Zinc in PDB 6wyq: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha, PDB code: 6wyq 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)	39.14 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.050, 123.790, 55.100, 90.00, 113.52, 90.00
R / Rfree (%)	17.6 / 22.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Iodine	(I)	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 4-Iodo-Saha (pdb code 6wyq). 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 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha, PDB code: 6wyq:
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 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha


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 4-Iodo-Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:12.9 occ:1.00 O20 A:UFJ504 1.9 12.1 1.0 OD2 A:ASP323 2.0 13.0 1.0 OD1 A:ASP230 2.1 7.2 1.0 ND1 A:HIS232 2.1 8.5 1.0 O01 A:UFJ504 2.3 11.4 1.0 OD2 A:ASP230 2.6 7.1 1.0 CG A:ASP230 2.6 8.0 1.0 N19 A:UFJ504 2.8 11.7 1.0 C02 A:UFJ504 2.8 12.1 1.0 CE1 A:HIS232 3.0 8.5 1.0 CG A:ASP323 3.1 11.0 1.0 CG A:HIS232 3.2 11.4 1.0 OD1 A:ASP323 3.5 16.9 1.0 CB A:HIS232 3.6 8.9 1.0 N A:HIS232 3.8 7.3 1.0 CA A:GLY361 4.0 9.0 1.0 CB A:ASP230 4.1 6.0 1.0 NE2 A:HIS232 4.1 9.1 1.0 N A:VAL231 4.2 7.6 1.0 CG1 A:VAL231 4.2 12.6 1.0 CD2 A:HIS232 4.3 10.7 1.0 C03 A:UFJ504 4.3 11.3 1.0 NE2 A:HIS192 4.3 5.2 1.0 CB A:ASP323 4.3 7.4 1.0 CA A:HIS232 4.3 7.1 1.0 N A:GLY361 4.4 7.2 1.0 CE2 A:TYR363 4.5 10.5 1.0 CE1 A:HIS192 4.7 8.7 1.0 OH A:TYR363 4.7 11.9 1.0 C A:VAL231 4.7 6.6 1.0 C04 A:UFJ504 4.8 12.3 1.0 C A:GLY361 4.8 9.9 1.0 C A:ASP230 4.8 8.6 1.0 CA A:VAL231 4.9 7.6 1.0 CA A:ASP230 4.9 6.0 1.0 N A:GLY362 5.0 9.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha


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 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:12.6 occ:1.00 O20 B:UFJ504 1.8 19.3 1.0 OD1 B:ASP230 2.1 9.9 1.0 OD2 B:ASP323 2.1 8.7 1.0 ND1 B:HIS232 2.2 8.1 1.0 O01 B:UFJ504 2.2 8.7 1.0 OD2 B:ASP230 2.6 7.2 1.0 N19 B:UFJ504 2.6 9.1 1.0 CG B:ASP230 2.7 7.8 1.0 C02 B:UFJ504 2.7 10.3 1.0 CE1 B:HIS232 3.0 12.8 1.0 CG B:ASP323 3.1 8.6 1.0 CG B:HIS232 3.2 9.7 1.0 OD1 B:ASP323 3.5 9.9 1.0 CB B:HIS232 3.6 6.9 1.0 N B:HIS232 3.9 7.9 1.0 CA B:GLY361 4.0 7.1 1.0 C03 B:UFJ504 4.1 10.0 1.0 CB B:ASP230 4.2 6.6 1.0 NE2 B:HIS232 4.2 12.7 1.0 CG1 B:VAL231 4.2 8.8 1.0 CD2 B:HIS232 4.3 7.9 1.0 NE2 B:HIS192 4.3 8.4 1.0 N B:VAL231 4.3 6.6 1.0 CA B:HIS232 4.4 9.7 1.0 CB B:ASP323 4.4 8.8 1.0 N B:GLY361 4.4 6.1 1.0 CE2 B:TYR363 4.5 10.9 1.0 C04 B:UFJ504 4.5 11.1 1.0 OH B:TYR363 4.5 10.9 1.0 CE1 B:HIS192 4.7 9.1 1.0 C B:GLY361 4.8 9.5 1.0 C B:VAL231 4.8 8.7 1.0 N B:GLY362 4.9 9.4 1.0 C B:ASP230 4.9 6.5 1.0 CA B:ASP230 4.9 7.4 1.0 CA B:VAL231 5.0 6.8 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