Zinc 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:

Calcium

(Ca)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex at 2.8 Angstrom, PDB code: 8bpb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 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 Zinc with other atoms in the Zn 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:Zn501 b:46.9 occ:1.00 O B:ACT504 1.9 22.2 1.0 OD2 B:ASP265 1.9 12.5 1.0 OD1 B:ASP177 1.9 20.0 1.0 ND1 B:HIS179 2.3 16.1 1.0 C B:ACT504 2.5 20.4 1.0 OXT B:ACT504 2.7 9.4 1.0 CG B:ASP177 2.7 9.0 1.0 OD2 B:ASP177 2.8 10.1 1.0 CG B:ASP265 3.0 6.0 1.0 CG B:HIS179 3.2 8.9 1.0 CE1 B:HIS179 3.3 10.7 1.0 OD1 B:ASP265 3.4 16.6 1.0 CB B:HIS179 3.5 1.0 1.0 N B:HIS179 3.7 4.7 1.0 CG2 B:ILE178 4.0 9.1 1.0 CH3 B:ACT504 4.0 19.9 1.0 CB B:ASP177 4.2 10.1 1.0 CB B:ASP265 4.2 0.7 1.0 CA B:HIS179 4.2 0.0 1.0 N B:ILE178 4.3 2.2 1.0 NE2 B:HIS179 4.4 14.8 1.0 CD2 B:HIS179 4.4 13.4 1.0 CA B:GLY302 4.4 1.8 1.0 C B:ILE178 4.7 1.8 1.0 OH B:TYR304 4.7 9.1 1.0 NE2 B:HIS141 4.7 9.0 1.0 NE2 B:HIS142 4.7 2.6 1.0 C B:ASP177 4.8 6.2 1.0 OE2 A:GLU436 4.8 20.2 1.0 CE2 B:TYR304 4.8 11.3 1.0 CA B:ILE178 4.9 8.8 1.0 N B:GLY302 4.9 9.1 1.0 CA B:ASP177 4.9 6.5 1.0 CB B:ILE178 5.0 7.6 1.0

Zinc binding site 2 out of 3 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 Zinc with other atoms in the Zn 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 C:Zn1101 b:72.6 occ:1.00 NE2 C:HIS318 2.1 61.7 1.0 SG C:CYS292 2.3 45.1 1.0 SG C:CYS315 2.3 59.6 1.0 SG C:CYS289 2.3 57.2 1.0 CD2 C:HIS318 2.6 55.5 1.0 CB C:CYS315 3.1 47.7 1.0 CE1 C:HIS318 3.1 57.0 1.0 CB C:CYS289 3.3 53.5 1.0 CB C:CYS292 3.6 48.0 1.0 CG C:HIS318 3.8 50.9 1.0 N C:CYS292 3.9 48.8 1.0 ND1 C:HIS318 3.9 55.1 1.0 N C:CYS315 4.0 48.7 1.0 CA C:CYS315 4.1 45.1 1.0 CA C:CYS292 4.3 49.3 1.0 O C:CYS292 4.4 55.6 1.0 O C:CYS315 4.6 51.2 1.0 C C:CYS315 4.6 45.0 1.0 C C:CYS292 4.7 53.1 1.0 CA C:CYS289 4.7 52.6 1.0 CB C:TYR291 4.8 50.0 1.0 CB C:LEU294 4.8 37.7 1.0 C C:TYR291 4.9 55.2 1.0 CD1 C:LEU294 5.0 43.0 1.0

Zinc binding site 3 out of 3 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 Zinc with other atoms in the Zn binding site number 3 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 C:Zn1102 b:80.6 occ:1.00 ND1 C:HIS297 2.1 38.4 1.0 SG C:CYS300 2.3 41.2 1.0 SG C:CYS277 2.3 48.4 1.0 SG C:CYS274 2.3 38.2 1.0 CB C:CYS274 2.8 36.1 1.0 CG C:HIS297 2.9 32.1 1.0 CE1 C:HIS297 3.1 33.0 1.0 CB C:HIS297 3.1 31.2 1.0 CB C:CYS300 3.3 28.4 1.0 CB C:CYS277 3.4 42.1 1.0 N C:CYS277 3.9 43.2 1.0 CD2 C:HIS297 4.0 28.2 1.0 NE2 C:HIS297 4.1 28.1 1.0 N C:HIS297 4.1 31.6 1.0 CA C:CYS277 4.3 44.4 1.0 CA C:HIS297 4.3 28.3 1.0 CA C:CYS274 4.3 35.4 1.0 CB C:THR276 4.6 40.5 1.0 CA C:CYS300 4.7 26.2 1.0 C C:THR276 4.8 39.6 1.0 N C:THR276 4.8 41.1 1.0 C C:CYS274 4.9 39.2 1.0 CA C:THR276 5.0 39.0 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