Zinc in PDB 6dvn: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137, PDB code: 6dvn was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.57 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.550, 95.500, 98.250, 90.00, 98.60, 90.00
R / Rfree (%)	18.8 / 22.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 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-137 (pdb code 6dvn). 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-137, PDB code: 6dvn:
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-137


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-137 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:21.2 occ:1.00 O04 A:HB7804 2.0 30.8 1.0 OD1 A:ASP612 2.1 15.5 1.0 OD2 A:ASP705 2.1 16.7 1.0 ND1 A:HIS614 2.2 11.7 1.0 O A:HOH903 2.3 18.8 1.0 N03 A:HB7804 2.5 17.5 1.0 OD2 A:ASP612 2.7 14.7 1.0 CG A:ASP612 2.7 15.6 1.0 CE1 A:HIS614 3.1 16.3 1.0 CG A:ASP705 3.2 20.6 1.0 CG A:HIS614 3.2 15.2 1.0 C02 A:HB7804 3.5 20.4 1.0 CB A:HIS614 3.5 12.7 1.0 OD1 A:ASP705 3.6 20.7 1.0 O01 A:HB7804 3.8 26.7 1.0 N A:HIS614 3.8 12.5 1.0 CG1 A:VAL613 4.2 13.9 1.0 CB A:ASP612 4.2 13.5 1.0 NE2 A:HIS573 4.2 17.1 1.0 NE2 A:HIS614 4.2 19.5 1.0 CA A:HIS614 4.3 14.7 1.0 CD2 A:HIS614 4.3 17.8 1.0 N A:VAL613 4.3 15.6 1.0 CB A:ASP705 4.4 12.7 1.0 NE2 A:HIS574 4.4 18.8 1.0 CE1 A:HIS573 4.5 17.8 1.0 CA A:GLY743 4.6 19.1 1.0 C05 A:HB7804 4.6 17.9 1.0 C A:VAL613 4.7 14.5 1.0 OH A:TYR745 4.8 21.4 1.0 C A:ASP612 4.9 13.0 1.0 CE2 A:TYR745 4.9 22.8 1.0 N A:GLY743 4.9 20.8 1.0 CA A:VAL613 4.9 13.6 1.0 CA A:ASP612 5.0 12.7 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-137


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-137 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:19.6 occ:1.00 O04 B:HB7804 2.0 33.4 1.0 OD1 B:ASP612 2.0 12.4 1.0 OD2 B:ASP705 2.1 25.6 1.0 ND1 B:HIS614 2.2 16.6 1.0 O B:HOH901 2.3 15.3 1.0 N03 B:HB7804 2.6 25.6 1.0 OD2 B:ASP612 2.7 13.7 1.0 CG B:ASP612 2.7 14.7 1.0 CE1 B:HIS614 3.1 16.3 1.0 CG B:ASP705 3.1 18.0 1.0 CG B:HIS614 3.2 17.2 1.0 CB B:HIS614 3.5 10.0 1.0 OD1 B:ASP705 3.5 14.6 1.0 C02 B:HB7804 3.6 26.3 1.0 N B:HIS614 3.8 11.0 1.0 O01 B:HB7804 3.8 28.2 1.0 CG1 B:VAL613 4.1 11.7 1.0 CB B:ASP612 4.2 14.4 1.0 NE2 B:HIS573 4.2 15.9 1.0 NE2 B:HIS614 4.2 17.9 1.0 N B:VAL613 4.3 8.2 1.0 CA B:HIS614 4.3 12.9 1.0 CD2 B:HIS614 4.3 17.1 1.0 CB B:ASP705 4.3 15.6 1.0 CE1 B:HIS573 4.5 14.4 1.0 NE2 B:HIS574 4.5 14.2 1.0 CA B:GLY743 4.6 18.3 1.0 C05 B:HB7804 4.7 22.3 1.0 C B:VAL613 4.7 11.9 1.0 OH B:TYR745 4.7 24.2 1.0 C B:ASP612 4.8 8.9 1.0 CA B:VAL613 4.9 9.5 1.0 N B:GLY743 4.9 18.7 1.0 CA B:ASP612 4.9 9.8 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-137


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-137 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:19.9 occ:1.00 O04 C:HB7804 2.0 36.5 1.0 OD2 C:ASP705 2.1 19.6 1.0 O C:HOH904 2.1 13.4 1.0 OD1 C:ASP612 2.2 15.8 1.0 ND1 C:HIS614 2.3 15.1 1.0 OD2 C:ASP612 2.7 20.1 1.0 N03 C:HB7804 2.7 21.3 1.0 CG C:ASP612 2.7 20.5 1.0 CG C:ASP705 3.2 24.3 1.0 CG C:HIS614 3.2 17.6 1.0 CE1 C:HIS614 3.3 16.2 1.0 CB C:HIS614 3.4 12.9 1.0 C02 C:HB7804 3.5 22.3 1.0 OD1 C:ASP705 3.7 19.3 1.0 O01 C:HB7804 3.7 31.6 1.0 N C:HIS614 3.8 13.5 1.0 NE2 C:HIS573 4.2 18.4 1.0 CG1 C:VAL613 4.2 14.6 1.0 CB C:ASP612 4.2 15.9 1.0 CA C:HIS614 4.2 14.4 1.0 CA C:GLY743 4.3 17.4 1.0 N C:VAL613 4.4 15.1 1.0 CD2 C:HIS614 4.4 19.2 1.0 CE1 C:HIS573 4.4 18.8 1.0 NE2 C:HIS614 4.4 22.5 1.0 CB C:ASP705 4.5 16.2 1.0 NE2 C:HIS574 4.5 21.0 1.0 C05 C:HB7804 4.7 21.5 1.0 N C:GLY743 4.7 20.2 1.0 C C:VAL613 4.8 13.3 1.0 OH C:TYR745 4.9 25.3 1.0 CE2 C:TYR745 4.9 23.6 1.0 C C:ASP612 4.9 16.5 1.0 CA C:VAL613 5.0 14.3 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-137


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-137 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:20.2 occ:1.00 O04 D:HB7804 2.0 38.8 1.0 OD1 D:ASP612 2.0 17.5 1.0 OD2 D:ASP705 2.0 20.1 1.0 ND1 D:HIS614 2.2 15.8 1.0 O D:HOH902 2.3 17.3 1.0 N03 D:HB7804 2.6 28.8 1.0 CG D:ASP612 2.7 15.3 1.0 OD2 D:ASP612 2.7 14.3 1.0 CE1 D:HIS614 3.1 18.2 1.0 CG D:ASP705 3.1 19.4 1.0 CG D:HIS614 3.2 16.2 1.0 OD1 D:ASP705 3.5 16.4 1.0 CB D:HIS614 3.6 13.4 1.0 C02 D:HB7804 3.6 26.6 1.0 N D:HIS614 3.8 12.2 1.0 O01 D:HB7804 3.9 25.7 1.0 CG1 D:VAL613 4.1 15.1 1.0 CB D:ASP612 4.2 13.0 1.0 NE2 D:HIS614 4.2 17.3 1.0 NE2 D:HIS573 4.2 13.4 1.0 CA D:GLY743 4.3 20.2 1.0 N D:VAL613 4.3 14.1 1.0 CD2 D:HIS614 4.3 16.9 1.0 CA D:HIS614 4.3 13.4 1.0 CB D:ASP705 4.3 14.5 1.0 CE1 D:HIS573 4.5 15.9 1.0 NE2 D:HIS574 4.6 16.1 1.0 OH D:TYR745 4.6 23.3 1.0 C05 D:HB7804 4.7 20.9 1.0 C D:VAL613 4.7 17.4 1.0 N D:GLY743 4.8 25.5 1.0 C D:ASP612 4.8 13.5 1.0 CE2 D:TYR745 4.9 18.0 1.0 CA D:VAL613 4.9 14.2 1.0 CA D:ASP612 4.9 10.0 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