Zinc in PDB 8eqi: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0, PDB code: 8eqi 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)	78.89 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.45, 92.03, 153.2, 90, 90, 90
R / Rfree (%)	23.6 / 27.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0 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 Complexed with Cyclopeptide DES4.2.0 (pdb code 8eqi). 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 Cyclopeptide DES4.2.0, PDB code: 8eqi:
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 Cyclopeptide DES4.2.0


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 Cyclopeptide DES4.2.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:9.5 occ:1.00 OD2 A:ASP705 1.9 7.7 1.0 OD1 A:ASP612 2.0 9.4 1.0 ND1 A:HIS614 2.1 7.3 1.0 SH F:U2M1 2.2 8.4 1.0 CG A:ASP612 2.7 8.3 1.0 OD2 A:ASP612 2.8 6.5 1.0 CG A:ASP705 3.0 7.7 1.0 CE1 A:HIS614 3.1 8.2 1.0 CG A:HIS614 3.2 10.1 1.0 CZ F:U2M1 3.4 7.9 1.0 OD1 A:ASP705 3.5 6.0 1.0 CB A:HIS614 3.5 10.7 1.0 CE F:U2M1 3.6 7.9 1.0 N A:HIS614 3.9 9.2 1.0 NE2 A:HIS573 4.0 8.7 1.0 CB A:ASP612 4.2 6.8 1.0 NE2 A:HIS614 4.2 6.9 1.0 CD2 A:HIS614 4.3 6.6 1.0 CB A:ASP705 4.3 8.0 1.0 CA A:GLY743 4.3 7.7 1.0 CE1 A:HIS573 4.3 6.8 1.0 CA A:HIS614 4.4 8.5 1.0 N A:VAL613 4.4 10.5 1.0 CE2 A:TYR745 4.4 8.2 1.0 CG1 A:VAL613 4.4 6.6 1.0 OH A:TYR745 4.4 7.8 1.0 NE2 A:HIS574 4.5 10.6 1.0 N A:GLY743 4.7 7.2 1.0 C A:ASP612 4.9 7.8 1.0 C A:VAL613 4.9 9.2 1.0 CA A:ASP612 4.9 7.6 1.0 CZ A:TYR745 4.9 8.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0


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 Cyclopeptide DES4.2.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:9.4 occ:1.00 OD2 B:ASP705 1.9 8.0 1.0 OD1 B:ASP612 2.0 10.2 1.0 ND1 B:HIS614 2.1 9.8 1.0 SH G:U2M1 2.2 11.8 1.0 CG B:ASP612 2.8 10.1 1.0 OD2 B:ASP612 2.9 7.9 1.0 CG B:ASP705 3.0 8.8 1.0 CE1 B:HIS614 3.0 10.5 1.0 CG B:HIS614 3.1 11.3 1.0 OD1 B:ASP705 3.5 6.6 1.0 CB B:HIS614 3.5 9.0 1.0 CZ G:U2M1 3.5 11.5 1.0 CE G:U2M1 3.7 12.5 1.0 N B:HIS614 3.9 9.5 1.0 NE2 B:HIS573 4.1 9.7 1.0 NE2 B:HIS614 4.2 9.5 1.0 CB B:ASP612 4.2 9.3 1.0 CD2 B:HIS614 4.2 11.1 1.0 CB B:ASP705 4.3 7.8 1.0 CA B:GLY743 4.3 9.7 1.0 CE2 B:TYR745 4.3 9.1 1.0 CA B:HIS614 4.3 9.7 1.0 N B:VAL613 4.4 11.0 1.0 CE1 B:HIS573 4.4 8.9 1.0 CG1 B:VAL613 4.4 8.1 1.0 NE2 B:HIS574 4.5 12.5 1.0 OH B:TYR745 4.5 8.4 1.0 N B:GLY743 4.7 8.0 1.0 C B:VAL613 4.9 10.4 1.0 C B:ASP612 4.9 9.7 1.0 CZ B:TYR745 4.9 9.1 1.0 CA B:ASP612 4.9 8.5 1.0

P.R.Watson, S.Gupta, P.Hosseinzadeh, B.P.Brown, D.Baker, D.W.Christianson. Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37027789
DOI: 10.1021/ACSCHEMBIO.3C00113