Iodine 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
Zinc	(Zn)	2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 2 binding sites of Iodine 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 Iodine binding site number: 1; 2;

Iodine 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 Iodine with other atoms in the I 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:I504 b:61.6 occ:1.00 I15 A:UFJ504 0.0 61.6 1.0 C14 A:UFJ504 2.1 26.2 1.0 C13 A:UFJ504 3.0 24.3 1.0 C16 A:UFJ504 3.0 19.6 1.0 OD2 A:ASP79 3.2 31.6 1.0 O B:ASP257 3.5 18.8 1.0 CB B:ASP257 3.8 15.0 1.0 CD A:PRO83 3.8 18.9 1.0 O A:SER81 4.0 28.7 1.0 CA A:HIS82 4.2 18.6 1.0 C12 A:UFJ504 4.3 22.0 1.0 C17 A:UFJ504 4.3 21.9 1.0 CG A:ASP79 4.4 24.5 1.0 C B:ASP257 4.4 13.4 1.0 C A:SER81 4.5 19.8 1.0 N A:HIS82 4.6 18.8 1.0 N A:PRO83 4.7 15.7 1.0 CA B:ASP257 4.7 12.4 1.0 CG B:ASP257 4.8 18.3 1.0 C11 A:UFJ504 4.8 20.0 1.0 CG A:PRO83 4.9 15.9 1.0 OD1 A:ASP79 4.9 24.9 1.0 CD2 A:HIS82 4.9 20.5 1.0 C A:HIS82 4.9 15.1 1.0

Iodine 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 Iodine with other atoms in the I 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:I504 b:44.7 occ:1.00 I15 B:UFJ504 0.0 44.7 1.0 C14 B:UFJ504 2.0 20.6 1.0 C13 B:UFJ504 2.9 18.5 1.0 C16 B:UFJ504 3.0 18.2 1.0 CB A:ASP257 3.9 20.5 1.0 CD B:PRO83 4.0 18.9 1.0 CG B:PRO83 4.1 18.9 1.0 O A:HOH701 4.2 17.6 1.0 C12 B:UFJ504 4.2 19.8 1.0 C17 B:UFJ504 4.3 16.9 1.0 CB B:PRO83 4.3 17.6 1.0 O A:ASP257 4.4 17.0 1.0 O A:GLU256 4.5 13.4 1.0 O B:HOH737 4.6 22.5 1.0 O B:SER81 4.6 24.8 1.0 CD1 B:LEU330 4.7 19.4 1.0 OD2 A:ASP257 4.7 34.1 1.0 C11 B:UFJ504 4.8 16.1 1.0 CG A:ASP257 4.8 25.9 1.0 C A:ASP257 4.8 17.0 1.0 N B:PRO83 4.8 17.6 1.0 CA A:ASP257 5.0 16.3 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