Zinc in PDB 8bpc: Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex with Saha at 2.8 Angstrom

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

The structure of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Core Complex with Saha 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 with Saha at 2.8 Angstrom (pdb code 8bpc). 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 with Saha at 2.8 Angstrom, PDB code: 8bpc:
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 with Saha 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 with Saha at 2.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:46.9 occ:1.00 OD2 B:ASP265 1.9 12.5 1.0 OD1 B:ASP177 1.9 20.0 1.0 O1 B:SHH501 2.1 9.9 1.0 ND1 B:HIS179 2.3 16.1 1.0 O2 B:SHH501 2.6 11.8 1.0 CG B:ASP177 2.7 9.0 1.0 OD2 B:ASP177 2.8 10.1 1.0 N1 B:SHH501 2.9 12.9 1.0 CG B:ASP265 3.0 6.0 1.0 C1 B:SHH501 3.1 11.9 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 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 C2 B:SHH501 4.5 8.5 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 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 C3 B:SHH501 4.9 11.0 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 with Saha 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 with Saha at 2.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 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 with Saha 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 with Saha at 2.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 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 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38276-0