Calcium in PDB 8bpa: Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom:
3.5.1.98;

The structure of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom (pdb code 8bpa). 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 Complex at 3.7 Angstrom, PDB code: 8bpa:
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 Complex at 3.7 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 Complex at 3.7 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:84.0 occ:1.00 O B:HIS179 2.1 77.4 1.0 OD1 B:ASP175 2.2 72.3 1.0 O B:ASP177 2.7 69.9 1.0 OG B:SER198 2.8 70.9 1.0 O B:PHE199 2.9 61.8 1.0 CG B:ASP175 3.0 72.3 1.0 C B:HIS179 3.3 77.4 1.0 CB B:HIS200 3.3 70.1 1.0 C B:PHE199 3.5 61.8 1.0 CA B:HIS180 3.7 78.3 1.0 C B:ASP177 3.7 69.9 1.0 OD2 B:ASP175 3.7 72.3 1.0 CB B:ASP175 3.9 72.3 1.0 N B:HIS180 3.9 78.3 1.0 N B:PHE199 3.9 61.8 1.0 CA B:HIS200 3.9 70.1 1.0 N B:ASP177 4.0 69.9 1.0 N B:HIS200 4.1 70.1 1.0 CB B:SER198 4.1 70.9 1.0 O B:ASP175 4.1 72.3 1.0 CG B:HIS200 4.2 70.1 1.0 ND1 B:HIS200 4.2 70.1 1.0 N B:GLY181 4.2 78.9 1.0 CA B:ASP177 4.3 69.9 1.0 C B:ASP175 4.4 72.3 1.0 C B:HIS180 4.4 78.3 1.0 N B:HIS179 4.4 77.4 1.0 CB B:ASP177 4.4 69.9 1.0 CA B:PHE199 4.4 61.8 1.0 C B:SER198 4.4 70.9 1.0 CA B:SER198 4.5 70.9 1.0 CA B:HIS179 4.5 77.4 1.0 C B:ILE178 4.5 74.7 1.0 O B:ILE178 4.7 74.7 1.0 CB B:HIS180 4.7 78.3 1.0 C B:ILE176 4.8 66.6 1.0 N B:ILE178 4.8 74.7 1.0 CA B:ASP175 4.8 72.3 1.0 N B:ILE176 4.9 66.6 1.0 ND1 B:HIS180 4.9 78.3 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 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 Complex at 3.7 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:92.6 occ:1.00 O B:VAL194 2.2 77.8 1.0 O B:PHE188 2.4 79.1 1.0 O B:THR191 3.2 74.4 1.0 C B:VAL194 3.3 77.8 1.0 O B:TYR223 3.4 78.7 1.0 C B:PHE188 3.6 79.1 1.0 CB B:PHE188 3.6 79.1 1.0 CG2 B:THR191 4.0 74.4 1.0 CG1 B:VAL194 4.0 77.8 1.0 CA B:VAL194 4.1 77.8 1.0 CB B:VAL194 4.1 77.8 1.0 N B:MET195 4.2 79.1 1.0 CA B:PHE188 4.2 79.1 1.0 C B:THR191 4.3 74.4 1.0 CA B:MET195 4.3 79.1 1.0 N B:VAL194 4.3 77.8 1.0 CG2 B:THR196 4.4 78.6 1.0 CB B:TYR223 4.5 78.7 1.0 C B:TYR223 4.5 78.7 1.0 N B:THR191 4.6 74.4 1.0 N B:TYR189 4.7 85.2 1.0 N B:THR196 4.8 78.6 1.0 C B:MET195 4.8 79.1 1.0 CA B:THR191 4.8 74.4 1.0 C B:TYR189 4.8 85.2 1.0 CA B:TYR189 4.9 85.2 1.0 CG B:PHE188 4.9 79.1 1.0 O B:TYR189 4.9 85.2 1.0 CB B:THR191 5.0 74.4 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