Zinc in PDB 6uo3: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42, PDB code: 6uo3 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)	43.09 / 1.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.750, 61.060, 121.650, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 19

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42 (pdb code 6uo3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42, PDB code: 6uo3:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Ar-42


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 1 (CD1) Complexed with Ar-42 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:6.9 occ:0.78 H231 A:QCP504 1.8 25.2 1.0 OD1 A:ASP230 2.0 7.8 1.0 OD2 A:ASP323 2.0 9.0 1.0 ND1 A:HIS232 2.1 7.9 1.0 O01 A:QCP504 2.2 12.9 1.0 O23 A:QCP504 2.2 21.0 1.0 N22 A:QCP504 2.6 20.0 1.0 C02 A:QCP504 2.6 18.4 1.0 CG A:ASP230 2.7 6.6 1.0 OD2 A:ASP230 2.7 8.8 1.0 CE1 A:HIS232 3.0 7.7 1.0 CG A:ASP323 3.0 8.4 1.0 CG A:HIS232 3.2 7.2 1.0 H221 A:QCP504 3.3 24.0 1.0 OD1 A:ASP323 3.4 8.2 1.0 CB A:HIS232 3.6 7.9 1.0 N A:HIS232 3.9 6.1 1.0 C03 A:QCP504 3.9 12.5 1.0 NE2 A:HIS232 4.1 8.0 1.0 CB A:ASP230 4.1 7.5 1.0 H211 A:QCP504 4.1 14.6 1.0 CA A:GLY361 4.2 7.5 1.0 CD2 A:HIS232 4.2 7.9 1.0 NE2 A:HIS192 4.3 9.5 1.0 CG1 A:VAL231 4.3 7.9 1.0 N A:VAL231 4.3 6.8 1.0 CA A:HIS232 4.4 7.1 1.0 CB A:ASP323 4.4 9.0 1.0 C21 A:QCP504 4.4 12.2 1.0 N A:GLY361 4.5 8.2 1.0 OH A:TYR363 4.6 11.7 1.0 CE2 A:TYR363 4.6 9.2 1.0 CE1 A:HIS192 4.6 9.2 1.0 C A:VAL231 4.8 5.9 1.0 NE2 A:HIS193 4.9 8.9 1.0 C A:ASP230 4.9 6.5 1.0 CA A:ASP230 4.9 6.8 1.0 C04 A:QCP504 4.9 12.2 1.0 CA A:VAL231 4.9 6.7 1.0 C A:GLY361 5.0 7.5 1.0

J.D.Osko, D.W.Christianson. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31755702
DOI: 10.1021/ACS.BIOCHEM.9B00934