Calcium in PDB 8c60: Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution:
3.5.1.98;

The structure of Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution 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 Full-Length Complex at 3.4 Angstrom Resolution (pdb code 8c60). 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 Full-Length Complex at 3.4 Angstrom Resolution, PDB code: 8c60:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


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 Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:107.2 occ:1.00 OD2 B:ASP175 2.4 55.2 1.0 O B:HIS179 2.4 42.4 1.0 O B:PHE199 2.4 45.7 1.0 O B:ASP177 2.6 45.7 1.0 OG B:SER198 2.9 43.6 1.0 C B:PHE199 3.1 32.2 1.0 CB B:HIS200 3.2 33.8 1.0 CG B:ASP175 3.3 55.2 1.0 C B:HIS179 3.5 39.0 1.0 N B:PHE199 3.6 30.8 1.0 CA B:HIS200 3.7 29.6 1.0 C B:ASP177 3.7 36.5 1.0 N B:HIS200 3.7 39.5 1.0 O B:ASP175 3.8 57.6 1.0 CA B:HIS180 3.9 45.2 1.0 ND1 B:HIS200 3.9 49.9 1.0 CG B:HIS200 4.0 34.4 1.0 CA B:PHE199 4.0 25.3 1.0 CB B:ASP175 4.0 48.3 1.0 OD1 B:ASP175 4.1 60.4 1.0 N B:HIS180 4.1 38.0 1.0 CB B:SER198 4.2 40.3 1.0 N B:ASP177 4.2 35.7 1.0 C B:ASP175 4.2 49.3 1.0 N B:GLY181 4.4 54.1 1.0 C B:SER198 4.4 42.5 1.0 CA B:ASP177 4.4 31.8 1.0 C B:ILE178 4.4 47.6 1.0 N B:HIS179 4.5 46.8 1.0 CA B:SER198 4.5 33.0 1.0 O B:ILE178 4.6 63.4 1.0 C B:HIS180 4.6 53.1 1.0 CA B:HIS179 4.6 46.3 1.0 C B:ILE176 4.6 29.3 1.0 CB B:ASP177 4.7 44.3 1.0 N B:ILE176 4.7 25.1 1.0 N B:ILE178 4.7 43.5 1.0 CA B:ASP175 4.8 44.8 1.0 CA B:ILE176 4.9 26.1 1.0 CA B:ILE178 4.9 43.9 1.0 CB B:PHE199 5.0 24.6 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of the Human SIN3B Full-Length Complex at 3.4 Angstrom Resolution


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 Full-Length Complex at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:93.9 occ:1.00 O B:PHE188 2.4 47.9 1.0 O B:VAL194 2.7 48.0 1.0 O B:TYR223 2.9 58.6 1.0 O B:THR191 3.2 34.1 1.0 C B:PHE188 3.6 46.5 1.0 C B:TYR223 3.8 44.5 1.0 C B:VAL194 3.8 29.0 1.0 CB B:TYR223 4.0 39.8 1.0 O B:TYR189 4.1 58.4 1.0 CB B:ALA224 4.3 44.1 1.0 C B:TYR189 4.3 50.5 1.0 CA B:MET195 4.3 47.1 1.0 CA B:TYR189 4.4 42.8 1.0 C B:THR191 4.4 32.5 1.0 CB B:PHE188 4.4 37.3 1.0 CG2 B:THR191 4.4 47.8 1.0 N B:TYR189 4.4 45.8 1.0 O B:GLY220 4.5 53.5 1.0 CA B:TYR223 4.5 39.6 1.0 N B:THR191 4.5 26.9 1.0 N B:MET195 4.6 41.2 1.0 N B:ALA224 4.6 35.0 1.0 CA B:PHE188 4.6 41.9 1.0 CG2 B:THR196 4.7 45.7 1.0 N B:THR196 4.7 35.4 1.0 CA B:ALA224 4.8 44.6 1.0 CB B:VAL194 4.8 29.0 1.0 CA B:VAL194 4.8 24.5 1.0 CG1 B:VAL194 4.8 42.5 1.0 CA B:THR191 5.0 33.2 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 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38276-0