Zinc in PDB 6dvm: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122, PDB code: 6dvm 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)	56.42 / 1.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.450, 95.180, 98.030, 90.00, 98.87, 90.00
R / Rfree (%)	14.8 / 17

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 (pdb code 6dvm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122, PDB code: 6dvm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


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 Ddk-122 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:9.1 occ:1.00 O19 A:HBJ804 1.9 32.9 1.0 OD2 A:ASP705 2.0 9.1 1.0 OD1 A:ASP612 2.0 7.1 1.0 O A:HOH901 2.1 14.9 1.0 ND1 A:HIS614 2.1 7.8 1.0 N18 A:HBJ804 2.4 11.9 1.0 CG A:ASP612 2.7 8.0 1.0 OD2 A:ASP612 2.7 9.1 1.0 CG A:ASP705 3.0 7.8 1.0 CE1 A:HIS614 3.0 8.2 1.0 CG A:HIS614 3.2 8.0 1.0 OD1 A:ASP705 3.4 8.6 1.0 C16 A:HBJ804 3.4 18.8 1.0 CB A:HIS614 3.6 7.2 1.0 O17 A:HBJ804 3.8 23.1 1.0 N A:HIS614 3.9 6.9 1.0 NE2 A:HIS573 4.1 10.1 1.0 NE2 A:HIS614 4.2 8.1 1.0 CB A:ASP612 4.2 8.2 1.0 CG1 A:VAL613 4.3 8.7 1.0 CD2 A:HIS614 4.3 10.3 1.0 CB A:ASP705 4.3 8.7 1.0 CA A:GLY743 4.3 8.7 1.0 N A:VAL613 4.4 6.0 1.0 CA A:HIS614 4.4 5.2 1.0 OH A:TYR745 4.5 14.7 1.0 NE2 A:HIS574 4.5 8.7 1.0 C15 A:HBJ804 4.6 11.1 1.0 CE1 A:HIS573 4.6 7.7 1.0 N A:GLY743 4.7 10.9 1.0 CE2 A:TYR745 4.7 10.3 1.0 C A:ASP612 4.9 8.0 1.0 C A:VAL613 4.9 6.2 1.0 CA A:ASP612 4.9 5.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


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 Ddk-122 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:7.8 occ:1.00 O19 B:HBJ804 1.8 20.7 0.8 OD2 B:ASP705 2.0 6.7 1.0 OD1 B:ASP612 2.0 6.5 1.0 ND1 B:HIS614 2.1 6.0 1.0 O B:HOH901 2.2 13.9 0.8 O19 B:HBJ804 2.3 12.5 0.2 N18 B:HBJ804 2.3 8.7 0.8 O17 B:HBJ804 2.5 12.7 0.2 CG B:ASP612 2.7 7.0 1.0 OD2 B:ASP612 2.7 5.8 1.0 N18 B:HBJ804 2.8 9.8 0.2 C16 B:HBJ804 2.9 11.6 0.2 CE1 B:HIS614 3.0 6.7 1.0 CG B:ASP705 3.0 6.7 1.0 CG B:HIS614 3.2 6.0 1.0 OD1 B:ASP705 3.3 7.4 1.0 C16 B:HBJ804 3.5 13.6 0.8 CB B:HIS614 3.6 6.0 1.0 O17 B:HBJ804 3.9 13.3 0.8 N B:HIS614 4.0 4.6 1.0 NE2 B:HIS614 4.2 6.4 1.0 NE2 B:HIS573 4.2 8.9 1.0 CB B:ASP612 4.2 6.2 1.0 C15 B:HBJ804 4.2 9.6 0.2 CD2 B:HIS614 4.3 6.7 1.0 CA B:GLY743 4.3 8.9 1.0 CB B:ASP705 4.3 6.7 1.0 CG1 B:VAL613 4.3 7.1 1.0 N B:VAL613 4.4 4.6 1.0 CA B:HIS614 4.4 5.3 1.0 OH B:TYR745 4.5 14.9 1.0 NE2 B:HIS574 4.5 7.6 1.0 CE1 B:HIS573 4.6 6.4 1.0 C15 B:HBJ804 4.6 9.0 0.8 N B:GLY743 4.7 8.6 1.0 CE2 B:TYR745 4.7 10.4 1.0 C20 B:HBJ804 4.8 9.6 0.2 C B:ASP612 4.9 4.4 1.0 C B:VAL613 4.9 6.3 1.0 CA B:ASP612 5.0 4.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:7.5 occ:1.00 O19 C:HBJ804 1.8 31.3 1.0 OD2 C:ASP705 2.0 6.3 1.0 O C:HOH904 2.0 12.6 1.0 ND1 C:HIS614 2.1 7.3 1.0 OD1 C:ASP612 2.1 6.4 1.0 N18 C:HBJ804 2.4 10.6 1.0 CG C:ASP612 2.7 5.5 1.0 OD2 C:ASP612 2.7 6.9 1.0 CE1 C:HIS614 2.9 8.0 1.0 CG C:ASP705 3.0 6.0 1.0 CG C:HIS614 3.2 8.0 1.0 C16 C:HBJ804 3.4 19.6 1.0 OD1 C:ASP705 3.4 7.1 1.0 CB C:HIS614 3.6 5.1 1.0 O17 C:HBJ804 3.7 21.4 1.0 N C:HIS614 3.9 6.5 1.0 NE2 C:HIS614 4.1 8.1 1.0 NE2 C:HIS573 4.1 8.0 1.0 CB C:ASP612 4.2 5.0 1.0 CD2 C:HIS614 4.2 6.3 1.0 CG1 C:VAL613 4.3 6.7 1.0 CB C:ASP705 4.3 7.0 1.0 CA C:GLY743 4.4 8.0 1.0 N C:VAL613 4.4 4.7 1.0 CA C:HIS614 4.4 4.7 1.0 NE2 C:HIS574 4.5 7.3 1.0 C15 C:HBJ804 4.5 10.6 1.0 OH C:TYR745 4.5 13.3 1.0 CE1 C:HIS573 4.6 5.9 1.0 N C:GLY743 4.7 8.0 1.0 CE2 C:TYR745 4.7 7.6 1.0 C C:VAL613 4.9 5.8 1.0 C C:ASP612 4.9 5.8 1.0 CA C:ASP612 4.9 4.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:7.7 occ:1.00 O19 D:HBJ804 1.8 32.2 1.0 OD2 D:ASP705 2.0 7.7 1.0 O D:HOH906 2.0 11.8 1.0 OD1 D:ASP612 2.1 6.2 1.0 ND1 D:HIS614 2.1 8.2 1.0 N18 D:HBJ804 2.4 10.1 1.0 CG D:ASP612 2.8 5.7 1.0 OD2 D:ASP612 2.8 6.7 1.0 CE1 D:HIS614 3.0 7.9 1.0 CG D:ASP705 3.0 6.2 1.0 CG D:HIS614 3.2 5.7 1.0 C16 D:HBJ804 3.4 16.1 1.0 OD1 D:ASP705 3.4 8.2 1.0 CB D:HIS614 3.6 4.8 1.0 O17 D:HBJ804 3.7 21.4 1.0 N D:HIS614 3.9 5.3 1.0 NE2 D:HIS573 4.1 8.3 1.0 NE2 D:HIS614 4.2 7.9 1.0 CB D:ASP612 4.2 5.2 1.0 CG1 D:VAL613 4.2 7.1 1.0 CD2 D:HIS614 4.3 6.7 1.0 CB D:ASP705 4.3 6.1 1.0 N D:VAL613 4.4 4.0 1.0 CA D:GLY743 4.4 8.7 1.0 CA D:HIS614 4.4 5.0 1.0 C15 D:HBJ804 4.5 12.5 1.0 NE2 D:HIS574 4.5 7.2 1.0 OH D:TYR745 4.6 13.6 1.0 CE1 D:HIS573 4.6 6.4 1.0 N D:GLY743 4.7 8.6 1.0 CE2 D:TYR745 4.7 8.0 1.0 C D:VAL613 4.9 7.0 1.0 C D:ASP612 4.9 4.0 1.0 CA D:ASP612 4.9 5.4 1.0

N.J.Porter, J.D.Osko, D.Diedrich, T.Kurz, J.M.Hooker, F.K.Hansen, D.W.Christianson. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. V. 61 8054 2018.
ISSN: ISSN 1520-4804
PubMed: 30118224
DOI: 10.1021/ACS.JMEDCHEM.8B01013