Zinc in PDB 5eef: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A, PDB code: 5eef was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.04 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.876, 123.717, 55.186, 90.00, 113.85, 90.00
R / Rfree (%)	21.1 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A (pdb code 5eef). 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A, PDB code: 5eef:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:31.5 occ:0.84 O1 A:TSN2002 1.9 33.8 1.0 OD2 A:ASP323 2.1 23.7 1.0 ND1 A:HIS232 2.1 23.2 1.0 OD1 A:ASP230 2.1 21.3 1.0 O2 A:TSN2002 2.4 32.4 1.0 N1 A:TSN2002 2.4 33.3 1.0 C13 A:TSN2002 2.6 32.7 1.0 CG A:ASP230 2.9 21.6 1.0 OD2 A:ASP230 2.9 22.0 1.0 CG A:HIS232 3.1 23.1 1.0 CE1 A:HIS232 3.1 23.9 1.0 CG A:ASP323 3.1 24.6 1.0 CB A:HIS232 3.4 23.0 1.0 OD1 A:ASP323 3.6 25.3 1.0 N A:HIS232 3.8 22.3 1.0 C12 A:TSN2002 3.8 32.5 1.0 CA A:GLY361 4.0 26.8 1.0 CG1 A:VAL231 4.1 22.3 1.0 NE2 A:HIS232 4.2 24.2 1.0 CD2 A:HIS232 4.2 23.6 1.0 CA A:HIS232 4.2 22.5 1.0 CB A:ASP230 4.3 22.1 1.0 CB A:ASP323 4.4 24.8 1.0 N A:VAL231 4.4 23.2 1.0 NE2 A:HIS192 4.5 20.3 1.0 N A:GLY361 4.5 25.4 1.0 C11 A:TSN2002 4.6 32.7 1.0 CE2 A:TYR363 4.6 37.7 1.0 C A:VAL231 4.8 22.3 1.0 CE1 A:HIS192 4.8 19.5 1.0 NE2 A:HIS193 4.8 24.1 1.0 C A:GLY361 4.9 28.3 1.0 N A:GLY362 4.9 30.1 1.0 CA A:VAL231 5.0 22.7 1.0 C A:ASP230 5.0 23.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:37.8 occ:1.00 O1 B:TSN2002 2.1 27.5 1.0 OD1 B:ASP230 2.1 23.6 1.0 OD2 B:ASP323 2.2 24.9 1.0 ND1 B:HIS232 2.2 25.5 1.0 O2 B:TSN2002 2.5 27.4 1.0 OD2 B:ASP230 2.7 21.9 1.0 CG B:ASP230 2.7 22.6 1.0 N1 B:TSN2002 2.7 27.4 1.0 C13 B:TSN2002 2.9 27.8 1.0 CG B:ASP323 3.1 24.6 1.0 CG B:HIS232 3.2 25.1 1.0 CE1 B:HIS232 3.2 25.8 1.0 OD1 B:ASP323 3.4 24.4 1.0 CB B:HIS232 3.5 23.9 1.0 N B:HIS232 3.8 22.0 1.0 CA B:GLY361 3.9 24.5 1.0 CB B:ASP230 4.2 22.3 1.0 CA B:HIS232 4.2 22.5 1.0 CG1 B:VAL231 4.2 28.7 1.0 C12 B:TSN2002 4.3 28.6 1.0 N B:VAL231 4.3 21.1 1.0 NE2 B:HIS232 4.3 26.0 1.0 NE2 B:HIS192 4.3 19.6 1.0 CD2 B:HIS232 4.3 25.6 1.0 N B:GLY361 4.4 23.5 1.0 CB B:ASP323 4.5 24.6 1.0 CE1 B:HIS192 4.5 19.2 1.0 OH B:TYR363 4.7 32.9 1.0 C B:VAL231 4.7 21.9 1.0 CE2 B:TYR363 4.7 30.8 1.0 C B:GLY361 4.7 26.1 1.0 NE2 B:HIS193 4.8 22.2 1.0 C11 B:TSN2002 4.8 29.4 1.0 C B:ASP230 4.8 21.5 1.0 CA B:VAL231 4.9 21.9 1.0 N B:GLY362 4.9 27.4 1.0 CA B:ASP230 4.9 22.0 1.0

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134