Zinc in PDB 1w22: Crystal Structure of Inhibited Human HDAC8

The structure of Crystal Structure of Inhibited Human HDAC8, PDB code: 1w22 was solved by A.Vannini, C.Volpari, E.Caroli Casavola, S.Di Marco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.0 / 2.5
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.746, 83.532, 94.653, 90.00, 97.48, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Inhibited Human HDAC8 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Inhibited Human HDAC8 (pdb code 1w22). 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 Inhibited Human HDAC8, PDB code: 1w22:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Inhibited Human HDAC8


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 Inhibited Human HDAC8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1375 b:25.7 occ:1.00 OD2 A:ASP267 2.0 21.4 1.0 ND1 A:HIS180 2.0 23.2 1.0 OD2 A:ASP178 2.1 18.8 1.0 O26 A:NHB1378 2.2 41.0 1.0 O25 A:NHB1378 2.2 41.2 1.0 C23 A:NHB1378 2.6 41.4 1.0 N24 A:NHB1378 2.6 41.1 1.0 CE1 A:HIS180 2.8 23.4 1.0 CG A:ASP267 3.1 26.2 1.0 CG A:ASP178 3.1 20.6 1.0 CG A:HIS180 3.1 22.1 1.0 OD1 A:ASP178 3.5 21.5 1.0 CB A:HIS180 3.6 19.2 1.0 OD1 A:ASP267 3.6 25.1 1.0 N A:HIS180 3.7 19.3 1.0 C20 A:NHB1378 3.9 44.0 1.0 NE2 A:HIS180 4.0 25.2 1.0 CD2 A:HIS180 4.1 22.8 1.0 N A:LEU179 4.1 21.8 1.0 CB A:ASP267 4.2 22.4 1.0 CA A:GLY304 4.3 21.2 1.0 CA A:HIS180 4.3 19.7 1.0 O A:HOH2154 4.3 45.5 1.0 CB A:LEU179 4.4 16.6 1.0 CB A:ASP178 4.4 19.7 1.0 OH A:TYR306 4.5 39.0 1.0 C A:LEU179 4.6 20.7 1.0 NE2 A:HIS142 4.6 23.1 1.0 CA A:LEU179 4.6 19.5 1.0 C21 A:NHB1378 4.6 45.6 1.0 N A:GLY304 4.6 21.7 1.0 CE1 A:TYR306 4.8 33.6 1.0 NE2 A:HIS143 4.8 24.3 1.0 C19 A:NHB1378 4.8 45.1 1.0 CE1 A:HIS142 4.9 25.3 1.0 C A:ASP178 5.0 20.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Inhibited Human HDAC8


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 Inhibited Human HDAC8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1375 b:27.4 occ:1.00 OD2 B:ASP178 2.0 16.4 1.0 OD2 B:ASP267 2.0 17.8 1.0 ND1 B:HIS180 2.0 21.5 1.0 O26 B:NHB1378 2.1 40.7 1.0 O25 B:NHB1378 2.5 43.9 1.0 N24 B:NHB1378 2.6 42.6 1.0 CE1 B:HIS180 2.8 21.8 1.0 C23 B:NHB1378 2.9 43.3 1.0 CG B:ASP178 3.0 20.8 1.0 CG B:ASP267 3.1 20.9 1.0 CG B:HIS180 3.1 20.4 1.0 OD1 B:ASP178 3.3 21.0 1.0 OD1 B:ASP267 3.4 24.9 1.0 N B:HIS180 3.6 21.2 1.0 CB B:HIS180 3.6 19.4 1.0 NE2 B:HIS180 3.9 22.9 1.0 N B:LEU179 3.9 22.3 1.0 CD2 B:HIS180 4.1 22.8 1.0 CB B:LEU179 4.1 20.6 1.0 CA B:HIS180 4.2 20.3 1.0 C20 B:NHB1378 4.3 45.2 1.0 CB B:ASP178 4.3 20.2 1.0 CA B:LEU179 4.4 20.6 1.0 CB B:ASP267 4.4 19.1 1.0 CA B:GLY304 4.4 19.6 1.0 C B:LEU179 4.4 20.6 1.0 NE2 B:HIS142 4.6 22.6 1.0 N B:GLY304 4.7 21.2 1.0 OH B:TYR306 4.7 29.0 1.0 C B:ASP178 4.8 22.7 1.0 NE2 B:HIS143 4.9 28.9 1.0 CE1 B:HIS142 5.0 24.3 1.0 CE1 B:TYR306 5.0 29.7 1.0

A.Vannini, C.Volpari, G.Filocamo, E.Caroli Casavola, M.Brunetti, D.Renzoni, P.Chakravarty, C.Paolini, R.De Francesco, P.Gallinari, C.Steinckuhler, S.Di Marco. Crystal Structure of A Eukaryotic Zn-Dependent Histone Deacetylase,Human HDAC8,Complexed with A Hydroxamic Acid Inhibitor Proc.Natl.Acad.Sci.Usa V. 101 15064 2004.
ISSN: ISSN 0027-8424
PubMed: 15477595
DOI: 10.1073/PNAS.0404603101