Zinc in PDB 4qa5: Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa5 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)	46.42 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.830, 97.760, 105.485, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.4

The structure of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 4qa5). 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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A188T/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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:16.4 occ:1.00 OD2 A:ASP178 1.9 14.9 1.0 OD2 A:ASP267 2.0 13.2 1.0 OH C:ALY505 2.1 16.1 1.0 ND1 A:HIS180 2.1 15.1 1.0 O A:HOH501 2.1 14.7 1.0 CG A:ASP178 2.8 17.2 1.0 CE1 A:HIS180 3.0 15.2 1.0 CH C:ALY505 3.0 18.7 1.0 OD1 A:ASP178 3.1 15.2 1.0 CG A:ASP267 3.1 15.2 1.0 CG A:HIS180 3.2 15.1 1.0 OD1 A:ASP267 3.4 15.0 1.0 CB A:HIS180 3.7 14.5 1.0 N A:HIS180 3.8 14.1 1.0 NZ C:ALY505 3.8 15.4 1.0 CE C:ALY505 3.9 13.7 1.0 CH3 C:ALY505 4.0 14.8 1.0 CA A:GLY304 4.1 14.1 1.0 NE2 A:HIS180 4.1 14.2 1.0 CB A:ASP178 4.2 15.9 1.0 N A:LEU179 4.3 13.0 1.0 CD2 A:HIS180 4.3 15.9 1.0 NE2 A:HIS142 4.3 17.2 1.0 CA A:HIS180 4.3 11.9 1.0 N A:GLY304 4.4 14.6 1.0 CB A:ASP267 4.4 11.2 1.0 CB A:LEU179 4.5 14.6 1.0 NE2 A:HIS143 4.7 16.5 1.0 C A:LEU179 4.7 16.1 1.0 CA A:LEU179 4.7 13.6 1.0 CE2 A:PHE306 4.8 14.9 1.0 CE1 A:HIS142 4.9 15.5 1.0 C A:ASP178 4.9 16.2 1.0 CA A:ASP178 5.0 14.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A188T/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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:17.3 occ:1.00 OD2 B:ASP178 2.0 15.0 1.0 OD2 B:ASP267 2.0 14.9 1.0 ND1 B:HIS180 2.1 11.8 1.0 OH D:ALY505 2.1 14.0 1.0 O B:HOH501 2.2 14.9 1.0 CG B:ASP178 2.8 13.8 1.0 CE1 B:HIS180 3.0 15.6 1.0 OD1 B:ASP178 3.0 14.2 1.0 CH D:ALY505 3.0 15.0 1.0 CG B:ASP267 3.1 17.1 1.0 CG B:HIS180 3.2 14.2 1.0 OD1 B:ASP267 3.4 15.9 1.0 CB B:HIS180 3.6 13.6 1.0 NZ D:ALY505 3.8 14.0 1.0 N B:HIS180 3.8 14.8 1.0 CE D:ALY505 3.9 13.9 1.0 CH3 D:ALY505 3.9 14.1 1.0 NE2 B:HIS180 4.1 16.3 1.0 CA B:GLY304 4.1 12.2 1.0 CD2 B:HIS180 4.2 15.6 1.0 CB B:ASP178 4.3 15.9 1.0 N B:LEU179 4.3 13.1 1.0 NE2 B:HIS142 4.3 18.3 1.0 N B:GLY304 4.4 13.6 1.0 CA B:HIS180 4.4 13.1 1.0 CB B:ASP267 4.4 14.3 1.0 CB B:LEU179 4.5 15.1 1.0 NE2 B:HIS143 4.6 15.0 1.0 C B:LEU179 4.7 16.4 1.0 CA B:LEU179 4.8 14.4 1.0 CE2 B:PHE306 4.8 15.3 1.0 CE1 B:HIS142 4.9 17.9 1.0 C B:ASP178 4.9 12.1 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