Zinc in PDB 6uob: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat, PDB code: 6uob 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)	56.45 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.270, 102.620, 112.900, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.8

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat 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) K330L Mutant Complexed with Resminostat (pdb code 6uob). 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) K330L Mutant Complexed with Resminostat, PDB code: 6uob:
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) K330L Mutant Complexed with Resminostat


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) K330L Mutant Complexed with Resminostat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:15.2 occ:1.00 O23 A:P7D505 1.8 28.5 0.5 O23 A:P7D505 1.9 28.6 0.5 OD2 A:ASP323 2.0 14.6 1.0 OD1 A:ASP230 2.0 11.5 1.0 ND1 A:HIS232 2.1 14.6 1.0 H20 A:P7D505 2.5 34.2 0.5 H20 A:P7D505 2.5 34.3 0.5 O21 A:P7D505 2.5 28.2 0.5 N22 A:P7D505 2.6 30.8 0.5 O21 A:P7D505 2.6 28.2 0.5 N22 A:P7D505 2.6 30.8 0.5 CG A:ASP230 2.7 12.7 1.0 OD2 A:ASP230 2.8 13.4 1.0 CE1 A:HIS232 2.9 14.7 1.0 C20 A:P7D505 3.0 26.7 0.5 CG A:ASP323 3.0 13.5 1.0 C20 A:P7D505 3.0 26.7 0.5 CG A:HIS232 3.1 10.5 1.0 H19 A:P7D505 3.3 37.0 0.5 H19 A:P7D505 3.3 37.0 0.5 OD1 A:ASP323 3.3 13.9 1.0 CB A:HIS232 3.6 11.4 1.0 N A:HIS232 3.8 9.7 1.0 NE2 A:HIS232 4.1 16.6 1.0 H16 A:P7D505 4.1 35.1 0.5 H16 A:P7D505 4.2 34.8 0.5 CB A:ASP230 4.2 11.4 1.0 CG1 A:VAL231 4.2 13.4 1.0 CD2 A:HIS232 4.2 17.0 1.0 NE2 A:HIS192 4.2 11.7 1.0 CA A:GLY361 4.2 12.4 1.0 C19 A:P7D505 4.3 23.2 0.5 C19 A:P7D505 4.3 23.2 0.5 N A:VAL231 4.3 10.6 1.0 CA A:HIS232 4.3 12.1 1.0 CB A:ASP323 4.4 15.7 1.0 OH A:TYR363 4.5 25.7 1.0 CE2 A:TYR363 4.6 18.3 1.0 CE1 A:HIS192 4.6 14.2 1.0 N A:GLY361 4.6 13.4 1.0 C18 A:P7D505 4.7 29.2 0.5 C18 A:P7D505 4.7 29.0 0.5 NE2 A:HIS193 4.7 14.1 1.0 C A:VAL231 4.8 12.1 1.0 C A:ASP230 4.9 9.7 1.0 CA A:ASP230 4.9 10.8 1.0 CA A:VAL231 5.0 11.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat


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) K330L Mutant Complexed with Resminostat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:13.9 occ:1.00 H20 B:P7D504 1.6 37.1 1.0 OD2 B:ASP323 2.0 11.2 1.0 O23 B:P7D504 2.0 30.9 1.0 OD1 B:ASP230 2.0 11.5 1.0 ND1 B:HIS232 2.1 11.3 1.0 O21 B:P7D504 2.2 22.9 1.0 N22 B:P7D504 2.6 33.5 1.0 CG B:ASP230 2.7 11.8 1.0 OD2 B:ASP230 2.7 11.7 1.0 C20 B:P7D504 2.8 26.9 1.0 CE1 B:HIS232 3.0 12.8 1.0 CG B:ASP323 3.0 11.5 1.0 CG B:HIS232 3.2 11.2 1.0 H19 B:P7D504 3.3 40.3 1.0 OD1 B:ASP323 3.3 13.6 1.0 CB B:HIS232 3.6 10.3 1.0 H16 B:P7D504 3.6 27.3 1.0 N B:HIS232 3.9 11.3 1.0 C19 B:P7D504 4.0 20.5 1.0 NE2 B:HIS232 4.1 12.7 1.0 CB B:ASP230 4.2 9.1 1.0 CA B:GLY361 4.2 10.3 1.0 C18 B:P7D504 4.2 22.8 1.0 CD2 B:HIS232 4.3 11.9 1.0 NE2 B:HIS192 4.3 14.3 1.0 CG1 B:VAL231 4.3 14.5 1.0 N B:VAL231 4.3 11.0 1.0 CB B:ASP323 4.3 10.2 1.0 CA B:HIS232 4.4 9.8 1.0 N B:GLY361 4.6 12.1 1.0 CE2 B:TYR363 4.6 14.7 1.0 NE2 B:HIS193 4.7 14.8 1.0 CE1 B:HIS192 4.7 16.4 1.0 OH B:TYR363 4.8 22.8 1.0 H17 B:P7D504 4.8 24.6 1.0 C B:VAL231 4.8 10.3 1.0 C B:ASP230 4.9 11.1 1.0 CA B:ASP230 5.0 11.0 1.0 C B:GLY361 5.0 14.3 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