Zinc in PDB 3rqd: Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8

All present enzymatic activity of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8:
3.5.1.98;

The structure of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8, PDB code: 3rqd was solved by K.E.Cole, D.P.Dowling, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.78 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.059, 88.302, 93.660, 90.00, 101.62, 90.00
R / Rfree (%)	20.2 / 24.5

The structure of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 (pdb code 3rqd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8, PDB code: 3rqd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.2 occ:1.00 OD2 A:ASP178 2.0 17.6 1.0 OD2 A:ASP267 2.0 14.7 1.0 ND1 A:HIS180 2.2 15.9 1.0 S C:02G1 2.3 16.5 1.0 CG A:ASP178 2.9 17.4 1.0 CG A:ASP267 3.0 20.8 1.0 CE1 A:HIS180 3.1 20.9 1.0 OD1 A:ASP178 3.2 19.1 1.0 CG A:HIS180 3.2 14.7 1.0 C7 C:02G1 3.2 12.9 1.0 OD1 A:ASP267 3.3 17.1 1.0 CB A:HIS180 3.6 18.1 1.0 N A:HIS180 3.7 16.0 1.0 C6 C:02G1 3.9 7.9 1.0 N A:LEU179 4.2 16.0 1.0 NE2 A:HIS180 4.2 15.9 1.0 NE2 A:HIS142 4.3 25.2 1.0 CB A:ASP178 4.3 16.7 1.0 CA A:GLY304 4.3 15.5 1.0 CD2 A:HIS180 4.3 15.7 1.0 CA A:HIS180 4.3 13.1 1.0 CB A:ASP267 4.3 14.7 1.0 NE2 A:HIS143 4.4 18.8 1.0 CB A:LEU179 4.5 17.8 1.0 CE2 A:TYR306 4.6 21.2 1.0 C A:LEU179 4.6 20.1 1.0 CA A:LEU179 4.7 17.8 1.0 CE1 A:HIS142 4.7 21.4 1.0 N A:GLY304 4.7 21.1 1.0 OH A:TYR306 4.8 14.6 1.0 C A:ASP178 4.9 16.4 1.0 C5 C:02G1 4.9 23.9 1.0 O A:HOH558 4.9 22.1 1.0 CA A:ASP178 5.0 18.9 1.0

Zinc binding site 2 out of 2 in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:15.4 occ:1.00 OD2 B:ASP178 2.0 18.2 1.0 OD2 B:ASP267 2.0 15.5 1.0 ND1 B:HIS180 2.2 17.3 1.0 S D:02G1 2.3 13.3 1.0 CG B:ASP178 2.9 15.8 1.0 CG B:ASP267 3.0 19.0 1.0 C7 D:02G1 3.0 13.8 1.0 CE1 B:HIS180 3.0 18.2 1.0 OD1 B:ASP178 3.2 18.2 1.0 CG B:HIS180 3.2 15.2 1.0 OD1 B:ASP267 3.3 15.1 1.0 CB B:HIS180 3.6 15.0 1.0 N B:HIS180 3.7 15.9 1.0 C6 D:02G1 3.8 16.5 1.0 N B:LEU179 4.1 16.2 1.0 NE2 B:HIS180 4.2 14.9 1.0 NE2 B:HIS142 4.3 21.3 1.0 CA B:GLY304 4.3 17.4 1.0 CB B:ASP178 4.3 16.0 1.0 CD2 B:HIS180 4.3 13.5 1.0 CA B:HIS180 4.3 12.6 1.0 CB B:ASP267 4.3 11.7 1.0 NE2 B:HIS143 4.5 16.5 1.0 CB B:LEU179 4.5 15.2 1.0 CE2 B:TYR306 4.6 20.5 1.0 C B:LEU179 4.6 21.3 1.0 CA B:LEU179 4.6 16.8 1.0 CE1 B:HIS142 4.7 19.8 1.0 N B:GLY304 4.7 17.9 1.0 OH B:TYR306 4.8 16.8 1.0 C5 D:02G1 4.8 19.0 1.0 C B:ASP178 4.8 16.7 1.0 CA B:ASP178 5.0 20.4 1.0

K.E.Cole, D.P.Dowling, M.A.Boone, A.J.Phillips, D.W.Christianson. Structural Basis of the Antiproliferative Activity of Largazole, A Depsipeptide Inhibitor of the Histone Deacetylases. J.Am.Chem.Soc. V. 133 12474 2011.
ISSN: ISSN 0002-7863
PubMed: 21790156
DOI: 10.1021/JA205972N