Zinc in PDB 6css: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclopentenylhydroxamate

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclopentenylhydroxamate, PDB code: 6css was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.32 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.791, 92.021, 96.640, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclopentenylhydroxamate 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 Cyclopentenylhydroxamate (pdb code 6css). 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 Cyclopentenylhydroxamate, PDB code: 6css:
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 Cyclopentenylhydroxamate


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 Cyclopentenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:4.8 occ:1.00 OD2 A:ASP705 2.0 5.8 1.0 O04 A:FBJ804 2.0 9.3 1.0 OD1 A:ASP612 2.0 3.2 1.0 ND1 A:HIS614 2.1 3.4 1.0 O01 A:FBJ804 2.5 21.4 1.0 N03 A:FBJ804 2.6 19.6 1.0 CG A:ASP612 2.7 4.0 1.0 OD2 A:ASP612 2.7 4.0 1.0 C02 A:FBJ804 2.8 20.6 1.0 CE1 A:HIS614 2.9 6.5 1.0 CG A:ASP705 3.0 3.6 1.0 CG A:HIS614 3.2 5.4 1.0 OD1 A:ASP705 3.4 5.1 1.0 CB A:HIS614 3.7 5.1 1.0 N A:HIS614 3.9 3.8 1.0 NE2 A:HIS614 4.1 4.6 1.0 CB A:ASP612 4.2 2.4 1.0 NE2 A:HIS573 4.2 6.0 1.0 CD2 A:HIS614 4.3 4.5 1.0 CG1 A:VAL613 4.3 3.2 1.0 CA A:GLY743 4.3 3.8 1.0 CB A:ASP705 4.3 2.0 1.0 N A:VAL613 4.3 3.2 1.0 C05 A:FBJ804 4.4 14.8 1.0 OH A:TYR745 4.4 12.8 1.0 CA A:HIS614 4.4 3.3 1.0 CE1 A:HIS573 4.5 3.9 1.0 CE2 A:TYR745 4.6 10.2 1.0 NE2 A:HIS574 4.6 5.6 1.0 N A:GLY743 4.7 4.4 1.0 C A:VAL613 4.8 4.6 1.0 C A:ASP612 4.8 3.5 1.0 C09 A:FBJ804 4.9 13.9 1.0 CA A:ASP612 4.9 1.2 1.0 CA A:VAL613 5.0 3.6 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 Cyclopentenylhydroxamate


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 Cyclopentenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:4.7 occ:1.00 OD1 B:ASP612 2.0 3.1 1.0 OD2 B:ASP705 2.0 5.1 1.0 O04 B:FBJ804 2.0 7.4 1.0 ND1 B:HIS614 2.1 3.2 1.0 O01 B:FBJ804 2.4 20.9 1.0 N03 B:FBJ804 2.6 16.0 1.0 CG B:ASP612 2.7 3.3 1.0 OD2 B:ASP612 2.7 3.9 1.0 C02 B:FBJ804 2.8 19.1 1.0 CE1 B:HIS614 3.0 5.8 1.0 CG B:ASP705 3.0 5.5 1.0 CG B:HIS614 3.2 5.1 1.0 OD1 B:ASP705 3.4 5.5 1.0 CB B:HIS614 3.6 5.2 1.0 N B:HIS614 3.9 2.5 1.0 NE2 B:HIS614 4.1 6.0 1.0 CB B:ASP612 4.1 3.2 1.0 NE2 B:HIS573 4.2 5.8 1.0 CD2 B:HIS614 4.3 5.0 1.0 CA B:GLY743 4.3 4.5 1.0 CG1 B:VAL613 4.3 3.7 1.0 N B:VAL613 4.3 2.8 1.0 CB B:ASP705 4.3 2.7 1.0 C05 B:FBJ804 4.3 11.8 1.0 CA B:HIS614 4.4 5.2 1.0 OH B:TYR745 4.4 11.6 1.0 CE1 B:HIS573 4.5 5.5 1.0 CE2 B:TYR745 4.6 8.1 1.0 NE2 B:HIS574 4.7 6.6 1.0 N B:GLY743 4.7 4.2 1.0 C B:VAL613 4.8 4.4 1.0 C B:ASP612 4.9 2.6 1.0 C09 B:FBJ804 4.9 14.7 1.0 CA B:ASP612 4.9 2.2 1.0 CZ B:TYR745 5.0 7.0 1.0

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367