Zinc in PDB 4qa6: Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa6 was solved by C.Decroos, C.B.Bowman, J.-A.S.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.77 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.832, 85.071, 94.444, 90.00, 97.55, 90.00
R / Rfree (%)	18.1 / 21.2

The structure of Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 4qa6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.2 occ:1.00 OD2 A:ASP178 2.0 23.2 1.0 OH C:ALY505 2.1 16.9 1.0 OD2 A:ASP267 2.1 20.3 1.0 O A:HOH642 2.1 22.6 1.0 ND1 A:HIS180 2.2 21.6 1.0 CG A:ASP178 2.9 22.4 1.0 CE1 A:HIS180 3.0 21.1 1.0 CH C:ALY505 3.0 20.6 1.0 OD1 A:ASP178 3.1 21.9 1.0 CG A:ASP267 3.2 22.6 1.0 CG A:HIS180 3.3 18.7 1.0 OD1 A:ASP267 3.6 20.5 1.0 CB A:HIS180 3.7 18.1 1.0 N A:HIS180 3.8 19.8 1.0 NZ C:ALY505 3.8 17.6 1.0 CE C:ALY505 3.9 17.4 1.0 CH3 C:ALY505 4.0 18.3 1.0 CA A:GLY304 4.1 17.7 1.0 NE2 A:HIS180 4.2 20.2 1.0 N A:LEU179 4.2 20.6 1.0 CB A:ASP178 4.3 19.7 1.0 CD2 A:HIS180 4.3 19.4 1.0 CA A:HIS180 4.4 18.4 1.0 N A:GLY304 4.4 17.8 1.0 CB A:ASP267 4.4 18.4 1.0 CB A:LEU179 4.5 19.3 1.0 NE2 A:HIS142 4.5 19.3 1.0 NE2 A:HIS143 4.6 18.6 1.0 C A:LEU179 4.7 21.1 1.0 CA A:LEU179 4.7 19.6 1.0 CE2 A:PHE306 4.8 18.1 1.0 C A:ASP178 5.0 21.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of I243N/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.3 occ:1.00 OD2 B:ASP178 2.0 23.0 1.0 OD2 B:ASP267 2.1 19.4 1.0 OH D:ALY505 2.1 18.2 1.0 ND1 B:HIS180 2.2 16.8 1.0 O B:HOH629 2.4 19.4 1.0 CG B:ASP178 2.9 19.8 1.0 CH D:ALY505 3.0 19.5 1.0 OD1 B:ASP178 3.0 21.3 1.0 CE1 B:HIS180 3.1 15.9 1.0 CG B:ASP267 3.1 20.5 1.0 CG B:HIS180 3.3 18.6 1.0 OD1 B:ASP267 3.6 20.7 1.0 CB B:HIS180 3.7 18.8 1.0 NZ D:ALY505 3.8 18.4 1.0 N B:HIS180 3.8 19.9 1.0 CE D:ALY505 3.9 18.5 1.0 CH3 D:ALY505 3.9 17.6 1.0 CA B:GLY304 4.1 21.7 1.0 NE2 B:HIS180 4.2 18.0 1.0 N B:LEU179 4.3 18.7 1.0 CB B:ASP178 4.3 21.4 1.0 CD2 B:HIS180 4.3 18.5 1.0 CA B:HIS180 4.3 17.2 1.0 NE2 B:HIS142 4.4 19.2 1.0 CB B:ASP267 4.4 18.8 1.0 N B:GLY304 4.5 19.6 1.0 NE2 B:HIS143 4.5 19.2 1.0 CB B:LEU179 4.6 18.1 1.0 C B:LEU179 4.7 20.2 1.0 CA B:LEU179 4.7 18.0 1.0 CE2 B:PHE306 4.8 18.3 1.0 CE1 B:HIS142 4.9 18.8 1.0 C B:ASP178 5.0 19.2 1.0

C.Decroos, C.M.Bowman, J.A.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia De Lange Syndrome Spectrum Disorders. Acs Chem.Biol. V. 9 2157 2014.
ISSN: ISSN 1554-8929
PubMed: 25075551
DOI: 10.1021/CB5003762