Zinc in PDB 6uo4: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Trichostatin A

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Trichostatin A, PDB code: 6uo4 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)	62.20 / 1.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.892, 124.407, 55.630, 90.00, 114.46, 90.00
R / Rfree (%)	18.2 / 19.6

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F 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) Y363F Mutant Complexed with Trichostatin A (pdb code 6uo4). 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) Y363F Mutant Complexed with Trichostatin A, PDB code: 6uo4:
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) Y363F 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) Y363F Mutant Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:12.5 occ:1.00 OD1 A:ASP230 1.9 10.8 1.0 OD2 A:ASP323 2.0 13.0 1.0 HO1 A:TSN504 2.0 17.0 1.0 O1 A:TSN504 2.1 14.2 1.0 ND1 A:HIS232 2.1 12.5 1.0 O2 A:TSN504 2.3 14.0 1.0 CG A:ASP230 2.7 10.1 1.0 N1 A:TSN504 2.7 13.9 1.0 C13 A:TSN504 2.8 12.4 1.0 OD2 A:ASP230 2.8 10.6 1.0 CE1 A:HIS232 3.0 11.1 1.0 CG A:ASP323 3.0 12.6 1.0 CG A:HIS232 3.2 12.2 1.0 OD1 A:ASP323 3.3 12.7 1.0 HN1 A:TSN504 3.4 16.7 1.0 CB A:HIS232 3.6 12.1 1.0 N A:HIS232 3.9 10.2 1.0 O A:HOH650 4.0 18.1 1.0 CA A:GLY361 4.1 15.4 1.0 C12 A:TSN504 4.1 15.7 1.0 NE2 A:HIS232 4.1 14.0 1.0 CB A:ASP230 4.2 8.7 1.0 CD2 A:HIS232 4.3 12.8 1.0 NE2 A:HIS192 4.3 10.9 1.0 N A:VAL231 4.3 11.2 1.0 CG1 A:VAL231 4.3 14.1 1.0 CB A:ASP323 4.3 13.2 1.0 CA A:HIS232 4.4 12.1 1.0 H111 A:TSN504 4.5 17.0 1.0 N A:GLY361 4.5 13.4 1.0 N A:GLY362 4.6 19.5 1.0 CE1 A:HIS192 4.6 9.8 1.0 C A:GLY361 4.7 14.3 1.0 H121 A:TSN504 4.7 18.9 1.0 C11 A:TSN504 4.7 14.1 1.0 C A:VAL231 4.8 11.0 1.0 C A:ASP230 4.8 9.4 1.0 CA A:ASP230 4.9 10.9 1.0 NE2 A:HIS193 4.9 11.4 1.0 CA A:VAL231 4.9 10.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F 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) Y363F Mutant Complexed with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:10.9 occ:1.00 OD2 B:ASP323 2.0 10.3 1.0 OD1 B:ASP230 2.0 8.8 1.0 HO1 B:TSN504 2.0 14.1 1.0 O1 B:TSN504 2.1 11.8 1.0 ND1 B:HIS232 2.1 11.6 1.0 O2 B:TSN504 2.3 13.2 1.0 N1 B:TSN504 2.7 13.2 1.0 CG B:ASP230 2.7 8.5 1.0 C13 B:TSN504 2.8 11.8 1.0 OD2 B:ASP230 2.8 9.0 1.0 CE1 B:HIS232 3.0 10.7 1.0 CG B:ASP323 3.0 10.9 1.0 CG B:HIS232 3.2 10.7 1.0 OD1 B:ASP323 3.4 10.7 1.0 HN1 B:TSN504 3.4 15.8 1.0 CB B:HIS232 3.6 10.6 1.0 N B:HIS232 3.9 9.4 1.0 O B:HOH684 4.0 12.6 1.0 CA B:GLY361 4.0 12.1 1.0 C12 B:TSN504 4.1 12.9 1.0 NE2 B:HIS232 4.1 10.6 1.0 CB B:ASP230 4.2 10.2 1.0 NE2 B:HIS192 4.2 10.6 1.0 CD2 B:HIS232 4.2 12.1 1.0 N B:VAL231 4.3 9.8 1.0 CB B:ASP323 4.3 10.3 1.0 CG1 B:VAL231 4.3 11.6 1.0 CA B:HIS232 4.4 10.3 1.0 H111 B:TSN504 4.4 14.2 1.0 N B:GLY361 4.5 10.3 1.0 CE1 B:HIS192 4.6 10.2 1.0 N B:GLY362 4.7 11.9 1.0 H121 B:TSN504 4.7 15.5 1.0 C11 B:TSN504 4.7 11.9 1.0 C B:GLY361 4.7 10.6 1.0 C B:VAL231 4.8 9.2 1.0 C B:ASP230 4.8 8.3 1.0 NE2 B:HIS193 4.9 11.6 1.0 CA B:ASP230 4.9 9.0 1.0 CA B:VAL231 4.9 9.8 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