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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexylhydroxamate, PDB code: 6csq 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)	66.61 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.622, 91.961, 96.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.3

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


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 Cyclohexylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:6.6 occ:1.00 OD2 A:ASP705 2.0 4.2 1.0 O04 A:F9P804 2.1 4.2 1.0 OD1 A:ASP612 2.1 3.0 1.0 ND1 A:HIS614 2.2 6.5 1.0 O01 A:F9P804 2.2 4.5 1.0 CG A:ASP612 2.8 4.9 1.0 OD2 A:ASP612 2.8 6.0 1.0 N03 A:F9P804 2.8 5.6 1.0 C02 A:F9P804 2.8 6.5 1.0 CE1 A:HIS614 3.0 6.2 1.0 CG A:ASP705 3.1 5.1 1.0 CG A:HIS614 3.3 4.4 1.0 OD1 A:ASP705 3.5 3.5 1.0 CB A:HIS614 3.7 4.6 1.0 N A:HIS614 3.9 4.7 1.0 NE2 A:HIS614 4.2 5.4 1.0 CG1 A:VAL613 4.2 3.4 1.0 C05 A:F9P804 4.2 6.3 1.0 CB A:ASP612 4.2 3.8 1.0 NE2 A:HIS573 4.3 5.8 1.0 CA A:GLY743 4.3 5.3 1.0 CB A:ASP705 4.3 4.7 1.0 N A:VAL613 4.3 5.0 1.0 O A:HOH1015 4.3 15.5 1.0 CD2 A:HIS614 4.4 5.3 1.0 OH A:TYR745 4.4 3.9 1.0 CA A:HIS614 4.4 6.1 1.0 CE1 A:HIS573 4.5 4.3 1.0 CE2 A:TYR745 4.6 3.9 1.0 C06 A:F9P804 4.7 8.6 1.0 N A:GLY743 4.7 4.9 1.0 C A:ASP612 4.9 4.2 1.0 C A:VAL613 4.9 5.4 1.0 CA A:ASP612 4.9 3.7 1.0 N A:GLY744 5.0 4.4 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 Cyclohexylhydroxamate


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 Cyclohexylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:8.6 occ:1.00 OD2 B:ASP705 2.0 4.9 1.0 OD1 B:ASP612 2.0 5.5 1.0 O04 B:F9P804 2.0 6.4 1.0 O01 B:F9P804 2.1 7.3 1.0 ND1 B:HIS614 2.2 5.5 1.0 CG B:ASP612 2.7 5.2 1.0 C02 B:F9P804 2.8 7.4 1.0 OD2 B:ASP612 2.8 5.2 1.0 N03 B:F9P804 2.8 5.8 1.0 CG B:ASP705 3.0 7.5 1.0 CE1 B:HIS614 3.1 6.8 1.0 CG B:HIS614 3.2 7.7 1.0 OD1 B:ASP705 3.4 4.3 1.0 CB B:HIS614 3.5 7.4 1.0 N B:HIS614 3.9 4.8 1.0 CB B:ASP612 4.2 4.4 1.0 C05 B:F9P804 4.2 6.5 1.0 NE2 B:HIS573 4.2 8.2 1.0 NE2 B:HIS614 4.2 6.3 1.0 CG1 B:VAL613 4.3 3.9 1.0 CD2 B:HIS614 4.3 6.8 1.0 CA B:GLY743 4.3 4.8 1.0 CA B:HIS614 4.3 6.8 1.0 CB B:ASP705 4.3 5.0 1.0 N B:VAL613 4.3 6.2 1.0 OH B:TYR745 4.4 6.3 1.0 CE1 B:HIS573 4.4 6.2 1.0 CE2 B:TYR745 4.6 5.7 1.0 C06 B:F9P804 4.7 6.1 1.0 O B:HOH1129 4.7 15.1 1.0 N B:GLY743 4.7 4.2 1.0 C B:VAL613 4.8 6.8 1.0 C B:ASP612 4.8 5.2 1.0 CA B:ASP612 4.9 5.6 1.0 NE2 B:HIS574 4.9 7.3 1.0 CA B:VAL613 5.0 6.3 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