4.6 9.3 1.0 N B:THR191 4.6 7.5 1.0 C B:TYR189 4.7 15.3 1.0 CB B:ALA224 4.7 8.2 1.0 N B:ALA224 4.7 2.1 1.0 N B:THR196 4.7 0.0 1.0 CA B:TYR189 4.8 6.6 1.0 CG2 B:THR196 4.8 11.5 1.0 CG B:TYR223 4.8 16.2 1.0 N B:VAL194 4.8 14.4 1.0 CB B:VAL194 4.9 9.1 1.0 N B:TYR189 4.9 18.1 1.0 CA B:PHE188 4.9 3.9 1.0 C B:MET195 4.9 4.5 1.0 CA B:THR191 4.9 0.1 1.0

M.S.M.Wan, R.Muhammad, M.G.Koliopoulos, T.I.Roumeliotis, J.S.Choudhary, C.Alfieri. Mechanism of Assembly, Activation and Lysine Selection By the SIN3B Histone Deacetylase Complex Nat Commun V. 14 2556 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38276-0