Zinc in PDB 6wyp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne, PDB code: 6wyp 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)	54.25 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.029, 95.170, 119.710, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne 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) K330L Mutant Complexed with Saha-Bpyne (pdb code 6wyp). 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) K330L Mutant Complexed with Saha-Bpyne, PDB code: 6wyp:

Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne


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) K330L Mutant Complexed with Saha-Bpyne within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:33.9 occ:1.00 OD2 A:ASP323 2.0 30.7 1.0 O35 A:UFS504 2.1 38.7 0.6 OD1 A:ASP230 2.1 35.2 1.0 O35 A:UFS504 2.1 38.6 0.4 ND1 A:HIS232 2.2 33.5 1.0 O01 A:UFS504 2.2 35.7 0.4 O01 A:UFS504 2.3 35.7 0.6 C02 A:UFS504 2.8 35.9 0.4 OD2 A:ASP230 2.8 30.8 1.0 CG A:ASP230 2.8 32.6 1.0 N34 A:UFS504 2.8 33.7 0.6 C02 A:UFS504 2.8 35.8 0.6 N34 A:UFS504 2.8 33.8 0.4 CE1 A:HIS232 3.0 35.5 1.0 CG A:HIS232 3.2 32.7 1.0 CG A:ASP323 3.2 33.4 1.0 CB A:HIS232 3.5 29.2 1.0 OD1 A:ASP323 3.7 32.6 1.0 N A:HIS232 3.9 29.4 1.0 CA A:GLY361 4.0 30.4 1.0 NE2 A:HIS232 4.2 34.2 1.0 C03 A:UFS504 4.2 34.4 0.4 C03 A:UFS504 4.2 34.4 0.6 CG1 A:VAL231 4.2 30.2 1.0 CD2 A:HIS232 4.2 31.8 1.0 CB A:ASP230 4.2 26.7 1.0 CA A:HIS232 4.3 34.9 1.0 CB A:ASP323 4.4 32.0 1.0 N A:VAL231 4.4 34.5 1.0 NE2 A:HIS192 4.4 33.6 1.0 N A:GLY361 4.5 30.6 1.0 OH A:TYR363 4.6 32.3 1.0 CE2 A:TYR363 4.6 36.3 1.0 CE1 A:HIS192 4.6 31.8 1.0 C04 A:UFS504 4.6 34.2 0.4 C04 A:UFS504 4.7 34.1 0.6 C A:VAL231 4.8 30.7 1.0 NE2 A:HIS193 4.9 37.1 1.0 CA A:VAL231 5.0 28.1 1.0 C A:GLY361 5.0 30.9 1.0

J.D.Osko, D.W.Christianson. Binding of Inhibitors to Active-Site Mutants of CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Acta Crystallogr.,Sect.F V. 76 428 2020.
ISSN: ESSN 2053-230X
PubMed: 32880591
DOI: 10.1107/S2053230X20010250