Zinc in PDB 5dc6: Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc6 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)	49.10 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.332, 98.206, 104.281, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.6

The structure of Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5dc6). 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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.5 occ:1.00 OD2 A:ASP178 1.9 15.7 1.0 OD2 A:ASP267 1.9 16.4 1.0 OH C:ALY5 2.0 17.1 1.0 ND1 A:HIS180 2.1 14.9 1.0 CG A:ASP178 2.8 17.0 1.0 O A:HOH507 2.8 29.4 0.4 CG A:ASP267 2.9 15.2 1.0 CE1 A:HIS180 2.9 14.8 1.0 OD1 A:ASP178 3.0 17.6 1.0 CH C:ALY5 3.1 16.5 1.0 CG A:HIS180 3.2 13.5 1.0 OD1 A:ASP267 3.2 14.7 1.0 CB A:HIS180 3.6 13.6 1.0 N A:HIS180 3.7 14.1 1.0 NZ C:ALY5 3.9 15.9 1.0 CE C:ALY5 3.9 16.1 1.0 CA A:GLY304 4.0 14.0 1.0 CH3 C:ALY5 4.0 19.5 1.0 N A:LEU179 4.1 14.2 1.0 NE2 A:HIS180 4.1 13.9 1.0 CB A:ASP178 4.2 18.3 1.0 CB A:ASP267 4.2 13.6 1.0 CD2 A:HIS180 4.2 14.6 1.0 N A:GLY304 4.3 14.3 1.0 CB A:LEU179 4.3 14.2 1.0 CA A:HIS180 4.3 14.0 1.0 CA A:LEU179 4.5 13.4 1.0 C A:LEU179 4.6 14.5 1.0 CE2 A:PHE306 4.7 17.0 1.0 C A:ASP178 4.8 17.7 1.0 NE2 A:HIS143 4.8 15.9 1.0 CA A:ASP178 4.9 16.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:18.0 occ:1.00 OD2 B:ASP267 1.9 16.9 1.0 OD2 B:ASP178 1.9 16.1 1.0 OH D:ALY5 2.0 17.1 1.0 ND1 B:HIS180 2.1 15.2 1.0 O B:HOH510 2.6 13.1 0.2 CG B:ASP178 2.8 17.9 1.0 CE1 B:HIS180 2.9 13.5 1.0 CG B:ASP267 2.9 17.2 1.0 OD1 B:ASP178 3.0 18.0 1.0 CH D:ALY5 3.0 17.9 1.0 CG B:HIS180 3.2 13.2 1.0 OD1 B:ASP267 3.3 16.4 1.0 CB B:HIS180 3.6 13.7 1.0 N B:HIS180 3.7 15.2 1.0 NZ D:ALY5 3.9 15.1 1.0 CE D:ALY5 4.0 15.1 1.0 CH3 D:ALY5 4.0 23.4 1.0 CA B:GLY304 4.0 16.8 1.0 NE2 B:HIS180 4.1 13.5 1.0 N B:LEU179 4.1 15.6 1.0 CB B:ASP178 4.2 18.3 1.0 CD2 B:HIS180 4.2 12.8 1.0 CB B:ASP267 4.3 13.8 1.0 N B:GLY304 4.3 17.3 1.0 CA B:HIS180 4.3 14.9 1.0 CB B:LEU179 4.3 15.0 1.0 C B:LEU179 4.6 17.4 1.0 CA B:LEU179 4.6 14.2 1.0 NE2 B:HIS143 4.7 18.4 1.0 CE2 B:PHE306 4.8 16.7 1.0 C B:ASP178 4.8 16.2 1.0 CA B:ASP178 4.9 16.5 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