Zinc in PDB 2v5x: Crystal Structure of HDAC8-Inhibitor Complex

The structure of Crystal Structure of HDAC8-Inhibitor Complex, PDB code: 2v5x was solved by S.Di Marco, A.Vannini, C.Volpari, P.Gallinari, P.Jones, M.Mattu, A.Carfi, R.Defrancesco, C.Steinkuhler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.298, 98.694, 110.474, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24

The structure of Crystal Structure of HDAC8-Inhibitor Complex also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of HDAC8-Inhibitor Complex (pdb code 2v5x). 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 HDAC8-Inhibitor Complex, PDB code: 2v5x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of HDAC8-Inhibitor Complex


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 HDAC8-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1377 b:24.5 occ:1.00 OD2 A:ASP267 1.9 26.0 1.0 OD2 A:ASP178 1.9 20.9 1.0 OBB A:V5X1380 2.1 28.7 1.0 ND1 A:HIS180 2.2 19.7 1.0 OBE A:V5X1380 2.2 29.8 1.0 NBA A:V5X1380 2.7 29.0 1.0 CAZ A:V5X1380 2.7 30.1 1.0 CG A:ASP178 2.9 22.6 1.0 CG A:ASP267 2.9 25.5 1.0 CE1 A:HIS180 3.0 20.0 1.0 OD1 A:ASP178 3.1 20.1 1.0 OD1 A:ASP267 3.2 21.5 1.0 CG A:HIS180 3.3 23.2 1.0 CB A:HIS180 3.7 24.7 1.0 N A:HIS180 3.9 25.3 1.0 CA A:GLY304 4.0 25.9 1.0 NE2 A:HIS180 4.2 18.9 1.0 CAY A:V5X1380 4.2 30.9 1.0 N A:GLY304 4.2 25.4 1.0 CB A:ASP178 4.3 24.4 1.0 CB A:ASP267 4.3 25.9 1.0 O A:HOH2152 4.3 37.0 1.0 N A:LEU179 4.3 24.3 1.0 CD2 A:HIS180 4.3 20.1 1.0 NE2 A:HIS142 4.4 22.4 1.0 CA A:HIS180 4.5 25.2 1.0 CB A:LEU179 4.5 23.8 1.0 OH A:TYR306 4.5 30.3 1.0 CAX A:V5X1380 4.7 32.9 1.0 C A:LEU179 4.7 24.9 1.0 CA A:LEU179 4.8 24.1 1.0 CE1 A:TYR306 4.8 26.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of HDAC8-Inhibitor Complex


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 HDAC8-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1377 b:24.9 occ:1.00 OD2 B:ASP178 2.0 21.0 1.0 OD2 B:ASP267 2.0 22.9 1.0 OBB B:V5X1380 2.2 27.5 1.0 OBE B:V5X1380 2.3 29.1 1.0 ND1 B:HIS180 2.3 24.4 1.0 NBA B:V5X1380 2.8 27.5 1.0 CAZ B:V5X1380 2.8 29.4 1.0 CG B:ASP178 2.9 26.6 1.0 CG B:ASP267 3.0 24.4 1.0 OD1 B:ASP178 3.0 27.1 1.0 CE1 B:HIS180 3.1 23.2 1.0 CG B:HIS180 3.3 24.9 1.0 OD1 B:ASP267 3.3 22.3 1.0 CB B:HIS180 3.7 25.8 1.0 N B:HIS180 3.9 26.6 1.0 CA B:GLY304 4.0 26.2 1.0 NE2 B:HIS180 4.2 23.5 1.0 CD2 B:HIS180 4.3 25.1 1.0 CB B:ASP178 4.3 27.1 1.0 N B:GLY304 4.3 26.6 1.0 CAY B:V5X1380 4.3 28.7 1.0 CB B:ASP267 4.4 24.7 1.0 NE2 B:HIS142 4.4 29.5 1.0 N B:LEU179 4.4 27.1 1.0 CA B:HIS180 4.4 25.9 1.0 O B:HOH2168 4.4 40.1 1.0 CB B:LEU179 4.5 27.1 1.0 OH B:TYR306 4.6 34.4 1.0 C B:LEU179 4.8 27.2 1.0 CA B:LEU179 4.8 27.1 1.0 CAX B:V5X1380 4.9 35.2 1.0 CE1 B:TYR306 4.9 30.6 1.0 C B:GLY304 5.0 26.0 1.0

A.Vannini, C.Volpari, P.Gallinari, P.Jones, M.Mattu, A.Carfi, R.Defrancesco, C.Steinkuhler, S.Di Marco. Substrate Binding to Histone Deacetylases As Revealed By Crystal Structure of HDAC8-Substrate Complex Embo Rep. V. 8 879 2007.
ISSN: ISSN 1469-221X
PubMed: 17721440
DOI: 10.1038/SJ.EMBOR.7401047