Zinc in PDB 2v5w: Crystal Structure of HDAC8-Substrate Complex

The structure of Crystal Structure of HDAC8-Substrate Complex, PDB code: 2v5w was solved by S.Di Marco, A.Vannini, C.Volpari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.304, 151.801, 57.552, 90.00, 117.02, 90.00
R / Rfree (%)	17.6 / 23

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

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of HDAC8-Substrate Complex (pdb code 2v5w). 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-Substrate Complex, PDB code: 2v5w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of HDAC8-Substrate 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-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1380 b:16.4 occ:1.00 OD2 A:ASP267 2.0 14.8 1.0 OD2 A:ASP178 2.0 15.4 1.0 OH I:ALY5 2.0 19.5 1.0 ND1 A:HIS180 2.1 10.9 1.0 O I:HOH2358 2.1 31.3 1.0 CE1 A:HIS180 2.9 13.9 1.0 CG A:ASP178 2.9 13.3 1.0 CH I:ALY5 3.0 22.5 1.0 CG A:ASP267 3.0 16.2 1.0 OD1 A:ASP178 3.0 13.3 1.0 CG A:HIS180 3.2 12.3 1.0 OD1 A:ASP267 3.3 16.4 1.0 CB A:HIS180 3.7 12.8 1.0 NZ I:ALY5 3.8 21.2 1.0 CH3 I:ALY5 3.8 22.4 1.0 N A:HIS180 3.8 12.7 1.0 NE2 A:HIS180 4.0 12.6 1.0 CE I:ALY5 4.1 19.9 1.0 CA A:GLY304 4.1 16.2 1.0 CD2 A:HIS180 4.2 14.0 1.0 CB A:ASP178 4.3 13.4 1.0 NE2 A:HIS142 4.3 15.5 1.0 N A:LEU179 4.3 13.6 1.0 CB A:ASP267 4.4 14.5 1.0 CA A:HIS180 4.4 12.1 1.0 N A:GLY304 4.4 16.0 1.0 CB A:LEU179 4.5 13.3 1.0 CA A:LEU179 4.7 13.0 1.0 C A:LEU179 4.8 13.0 1.0 NE2 A:HIS143 4.8 14.9 1.0 CE1 A:PHE306 4.8 18.1 1.0 CE1 A:HIS142 4.8 15.2 1.0 C A:ASP178 4.9 13.7 1.0 CA A:ASP178 5.0 13.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of HDAC8-Substrate 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-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1379 b:16.8 occ:1.00 OD2 B:ASP267 1.9 13.9 1.0 OD2 B:ASP178 2.0 13.5 1.0 OH L:ALY5 2.0 17.8 1.0 ND1 B:HIS180 2.1 11.7 1.0 O L:HOH2356 2.2 25.2 1.0 CE1 B:HIS180 2.8 13.3 1.0 CG B:ASP178 2.9 15.0 1.0 CH L:ALY5 3.0 23.1 1.0 CG B:ASP267 3.0 14.3 1.0 OD1 B:ASP178 3.1 14.2 1.0 CG B:HIS180 3.2 11.2 1.0 OD1 B:ASP267 3.4 13.5 1.0 CB B:HIS180 3.7 12.9 1.0 N B:HIS180 3.8 12.5 1.0 NZ L:ALY5 3.8 21.2 1.0 CE L:ALY5 3.9 19.9 1.0 CH3 L:ALY5 4.0 24.0 1.0 NE2 B:HIS180 4.0 13.2 1.0 CA B:GLY304 4.1 14.2 1.0 CD2 B:HIS180 4.2 12.7 1.0 N B:LEU179 4.2 12.9 1.0 CB B:ASP178 4.3 13.4 1.0 CB B:ASP267 4.3 13.9 1.0 NE2 B:HIS142 4.4 18.2 1.0 N B:GLY304 4.4 14.1 1.0 CA B:HIS180 4.4 12.8 1.0 CB B:LEU179 4.4 13.2 1.0 CA B:LEU179 4.6 12.5 1.0 C B:LEU179 4.6 12.8 1.0 NE2 B:HIS143 4.7 11.4 1.0 CE1 B:PHE306 4.8 13.3 1.0 CE1 B:HIS142 4.8 18.6 1.0 C B:ASP178 4.9 12.3 1.0 CA B:ASP178 5.0 13.3 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