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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp 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)	48.28 / 1.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.700, 91.830, 96.549, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate (pdb code 6csp). 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 Cyclohexenylhydroxamate, PDB code: 6csp:
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 Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:5.9 occ:1.00 H13 A:FBM807 1.8 8.5 1.0 OD2 A:ASP705 1.9 5.8 1.0 O04 A:FBM807 2.0 7.1 1.0 OD1 A:ASP612 2.1 4.5 1.0 ND1 A:HIS614 2.1 5.2 1.0 O01 A:FBM807 2.2 10.1 1.0 N03 A:FBM807 2.7 9.7 1.0 C02 A:FBM807 2.7 10.0 1.0 CG A:ASP612 2.8 5.0 1.0 OD2 A:ASP612 2.8 5.3 1.0 CE1 A:HIS614 2.9 5.1 1.0 CG A:ASP705 3.0 4.5 1.0 HE1 A:HIS614 3.1 6.1 1.0 HB2 A:HIS614 3.1 5.8 1.0 CG A:HIS614 3.2 4.2 1.0 H A:HIS614 3.3 5.4 1.0 HA3 A:GLY743 3.4 5.4 1.0 OD1 A:ASP705 3.4 5.2 1.0 H12 A:FBM807 3.4 11.6 1.0 HG12 A:VAL613 3.4 5.5 1.0 HE2 A:HIS573 3.4 6.9 1.0 HH A:TYR745 3.6 9.6 1.0 CB A:HIS614 3.6 4.8 1.0 HE2 A:TYR745 3.8 7.1 1.0 N A:HIS614 4.0 4.5 1.0 H A:VAL613 4.0 4.9 1.0 NE2 A:HIS614 4.1 6.5 1.0 C05 A:FBM807 4.1 9.4 1.0 NE2 A:HIS573 4.2 5.7 1.0 H A:GLY743 4.2 5.3 1.0 CB A:ASP612 4.2 4.2 1.0 HE1 A:HIS573 4.2 6.6 1.0 CD2 A:HIS614 4.2 5.7 1.0 H1 A:FBM807 4.2 12.1 1.0 CB A:ASP705 4.3 4.8 1.0 CA A:GLY743 4.3 4.5 1.0 CG1 A:VAL613 4.3 4.6 1.0 HG13 A:VAL613 4.4 5.5 1.0 HB3 A:HIS614 4.4 5.8 1.0 N A:VAL613 4.4 4.1 1.0 OH A:TYR745 4.4 8.0 1.0 CA A:HIS614 4.4 4.2 1.0 HB2 A:ASP705 4.4 5.8 1.0 HB3 A:ASP705 4.5 5.8 1.0 HB3 A:ASP612 4.5 5.0 1.0 H A:GLY744 4.6 6.9 1.0 CE1 A:HIS573 4.6 5.5 1.0 CE2 A:TYR745 4.6 5.9 1.0 O A:HOH1173 4.6 16.2 1.0 N A:GLY743 4.7 4.5 1.0 C10 A:FBM807 4.7 10.1 1.0 NE2 A:HIS574 4.7 6.0 1.0 H2 A:FBM807 4.8 12.1 1.0 HB2 A:ASP612 4.8 5.0 1.0 HG11 A:VAL613 4.8 5.5 1.0 HA2 A:GLY743 4.8 5.4 1.0 HE2 A:HIS614 4.9 7.8 1.0 HA A:ASP612 4.9 4.9 1.0 C A:ASP612 4.9 4.0 1.0 HA3 A:GLY703 4.9 4.8 1.0 C A:VAL613 4.9 4.5 1.0 CA A:ASP612 4.9 4.0 1.0 CZ A:TYR745 5.0 6.3 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 Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:6.0 occ:1.00 H13 B:FBM805 1.8 9.3 1.0 OD2 B:ASP705 2.0 5.8 1.0 O04 B:FBM805 2.0 7.7 1.0 OD1 B:ASP612 2.1 4.3 1.0 ND1 B:HIS614 2.1 5.2 1.0 O01 B:FBM805 2.2 10.3 1.0 N03 B:FBM805 2.7 9.4 1.0 CG B:ASP612 2.8 4.0 1.0 C02 B:FBM805 2.8 9.4 1.0 OD2 B:ASP612 2.8 4.9 1.0 CE1 B:HIS614 3.0 6.3 1.0 CG B:ASP705 3.0 5.2 1.0 HE1 B:HIS614 3.1 7.5 1.0 HB2 B:HIS614 3.1 5.5 1.0 CG B:HIS614 3.2 4.3 1.0 H B:HIS614 3.3 5.3 1.0 HA3 B:GLY743 3.4 5.1 1.0 OD1 B:ASP705 3.4 5.7 1.0 HG12 B:VAL613 3.4 7.3 1.0 HE2 B:HIS573 3.4 6.5 1.0 H12 B:FBM805 3.4 11.3 1.0 HH B:TYR745 3.6 8.7 1.0 CB B:HIS614 3.6 4.6 1.0 HE2 B:TYR745 3.8 7.7 1.0 N B:HIS614 4.0 4.5 1.0 H B:VAL613 4.0 5.2 1.0 NE2 B:HIS614 4.1 6.6 1.0 C05 B:FBM805 4.1 8.8 1.0 NE2 B:HIS573 4.1 5.4 1.0 H B:GLY743 4.2 5.5 1.0 H1 B:FBM805 4.2 11.6 1.0 CB B:ASP612 4.2 3.9 1.0 HE1 B:HIS573 4.2 7.1 1.0 CD2 B:HIS614 4.2 5.7 1.0 CG1 B:VAL613 4.3 6.1 1.0 CA B:GLY743 4.3 4.3 1.0 CB B:ASP705 4.3 4.9 1.0 HG13 B:VAL613 4.3 7.3 1.0 HB3 B:HIS614 4.4 5.5 1.0 OH B:TYR745 4.4 7.2 1.0 N B:VAL613 4.4 4.4 1.0 CA B:HIS614 4.4 4.6 1.0 HB2 B:ASP705 4.5 5.8 1.0 HB3 B:ASP705 4.5 5.8 1.0 HB3 B:ASP612 4.5 4.6 1.0 CE1 B:HIS573 4.6 5.9 1.0 H B:GLY744 4.6 6.5 1.0 CE2 B:TYR745 4.6 6.5 1.0 N B:GLY743 4.6 4.6 1.0 C10 B:FBM805 4.7 9.7 1.0 O B:HOH1206 4.7 18.0 1.0 NE2 B:HIS574 4.8 5.8 1.0 H2 B:FBM805 4.8 11.6 1.0 HB2 B:ASP612 4.8 4.6 1.0 HG11 B:VAL613 4.8 7.3 1.0 HA2 B:GLY743 4.8 5.1 1.0 HE2 B:HIS614 4.9 7.9 1.0 HA B:ASP612 4.9 4.8 1.0 C B:ASP612 4.9 4.4 1.0 C B:VAL613 4.9 4.7 1.0 HA3 B:GLY703 4.9 5.7 1.0 CA B:ASP612 4.9 4.0 1.0 CZ B:TYR745 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