Zinc in PDB 8i03: Cryo-Em Structure of the SIN3L Complex From S. Pombe

All present enzymatic activity of Cryo-Em Structure of the SIN3L Complex From S. Pombe:
3.5.1.98;

The structure of Cryo-Em Structure of the SIN3L Complex From S. Pombe also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the SIN3L Complex From S. Pombe (pdb code 8i03). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of the SIN3L Complex From S. Pombe, PDB code: 8i03:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the SIN3L Complex From S. Pombe


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 SIN3L Complex From S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:23.8 occ:1.00 OD2 C:ASP173 1.9 6.6 1.0 ND1 C:HIS175 2.1 5.1 1.0 OD1 C:ASP173 2.1 6.6 1.0 CG C:ASP173 2.3 6.6 1.0 OD2 C:ASP261 2.5 6.3 1.0 CE1 C:HIS175 2.8 5.1 1.0 CG C:HIS175 3.3 5.1 1.0 CG C:ASP261 3.4 6.3 1.0 OD1 C:ASP261 3.7 6.3 1.0 CB C:ASP173 3.8 6.6 1.0 CB C:HIS175 3.8 5.1 1.0 NE2 C:HIS175 4.0 5.1 1.0 N C:HIS175 4.1 5.1 1.0 CD2 C:HIS175 4.2 5.1 1.0 N C:VAL174 4.3 5.9 1.0 NE2 C:HIS137 4.3 4.0 1.0 CA C:GLY298 4.4 4.7 1.0 OH C:TYR300 4.4 5.0 1.0 NE2 C:HIS138 4.6 3.2 1.0 CA C:HIS175 4.6 5.1 1.0 CG1 C:VAL174 4.6 5.9 1.0 CA C:ASP173 4.7 6.6 1.0 C C:ASP173 4.7 6.6 1.0 CE1 C:HIS137 4.8 4.0 1.0 CB C:ASP261 4.8 6.3 1.0 N C:GLY298 4.8 4.7 1.0 CE2 C:TYR300 4.9 5.0 1.0 C C:VAL174 5.0 5.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the SIN3L Complex From S. Pombe


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 SIN3L Complex From S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:29.2 occ:1.00 OD1 D:ASP173 2.0 8.9 1.0 ND1 D:HIS175 2.2 4.4 1.0 OD2 D:ASP173 2.4 8.9 1.0 CG D:ASP173 2.5 8.9 1.0 OD2 D:ASP261 2.5 6.2 1.0 CE1 D:HIS175 3.1 4.4 1.0 CG D:HIS175 3.2 4.4 1.0 CG D:ASP261 3.6 6.2 1.0 CB D:HIS175 3.6 4.4 1.0 OD1 D:ASP261 3.9 6.2 1.0 CB D:ASP173 4.0 8.9 1.0 N D:HIS175 4.0 4.4 1.0 NE2 D:HIS175 4.2 4.4 1.0 CA D:GLY298 4.2 3.8 1.0 NE2 D:HIS138 4.3 5.6 1.0 CE1 D:HIS137 4.3 5.0 1.0 CD2 D:HIS175 4.3 4.4 1.0 NE2 D:HIS137 4.3 5.0 1.0 OH D:TYR300 4.3 3.6 1.0 CA D:HIS175 4.4 4.4 1.0 N D:GLY298 4.6 3.8 1.0 N D:VAL174 4.6 5.8 1.0 CA D:ASP173 4.8 8.9 1.0 CB D:ASP261 4.8 6.2 1.0 C D:ASP173 4.9 8.9 1.0 CE2 D:TYR300 5.0 3.6 1.0

C.Wang, Z.Guo, C.Chu, Y.Lu, X.Zhang, X.Zhan. Two Assembly Modes For SIN3 Histone Deacetylase Complexes. Cell Discov V. 9 42 2023.
ISSN: ESSN 2056-5968
PubMed: 37076472
DOI: 10.1038/S41421-023-00539-X