Zinc in PDB 8ifg: Cryo-Em Structure of the CLR6S (CLR6-Hdac) Complex From S. Pombe

All present enzymatic activity of Cryo-Em Structure of the CLR6S (CLR6-Hdac) Complex From S. Pombe:
3.5.1.98;

The binding sites of Zinc atom in the Cryo-Em Structure of the CLR6S (CLR6-Hdac) Complex From S. Pombe (pdb code 8ifg). 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 CLR6S (CLR6-Hdac) Complex From S. Pombe, PDB code: 8ifg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of the CLR6S (CLR6-Hdac) 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 CLR6S (CLR6-Hdac) Complex From S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:65.6 occ:1.00 ND1 C:HIS175 2.0 41.1 1.0 OD1 C:ASP173 2.0 42.4 1.0 OD2 C:ASP261 2.1 43.4 1.0 OD2 C:ASP173 2.2 42.4 1.0 O C:HOH601 2.3 45.4 1.0 CG C:ASP173 2.4 42.4 1.0 CE1 C:HIS175 2.6 41.1 1.0 CG C:ASP261 3.2 43.4 1.0 CG C:HIS175 3.3 41.1 1.0 OD1 C:ASP261 3.7 43.4 1.0 NE2 C:HIS175 3.8 41.1 1.0 CB C:ASP173 3.9 42.4 1.0 CB C:HIS175 3.9 41.1 1.0 OH C:TYR300 4.1 45.2 1.0 N C:HIS175 4.1 41.1 1.0 CD2 C:HIS175 4.2 41.1 1.0 NE2 C:HIS137 4.3 43.6 1.0 CA C:GLY298 4.3 43.4 1.0 NE2 C:HIS138 4.4 44.4 1.0 CB C:ASP261 4.4 43.4 1.0 N C:VAL174 4.4 40.8 1.0 CG1 C:VAL174 4.4 40.8 1.0 CA C:HIS175 4.7 41.1 1.0 N C:GLY298 4.7 43.4 1.0 CA C:ASP173 4.8 42.4 1.0 CZ C:TYR300 4.8 45.2 1.0 CE1 C:HIS137 4.9 43.6 1.0 CE2 C:TYR300 4.9 45.2 1.0 C C:ASP173 4.9 42.4 1.0 C C:VAL174 5.0 40.8 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of the CLR6S (CLR6-Hdac) 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 CLR6S (CLR6-Hdac) Complex From S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn701 b:58.5 occ:1.00 ND1 P:HIS433 2.2 43.8 1.0 SG P:CYS412 2.2 47.5 1.0 SG P:CYS409 2.2 47.5 1.0 SG P:CYS436 2.3 44.3 1.0 CB P:CYS409 3.0 47.5 1.0 CE1 P:HIS433 3.1 43.8 1.0 CG P:HIS433 3.1 43.8 1.0 CB P:CYS412 3.4 47.5 1.0 CB P:HIS433 3.5 43.8 1.0 CB P:CYS436 3.6 44.3 1.0 N P:CYS412 3.7 47.5 1.0 CA P:CYS412 4.1 47.5 1.0 N P:HIS433 4.2 43.8 1.0 NE2 P:HIS433 4.2 43.8 1.0 CD2 P:HIS433 4.3 43.8 1.0 CA P:CYS409 4.5 47.5 1.0 CA P:HIS433 4.5 43.8 1.0 CD2 A:PHE230 4.7 46.0 1.0 CB P:ARG411 4.7 47.1 1.0 CE2 A:PHE230 4.8 46.0 1.0 C P:ARG411 4.8 47.1 1.0 N P:ARG411 4.8 47.1 1.0 C P:CYS412 4.8 47.5 1.0 N P:HIS413 4.9 47.3 1.0 CA P:CYS436 4.9 44.3 1.0 C P:CYS409 4.9 47.5 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of the CLR6S (CLR6-Hdac) Complex From S. Pombe


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 CLR6S (CLR6-Hdac) Complex From S. Pombe within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn702 b:54.8 occ:1.00 NE2 P:HIS456 2.0 46.5 1.0 SG P:CYS453 2.2 46.7 1.0 SG P:CYS428 2.2 49.9 1.0 SG P:CYS425 2.3 49.8 1.0 CE1 P:HIS456 2.9 46.5 1.0 CD2 P:HIS456 3.0 46.5 1.0 CB P:CYS453 3.0 46.7 1.0 CB P:CYS425 3.3 49.8 1.0 CB P:CYS428 3.6 49.9 1.0 N P:CYS453 3.7 46.7 1.0 CA P:CYS453 3.9 46.7 1.0 N P:CYS428 3.9 49.9 1.0 ND1 P:HIS456 3.9 46.5 1.0 CG P:HIS456 4.0 46.5 1.0 CA P:CYS428 4.3 49.9 1.0 C P:CYS453 4.5 46.7 1.0 O P:CYS453 4.5 46.7 1.0 CB P:TYR427 4.6 48.1 1.0 CA P:CYS425 4.7 49.8 1.0 C P:TYR427 4.7 48.1 1.0 CB P:SER430 4.8 49.8 1.0 C P:LYS452 4.9 46.4 1.0 C P:CYS428 4.9 49.9 1.0

X.Wang, Y.Wang, S.Liu, Y.Zhang, K.Xu, L.Ji, R.D.Kornberg, H.Zhang. Class I Histone Deacetylase Complex: Structure and Functional Correlates. Proc Natl Acad Sci U S A V. 120 98120 2023.
ISSN: ESSN 1091-6490
PubMed: 37459529
DOI: 10.1073/PNAS.2307598120