Zinc in PDB 6uo2: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A, PDB code: 6uo2 was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.68 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.030, 124.261, 55.520, 90.00, 114.09, 90.00
R / Rfree (%)	18.7 / 22.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A 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 1 (CD1) Complexed with Trichostatin A (pdb code 6uo2). 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 (CD1) Complexed with Trichostatin A, PDB code: 6uo2:
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 (CD1) Complexed 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 (CD1) Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.0 occ:1.00 O1 A:TSN504 1.8 21.6 1.0 OD1 A:ASP230 2.0 15.9 1.0 ND1 A:HIS232 2.1 14.8 1.0 OD2 A:ASP323 2.1 18.3 1.0 O2 A:TSN504 2.4 25.5 1.0 HO1 A:TSN504 2.5 25.9 1.0 N1 A:TSN504 2.6 28.0 1.0 CG A:ASP230 2.7 16.2 1.0 OD2 A:ASP230 2.7 16.9 1.0 C13 A:TSN504 2.8 21.9 1.0 CE1 A:HIS232 2.9 21.3 1.0 CG A:ASP323 3.0 20.1 1.0 CG A:HIS232 3.2 23.1 1.0 OD1 A:ASP323 3.3 16.6 1.0 HN1 A:TSN504 3.4 33.6 1.0 CB A:HIS232 3.6 15.0 1.0 N A:HIS232 3.8 15.1 1.0 CA A:GLY361 4.0 19.5 1.0 NE2 A:HIS232 4.1 20.5 1.0 CB A:ASP230 4.2 14.4 1.0 C12 A:TSN504 4.2 28.3 1.0 CG1 A:VAL231 4.2 17.1 1.0 CD2 A:HIS232 4.2 21.2 1.0 N A:VAL231 4.3 15.2 1.0 CA A:HIS232 4.3 15.8 1.0 NE2 A:HIS192 4.3 16.4 1.0 CB A:ASP323 4.4 21.9 1.0 H111 A:TSN504 4.4 34.6 1.0 N A:GLY361 4.4 16.9 1.0 CE2 A:TYR363 4.6 22.4 1.0 CE1 A:HIS192 4.7 15.1 1.0 OH A:TYR363 4.7 25.1 1.0 C11 A:TSN504 4.7 28.9 1.0 C A:VAL231 4.8 18.2 1.0 C A:GLY361 4.8 22.1 1.0 H121 A:TSN504 4.8 34.0 1.0 C A:ASP230 4.8 15.8 1.0 N A:GLY362 4.9 21.0 1.0 CA A:ASP230 4.9 12.4 1.0 NE2 A:HIS193 4.9 16.7 1.0 CA A:VAL231 4.9 18.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed 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 (CD1) Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:19.5 occ:1.00 O1 B:TSN504 1.9 23.6 1.0 OD1 B:ASP230 2.0 14.4 1.0 OD2 B:ASP323 2.0 16.6 1.0 ND1 B:HIS232 2.1 13.7 1.0 O2 B:TSN504 2.4 23.6 1.0 HO1 B:TSN504 2.6 28.3 1.0 N1 B:TSN504 2.6 28.0 1.0 CG B:ASP230 2.7 17.2 1.0 OD2 B:ASP230 2.7 19.3 1.0 C13 B:TSN504 2.8 21.4 1.0 CE1 B:HIS232 3.0 21.4 1.0 CG B:ASP323 3.0 19.6 1.0 CG B:HIS232 3.2 20.0 1.0 HN1 B:TSN504 3.3 33.6 1.0 OD1 B:ASP323 3.4 18.8 1.0 CB B:HIS232 3.6 17.7 1.0 N B:HIS232 3.9 15.9 1.0 CA B:GLY361 4.0 18.7 1.0 C12 B:TSN504 4.1 25.2 1.0 CB B:ASP230 4.1 13.9 1.0 NE2 B:HIS232 4.2 20.1 1.0 NE2 B:HIS192 4.3 17.7 1.0 CD2 B:HIS232 4.3 20.5 1.0 N B:VAL231 4.3 17.3 1.0 H111 B:TSN504 4.3 30.5 1.0 CB B:ASP323 4.4 18.8 1.0 CG1 B:VAL231 4.4 18.1 1.0 CA B:HIS232 4.4 18.1 1.0 N B:GLY361 4.4 17.8 1.0 CE2 B:TYR363 4.5 24.4 1.0 OH B:TYR363 4.6 27.0 1.0 CE1 B:HIS192 4.6 14.8 1.0 C11 B:TSN504 4.7 25.4 1.0 C B:GLY361 4.8 21.0 1.0 H121 B:TSN504 4.8 30.3 1.0 C B:VAL231 4.8 19.8 1.0 N B:GLY362 4.9 23.8 1.0 C B:ASP230 4.9 14.9 1.0 CA B:ASP230 4.9 14.6 1.0 NE2 B:HIS193 4.9 18.0 1.0 CA B:VAL231 5.0 18.4 1.0

J.D.Osko, D.W.Christianson. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31755702
DOI: 10.1021/ACS.BIOCHEM.9B00934