Zinc in PDB 5ef8: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat:
3.5.1.98;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat, PDB code: 5ef8 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)	49.71 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.168, 140.396, 91.856, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.4

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat (pdb code 5ef8). 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 2 in Complex with Panobinostat, PDB code: 5ef8:
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 2 in Complex with Panobinostat


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 2 in Complex with Panobinostat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:34.2 occ:1.00 OD2 A:ASP705 2.0 22.5 1.0 O2 A:LBH2004 2.1 50.9 1.0 ND1 A:HIS614 2.1 28.6 1.0 N3 A:LBH2004 2.1 46.4 1.0 OD1 A:ASP612 2.2 26.5 1.0 OD2 A:ASP612 2.7 27.9 1.0 CG A:ASP612 2.8 25.4 1.0 C21 A:LBH2004 3.0 43.7 1.0 CE1 A:HIS614 3.0 28.2 1.0 CG A:HIS614 3.1 28.4 1.0 CG A:ASP705 3.2 21.6 1.0 O1 A:LBH2004 3.5 43.2 1.0 CB A:HIS614 3.5 25.7 1.0 OD1 A:ASP705 3.7 22.9 1.0 N A:HIS614 3.9 20.9 1.0 C20 A:LBH2004 4.0 41.4 1.0 NE2 A:HIS614 4.1 28.2 1.0 CD2 A:HIS614 4.2 29.6 1.0 CA A:GLY743 4.2 23.2 1.0 NE2 A:HIS573 4.3 23.9 1.0 CB A:ASP612 4.3 21.6 1.0 CA A:HIS614 4.4 23.3 1.0 CG1 A:VAL613 4.4 22.8 1.0 OH A:TYR745 4.4 35.2 1.0 CB A:ASP705 4.4 21.9 1.0 N A:VAL613 4.5 20.6 1.0 CE1 A:HIS573 4.5 22.4 1.0 CE2 A:TYR745 4.6 30.0 1.0 N A:GLY743 4.7 21.4 1.0 C19 A:LBH2004 4.7 39.5 1.0 NE2 A:HIS574 4.7 26.8 1.0 C A:VAL613 4.9 22.4 1.0 C A:ASP612 4.9 21.8 1.0

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


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 2 in Complex with Panobinostat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:39.1 occ:1.00 OD2 B:ASP705 1.9 21.6 1.0 O2 B:LBH2004 2.0 43.6 1.0 OD1 B:ASP612 2.1 22.1 1.0 ND1 B:HIS614 2.2 27.8 1.0 N3 B:LBH2004 2.5 40.6 1.0 O1 B:LBH2004 2.6 39.2 1.0 C21 B:LBH2004 2.8 38.6 1.0 CG B:ASP612 2.9 23.1 1.0 OD2 B:ASP612 3.0 24.9 1.0 CE1 B:HIS614 3.1 28.5 1.0 CG B:ASP705 3.1 21.2 1.0 CG B:HIS614 3.2 26.2 1.0 CB B:HIS614 3.6 22.0 1.0 OD1 B:ASP705 3.6 21.9 1.0 N B:HIS614 3.9 22.8 1.0 C20 B:LBH2004 4.1 36.3 1.0 CA B:GLY743 4.2 23.3 1.0 CG1 B:VAL613 4.2 24.9 1.0 NE2 B:HIS614 4.2 28.3 1.0 CB B:ASP705 4.3 23.0 1.0 CB B:ASP612 4.3 20.6 1.0 CD2 B:HIS614 4.3 27.5 1.0 N B:VAL613 4.4 17.9 1.0 NE2 B:HIS573 4.4 20.4 1.0 CA B:HIS614 4.4 19.4 1.0 OH B:TYR745 4.5 33.9 1.0 CE1 B:HIS573 4.6 20.5 1.0 C19 B:LBH2004 4.6 34.6 1.0 CE2 B:TYR745 4.6 32.1 1.0 N B:GLY743 4.7 22.5 1.0 C B:VAL613 4.9 21.5 1.0 NE2 B:HIS574 4.9 22.6 1.0 C B:ASP612 4.9 21.0 1.0 C B:GLY743 4.9 22.2 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