Zinc in PDB 5dc7: Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc7 was solved by C.Decroos, M.S.Lee, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.845, 97.748, 103.616, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.6

The structure of Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5dc7). 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 D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of D176A-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 D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:60.1 occ:1.00 OD2 A:ASP178 2.0 31.9 1.0 OD2 A:ASP267 2.1 31.7 1.0 ND1 A:HIS180 2.2 25.4 1.0 OH C:ALY5 2.3 41.5 1.0 CG A:ASP178 3.0 31.6 1.0 CG A:ASP267 3.1 25.8 1.0 CE1 A:HIS180 3.1 24.7 1.0 CH C:ALY5 3.1 29.2 1.0 CG A:HIS180 3.2 25.6 1.0 OD1 A:ASP178 3.3 27.2 1.0 CB A:HIS180 3.5 22.9 1.0 OD1 A:ASP267 3.6 27.8 1.0 N A:HIS180 3.6 27.8 1.0 NZ C:ALY5 3.8 31.0 1.0 CE C:ALY5 3.8 22.4 1.0 N A:LEU179 4.1 27.4 1.0 CH3 C:ALY5 4.1 27.5 1.0 CA A:GLY304 4.2 22.5 1.0 CA A:HIS180 4.2 28.4 1.0 NE2 A:HIS180 4.2 26.1 1.0 CB A:LEU179 4.3 23.1 1.0 CB A:ASP267 4.3 19.8 1.0 CB A:ASP178 4.3 31.5 1.0 CD2 A:HIS180 4.3 28.4 1.0 N A:GLY304 4.5 23.6 1.0 C A:LEU179 4.5 26.7 1.0 CA A:LEU179 4.5 25.6 1.0 NE2 A:HIS143 4.5 31.3 1.0 CE2 A:PHE306 4.8 27.0 1.0 C A:ASP178 4.8 32.1 1.0 CA A:ASP178 5.0 27.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of D176A-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 D176A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:59.2 occ:1.00 OD2 B:ASP178 2.0 35.1 1.0 OD2 B:ASP267 2.1 31.5 1.0 ND1 B:HIS180 2.1 29.0 1.0 OH D:ALY5 2.1 31.0 1.0 CG B:ASP178 2.9 34.7 1.0 CE1 B:HIS180 3.0 25.2 1.0 CH D:ALY5 3.1 29.4 1.0 CG B:ASP267 3.1 32.5 1.0 CG B:HIS180 3.2 25.3 1.0 OD1 B:ASP178 3.2 30.1 1.0 OD1 B:ASP267 3.6 31.2 1.0 N B:HIS180 3.6 25.1 1.0 CB B:HIS180 3.6 21.6 1.0 CE D:ALY5 3.8 27.0 1.0 NZ D:ALY5 3.8 30.3 1.0 CA B:GLY304 4.0 26.4 1.0 N B:LEU179 4.1 28.6 1.0 NE2 B:HIS180 4.1 27.3 1.0 CH3 D:ALY5 4.2 30.5 1.0 CA B:HIS180 4.2 29.2 1.0 CD2 B:HIS180 4.3 25.0 1.0 CB B:ASP178 4.3 35.1 1.0 CB B:LEU179 4.3 28.3 1.0 N B:GLY304 4.4 29.7 1.0 CB B:ASP267 4.4 26.2 1.0 C B:LEU179 4.5 28.9 1.0 CA B:LEU179 4.5 27.7 1.0 NE2 B:HIS143 4.5 27.3 1.0 CE2 B:PHE306 4.6 24.4 1.0 C B:ASP178 4.9 35.5 1.0 CZ B:PHE306 4.9 21.9 1.0 CA B:ASP178 5.0 25.6 1.0

S.M.Gantt, C.Decroos, M.S.Lee, L.E.Gullett, C.M.Bowman, D.W.Christianson, C.A.Fierke. General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry V. 55 820 2016.
ISSN: ISSN 0006-2960
PubMed: 26806311
DOI: 10.1021/ACS.BIOCHEM.5B01327