Zinc in PDB 7jom: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317, PDB code: 7jom was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.43 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.46, 96.45, 96.45, 90, 90, 90
R / Rfree (%)	16.8 / 20.7

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Potassium	(K)	5 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 (pdb code 7jom). 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 Complexed with to-317, PDB code: 7jom:
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 Complexed with to-317


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 Complexed with to-317 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn907 b:8.9 occ:1.00 OD1 A:ASP612 2.0 5.7 1.0 OD2 A:ASP705 2.0 8.3 1.0 O A:HOH1034 2.1 20.8 1.0 ND1 A:HIS614 2.1 10.8 1.0 O04 A:TO3901 2.4 25.5 1.0 N03 A:TO3901 2.6 16.4 1.0 CG A:ASP612 2.7 5.8 1.0 OD2 A:ASP612 2.7 7.2 1.0 CE1 A:HIS614 3.0 9.4 1.0 CG A:ASP705 3.0 8.1 1.0 CG A:HIS614 3.2 7.2 1.0 OD1 A:ASP705 3.4 7.1 1.0 C02 A:TO3901 3.4 17.1 1.0 CB A:HIS614 3.7 6.0 1.0 O01 A:TO3901 3.9 26.2 1.0 N A:HIS614 4.0 4.7 1.0 NE2 A:HIS573 4.1 5.8 1.0 NE2 A:HIS614 4.1 6.0 1.0 CB A:ASP612 4.2 5.3 1.0 CG1 A:VAL613 4.3 4.9 1.0 CD2 A:HIS614 4.3 9.2 1.0 CA A:GLY743 4.3 7.1 1.0 CB A:ASP705 4.4 6.6 1.0 N A:VAL613 4.4 4.3 1.0 CA A:HIS614 4.4 4.8 1.0 C05 A:TO3901 4.5 11.6 1.0 CE1 A:HIS573 4.5 4.9 1.0 OH A:TYR745 4.7 16.5 1.0 N A:GLY743 4.7 7.0 1.0 NE2 A:HIS574 4.7 5.8 1.0 CE2 A:TYR745 4.8 10.4 1.0 C A:ASP612 4.9 4.9 1.0 C A:VAL613 4.9 5.5 1.0 CA A:ASP612 4.9 6.4 1.0 C06 A:TO3901 5.0 12.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317


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 Complexed with to-317 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn804 b:8.6 occ:1.00 O B:HOH930 2.0 15.5 1.0 OD2 B:ASP705 2.0 9.0 1.0 OD1 B:ASP612 2.1 5.5 1.0 ND1 B:HIS614 2.1 9.8 1.0 O04 B:TO3801 2.4 28.0 1.0 N03 B:TO3801 2.6 12.2 1.0 OD2 B:ASP612 2.7 7.9 1.0 CG B:ASP612 2.7 4.3 1.0 CE1 B:HIS614 3.0 8.0 1.0 CG B:ASP705 3.0 9.7 1.0 CG B:HIS614 3.2 6.7 1.0 C02 B:TO3801 3.3 14.4 1.0 OD1 B:ASP705 3.4 7.5 1.0 CB B:HIS614 3.6 5.8 1.0 O01 B:TO3801 3.8 23.9 1.0 N B:HIS614 4.0 5.2 1.0 NE2 B:HIS573 4.1 6.4 1.0 NE2 B:HIS614 4.2 6.8 1.0 CB B:ASP612 4.2 5.2 1.0 CD2 B:HIS614 4.3 6.2 1.0 CA B:GLY743 4.3 8.2 1.0 CG1 B:VAL613 4.3 6.3 1.0 CB B:ASP705 4.4 5.8 1.0 N B:VAL613 4.4 3.8 1.0 C05 B:TO3801 4.4 9.8 1.0 CA B:HIS614 4.4 5.6 1.0 CE1 B:HIS573 4.5 6.2 1.0 NE2 B:HIS574 4.6 6.4 1.0 N B:GLY743 4.7 8.4 1.0 CE2 B:TYR745 4.7 7.4 1.0 OH B:TYR745 4.8 12.5 1.0 C B:ASP612 4.9 7.3 1.0 C B:VAL613 4.9 8.0 1.0 C32 B:TO3801 4.9 10.5 1.0 CA B:ASP612 4.9 6.3 1.0

P.R.Watson, D.W.Christianson. Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 To Be Published.