Potassium in PDB 5wgk: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb, PDB code: 5wgk was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 1.82
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.670, 83.970, 94.570, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb also contains other interesting chemical elements:

Iodine	(I)	12 atoms
Zinc	(Zn)	1 atom

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb (pdb code 5wgk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb, PDB code: 5wgk:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:K813 b:6.8 occ:1.00 O A:ASP612 2.6 6.0 1.0 O A:LEU634 2.7 6.1 1.0 O A:HIS614 2.7 4.9 1.0 OG A:SER633 2.8 7.4 1.0 O A:ASP610 2.8 4.5 1.0 OD1 A:ASP610 2.9 7.4 1.0 CG A:ASP610 3.3 5.8 1.0 C A:ASP610 3.5 6.3 1.0 C A:ASP612 3.6 5.2 1.0 C A:HIS614 3.7 4.2 1.0 C A:LEU634 3.7 4.2 1.0 CB A:ASP610 3.8 5.4 1.0 N A:ASP612 3.9 4.6 1.0 OD2 A:ASP610 3.9 7.3 1.0 N A:LEU634 3.9 6.9 1.0 CB A:HIS635 4.0 5.0 1.0 CB A:SER633 4.0 7.3 1.0 CA A:ASP612 4.1 4.2 1.0 C A:TRP611 4.2 4.8 1.0 N A:TRP611 4.2 7.4 1.0 CB A:ASP612 4.2 5.7 1.0 CA A:HIS615 4.3 3.2 1.0 CA A:ASP610 4.3 3.3 1.0 CA A:TRP611 4.3 5.4 1.0 CA A:SER633 4.3 3.7 1.0 N A:HIS615 4.4 4.6 1.0 ND1 A:HIS635 4.4 7.5 1.0 N A:HIS614 4.4 6.2 1.0 N A:GLY616 4.4 5.1 1.0 CA A:HIS635 4.4 4.3 1.0 O A:HOH952 4.5 6.5 1.0 C A:SER633 4.5 7.6 1.0 CA A:LEU634 4.5 3.2 1.0 N A:HIS635 4.5 4.5 1.0 CG A:HIS635 4.7 6.4 1.0 C A:VAL613 4.7 6.3 1.0 OH A:TYR631 4.7 6.4 1.0 CA A:HIS614 4.7 5.8 1.0 N A:VAL613 4.7 4.1 1.0 C A:HIS615 4.7 5.6 1.0 CE1 A:HIS573 4.8 5.9 1.0 O A:TRP611 4.9 5.7 1.0 ND1 A:HIS573 4.9 6.4 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:K814 b:11.6 occ:1.00 O A:PHE623 2.7 7.9 1.0 O A:HOH960 2.7 8.7 1.0 O A:VAL629 2.7 10.4 1.0 O A:TYR662 2.8 5.9 1.0 O A:ASP626 2.9 10.2 0.6 O A:HOH1066 2.9 7.1 1.0 O A:ASP626 3.0 12.1 0.4 C A:TYR662 3.5 6.2 1.0 CB A:TYR662 3.6 5.2 1.0 C A:PHE623 3.7 9.9 1.0 CB A:PHE623 3.8 6.2 1.0 C A:VAL629 3.9 7.0 1.0 C A:ASP626 4.0 11.2 0.6 C A:ASP626 4.1 11.1 0.4 CA A:TYR662 4.2 7.5 1.0 N A:TYR631 4.4 5.7 1.0 CA A:PHE623 4.4 9.4 1.0 N A:ASN663 4.4 5.9 1.0 CB A:ASP626 4.4 13.3 0.4 N A:ASP626 4.4 11.3 0.6 N A:ASP626 4.5 11.3 0.4 CA A:ASP626 4.6 10.6 0.4 CA A:LEU630 4.6 5.5 1.0 N A:GLU624 4.6 6.6 0.5 N A:GLU624 4.6 6.6 0.5 CA A:GLU624 4.6 8.4 0.5 CA A:ASP626 4.6 10.6 0.6 O A:GLU624 4.6 11.5 0.5 CA A:GLU624 4.6 8.4 0.5 CB A:ASP626 4.6 13.4 0.6 O A:GLU624 4.7 11.5 0.5 C A:GLU624 4.7 9.9 0.5 N A:LEU630 4.7 7.0 1.0 C A:GLU624 4.7 9.9 0.5 CA A:ASN663 4.7 7.8 1.0 CB A:ASN663 4.8 4.5 1.0 O A:GLY659 4.8 11.4 1.0 CB A:TYR631 4.8 4.0 1.0 C A:LEU630 4.9 5.5 1.0 CG A:TYR662 4.9 6.9 1.0 CA A:VAL629 5.0 8.5 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:K815 b:16.6 occ:1.00 OE1 A:GLU624 2.6 18.8 0.5 O A:HOH1141 3.3 14.3 1.0 CD A:GLU624 3.4 13.9 0.5 N A:GLY655 3.4 6.4 1.0 CG A:GLU624 3.6 7.0 0.5 CA A:GLY655 3.7 8.9 1.0 C A:GLY655 3.9 13.1 1.0 CB A:LYS653 3.9 6.8 1.0 CG A:LEU656 3.9 19.5 1.0 N A:VAL654 4.0 6.5 1.0 CA A:LYS653 4.0 7.0 1.0 C A:LYS653 4.0 9.8 1.0 O A:GLY655 4.1 13.3 1.0 CD2 A:LEU656 4.1 19.8 1.0 OE2 A:GLU624 4.5 12.2 0.5 N A:LEU656 4.5 10.7 1.0 CD1 A:LEU656 4.5 22.0 1.0 C A:VAL654 4.6 9.0 1.0 O A:LYS653 4.6 7.7 1.0 O A:HOH1085 4.6 21.5 1.0 NE2 A:GLN620 4.7 8.4 1.0 CG A:LYS653 4.9 12.2 1.0 CD A:LYS653 4.9 17.3 1.0 CA A:VAL654 4.9 7.7 1.0

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114