Zinc in PDB 6wyo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double Mutant Complexed with Trichostatin A

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double Mutant Complexed with Trichostatin A, PDB code: 6wyo 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)	50.09 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.087, 123.993, 55.012, 90.00, 114.42, 90.00
R / Rfree (%)	17.1 / 23.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double Mutant 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) H82F F202Y Double Mutant Complexed with Trichostatin A (pdb code 6wyo). 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) H82F F202Y Double Mutant Complexed with Trichostatin A, PDB code: 6wyo:
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) H82F F202Y Double Mutant 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) H82F F202Y Double Mutant Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.0 occ:1.00 O1 A:TSN504 2.0 29.1 1.0 OD2 A:ASP323 2.0 20.2 1.0 OD1 A:ASP230 2.0 17.9 1.0 ND1 A:HIS232 2.1 24.6 1.0 O2 A:TSN504 2.5 26.0 1.0 OD2 A:ASP230 2.6 20.7 1.0 N1 A:TSN504 2.6 29.2 1.0 CG A:ASP230 2.6 19.7 1.0 C13 A:TSN504 2.8 27.2 1.0 CE1 A:HIS232 2.9 25.1 1.0 CG A:ASP323 3.0 23.3 1.0 CG A:HIS232 3.2 23.6 1.0 OD1 A:ASP323 3.3 25.8 1.0 CB A:HIS232 3.6 19.4 1.0 N A:HIS232 3.8 17.6 1.0 NE2 A:HIS232 4.1 23.7 1.0 CB A:ASP230 4.1 19.8 1.0 C12 A:TSN504 4.1 27.5 1.0 CA A:GLY361 4.2 28.9 1.0 CD2 A:HIS232 4.2 23.8 1.0 CG1 A:VAL231 4.2 17.1 1.0 N A:VAL231 4.3 19.5 1.0 CB A:ASP323 4.3 18.0 1.0 CA A:HIS232 4.3 19.3 1.0 NE2 A:HIS192 4.4 21.2 1.0 N A:GLY361 4.5 25.0 1.0 CE2 A:TYR363 4.6 36.2 1.0 CE1 A:HIS192 4.7 20.9 1.0 C11 A:TSN504 4.7 28.7 1.0 OH A:TYR363 4.7 38.3 1.0 C A:VAL231 4.7 20.6 1.0 C A:ASP230 4.8 19.3 1.0 CA A:ASP230 4.9 20.8 1.0 CA A:VAL231 4.9 19.3 1.0 NE2 A:HIS193 4.9 19.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double Mutant 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) H82F F202Y Double Mutant Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:25.4 occ:1.00 O1 B:TSN504 2.0 28.0 1.0 ND1 B:HIS232 2.0 22.4 1.0 OD2 B:ASP323 2.0 20.1 1.0 OD1 B:ASP230 2.2 22.0 1.0 O2 B:TSN504 2.5 25.0 1.0 N1 B:TSN504 2.6 27.1 1.0 OD2 B:ASP230 2.8 20.6 1.0 C13 B:TSN504 2.8 25.1 1.0 CG B:ASP230 2.8 19.8 1.0 CE1 B:HIS232 2.9 27.1 1.0 CG B:ASP323 3.1 28.2 1.0 CG B:HIS232 3.1 21.9 1.0 OD1 B:ASP323 3.5 26.5 1.0 CB B:HIS232 3.6 22.3 1.0 N B:HIS232 3.8 16.6 1.0 NE2 B:HIS232 4.0 20.8 1.0 C12 B:TSN504 4.1 22.8 1.0 CA B:GLY361 4.1 29.4 1.0 CG1 B:VAL231 4.2 19.4 1.0 CD2 B:HIS232 4.2 22.1 1.0 N B:VAL231 4.2 22.5 1.0 CB B:ASP230 4.3 20.0 1.0 CA B:HIS232 4.3 17.7 1.0 CB B:ASP323 4.4 22.9 1.0 NE2 B:HIS192 4.5 16.2 1.0 N B:GLY361 4.5 31.2 1.0 CE2 B:TYR363 4.6 29.6 1.0 OH B:TYR363 4.7 40.1 1.0 C B:VAL231 4.7 20.4 1.0 C11 B:TSN504 4.8 31.3 1.0 CA B:VAL231 4.9 19.8 1.0 CE1 B:HIS192 4.9 20.5 1.0 C B:ASP230 4.9 19.2 1.0 NE2 B:HIS193 4.9 18.8 1.0 C B:GLY361 4.9 30.0 1.0

J.D.Osko, D.W.Christianson. Binding of Inhibitors to Active-Site Mutants of CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Acta Crystallogr.,Sect.F V. 76 428 2020.
ISSN: ESSN 2053-230X
PubMed: 32880591
DOI: 10.1107/S2053230X20010250