Potassium in PDB 6csp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp 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)	48.28 / 1.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.700, 91.830, 96.549, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.3

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

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate (pdb code 6csp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:4.9 occ:1.00 O A:ASP612 2.6 4.4 1.0 O A:LEU634 2.7 4.3 1.0 O A:HIS614 2.7 4.1 1.0 OD1 A:ASP610 2.8 4.0 1.0 OG A:SER633 2.8 4.8 1.0 HG A:SER633 2.8 5.7 1.0 O A:ASP610 2.8 4.4 1.0 HB3 A:HIS635 3.0 5.5 1.0 CG A:ASP610 3.3 3.8 1.0 HB3 A:ASP612 3.5 5.0 1.0 HA A:HIS615 3.5 4.9 1.0 C A:ASP610 3.5 3.7 1.0 HB3 A:ASP610 3.5 4.6 1.0 H A:LEU634 3.6 5.1 1.0 C A:HIS614 3.6 4.3 1.0 C A:ASP612 3.6 4.0 1.0 C A:LEU634 3.7 4.1 1.0 H A:ASP612 3.8 4.7 1.0 CB A:ASP610 3.8 3.8 1.0 N A:ASP612 3.9 3.9 1.0 HA A:SER633 3.9 5.0 1.0 OD2 A:ASP610 3.9 4.5 1.0 HA A:TRP611 3.9 5.5 1.0 H A:GLY616 3.9 5.3 1.0 N A:LEU634 4.0 4.2 1.0 CB A:HIS635 4.0 4.6 1.0 CB A:SER633 4.0 5.0 1.0 HE1 A:HIS573 4.1 6.6 1.0 CA A:ASP612 4.2 4.0 1.0 N A:TRP611 4.2 3.7 1.0 HA A:HIS635 4.2 5.9 1.0 CA A:HIS615 4.2 4.1 1.0 C A:TRP611 4.2 3.8 1.0 CB A:ASP612 4.3 4.2 1.0 HB2 A:SER633 4.3 6.0 1.0 N A:HIS615 4.3 4.0 1.0 CA A:ASP610 4.3 3.9 1.0 ND1 A:HIS635 4.3 5.2 1.0 CA A:SER633 4.3 4.2 1.0 CA A:TRP611 4.3 4.6 1.0 HD1 A:HIS573 4.4 5.4 1.0 N A:HIS614 4.4 4.5 1.0 N A:GLY616 4.4 4.5 1.0 H A:HIS614 4.5 5.4 1.0 HH A:TYR631 4.5 6.2 1.0 CA A:HIS635 4.5 4.9 1.0 C A:SER633 4.5 4.2 1.0 CA A:LEU634 4.5 4.1 1.0 HB2 A:HIS635 4.6 5.5 1.0 N A:HIS635 4.6 4.1 1.0 O A:HOH965 4.6 6.7 1.0 CG A:HIS635 4.6 5.2 1.0 C A:VAL613 4.6 4.5 1.0 CA A:HIS614 4.7 4.2 1.0 C A:HIS615 4.7 4.2 1.0 OH A:TYR631 4.7 5.2 1.0 HB3 A:SER633 4.7 6.0 1.0 N A:VAL613 4.7 4.1 1.0 HB2 A:ASP610 4.7 4.6 1.0 CE1 A:HIS573 4.8 5.5 1.0 HB2 A:ASP612 4.8 5.0 1.0 HA A:ASP610 4.8 4.6 1.0 H A:TRP611 4.9 4.4 1.0 ND1 A:HIS573 4.9 4.5 1.0 HA A:VAL613 4.9 5.2 1.0 O A:TRP611 4.9 4.2 1.0 HB2 A:LEU634 5.0 6.3 1.0 H A:HIS615 5.0 4.8 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:K803 b:6.8 occ:1.00 O A:VAL629 2.7 7.0 1.0 O A:PHE623 2.7 5.5 1.0 O A:HOH1044 2.7 6.7 1.0 O A:TYR662 2.8 5.6 1.0 O A:ASP626 2.9 8.9 1.0 O A:HOH1067 3.0 6.0 1.0 HB3 A:PHE623 3.1 6.8 1.0 HB3 A:TYR662 3.1 7.7 1.0 HB2 A:TYR662 3.4 7.7 1.0 C A:TYR662 3.6 5.2 1.0 HB2 A:PHE623 3.6 6.8 1.0 C A:PHE623 3.6 4.7 1.0 CB A:TYR662 3.7 6.4 1.0 H A:TYR631 3.7 5.0 1.0 CB A:PHE623 3.7 5.7 1.0 H A:ASP626 3.7 8.7 1.0 HA A:LEU630 3.8 6.8 1.0 HB3 A:ASP626 3.9 10.3 1.0 C A:VAL629 3.9 5.8 1.0 HA A:GLU624 4.0 6.9 1.0 HB2 A:ASN663 4.0 7.0 1.0 C A:ASP626 4.0 7.8 1.0 CA A:TYR662 4.2 6.0 1.0 HB3 A:TYR631 4.3 6.7 1.0 CA A:PHE623 4.3 5.6 1.0 N A:TYR631 4.3 4.2 1.0 HB2 A:TYR631 4.4 6.7 1.0 N A:ASN663 4.4 5.7 1.0 HB A:VAL629 4.4 7.0 1.0 HA A:ASN663 4.4 6.2 1.0 N A:ASP626 4.5 7.3 1.0 N A:GLU624 4.5 5.3 1.0 CA A:LEU630 4.6 5.7 1.0 H A:VAL629 4.6 6.5 1.0 CA A:GLU624 4.6 5.8 1.0 HA3 A:GLY659 4.6 7.9 1.0 CA A:ASP626 4.6 7.8 1.0 C A:GLU624 4.7 6.6 1.0 N A:LEU630 4.7 5.2 1.0 CB A:ASP626 4.7 8.6 1.0 O A:GLU624 4.7 6.5 1.0 HA A:ASP627 4.7 9.3 1.0 CB A:TYR631 4.7 5.6 1.0 HA A:PHE623 4.8 6.7 1.0 CA A:ASN663 4.8 5.2 1.0 CB A:ASN663 4.8 5.9 1.0 HA A:TYR662 4.8 7.2 1.0 HA2 A:GLY659 4.9 7.9 1.0 C A:LEU630 4.9 5.5 1.0 HG12 A:VAL629 4.9 8.0 1.0 O A:GLY659 4.9 6.8 1.0 CA A:VAL629 4.9 5.5 1.0 CG A:PHE623 5.0 5.4 1.0 CG A:TYR662 5.0 7.3 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:K802 b:5.7 occ:1.00 O B:ASP612 2.6 4.6 1.0 O B:LEU634 2.7 5.8 1.0 O B:HIS614 2.7 4.8 1.0 OD1 B:ASP610 2.7 4.4 1.0 OG B:SER633 2.8 5.3 1.0 HG B:SER633 2.8 6.3 1.0 O B:ASP610 2.8 4.8 1.0 HB3 B:HIS635 3.1 6.6 1.0 CG B:ASP610 3.3 4.4 1.0 HB3 B:ASP612 3.5 4.6 1.0 C B:ASP610 3.5 4.5 1.0 HA B:HIS615 3.5 5.2 1.0 HB3 B:ASP610 3.5 5.4 1.0 H B:LEU634 3.6 6.3 1.0 C B:ASP612 3.6 4.4 1.0 C B:HIS614 3.7 4.7 1.0 C B:LEU634 3.7 5.0 1.0 CB B:ASP610 3.8 4.5 1.0 N B:ASP612 3.9 4.5 1.0 H B:ASP612 3.9 5.4 1.0 HA B:SER633 3.9 5.7 1.0 H B:GLY616 3.9 5.4 1.0 OD2 B:ASP610 3.9 4.8 1.0 HA B:TRP611 3.9 6.0 1.0 N B:LEU634 4.0 5.3 1.0 CB B:SER633 4.0 5.4 1.0 CB B:HIS635 4.0 5.5 1.0 HE1 B:HIS573 4.1 7.1 1.0 CA B:ASP612 4.1 4.0 1.0 N B:TRP611 4.2 4.3 1.0 C B:TRP611 4.2 4.2 1.0 HA B:HIS635 4.2 6.3 1.0 HB2 B:SER633 4.2 6.4 1.0 CA B:HIS615 4.2 4.3 1.0 CB B:ASP612 4.3 3.9 1.0 CA B:ASP610 4.3 4.2 1.0 N B:HIS615 4.3 4.8 1.0 ND1 B:HIS635 4.3 5.9 1.0 CA B:SER633 4.3 4.8 1.0 CA B:TRP611 4.3 5.0 1.0 HD1 B:HIS573 4.4 6.3 1.0 N B:HIS614 4.4 4.5 1.0 H B:HIS614 4.4 5.3 1.0 HH B:TYR631 4.5 6.0 1.0 N B:GLY616 4.5 4.5 1.0 CA B:HIS635 4.5 5.3 1.0 C B:SER633 4.5 5.5 1.0 CA B:LEU634 4.5 5.3 1.0 N B:HIS635 4.6 5.1 1.0 O B:HOH935 4.6 7.1 1.0 HB2 B:HIS635 4.6 6.6 1.0 CG B:HIS635 4.6 5.4 1.0 C B:VAL613 4.7 4.7 1.0 OH B:TYR631 4.7 5.0 1.0 CA B:HIS614 4.7 4.6 1.0 HB3 B:SER633 4.7 6.4 1.0 C B:HIS615 4.7 4.5 1.0 N B:VAL613 4.7 4.4 1.0 HB2 B:ASP610 4.7 5.4 1.0 CE1 B:HIS573 4.8 5.9 1.0 HA B:ASP610 4.8 5.1 1.0 HB2 B:ASP612 4.8 4.6 1.0 H B:TRP611 4.9 5.1 1.0 ND1 B:HIS573 4.9 5.2 1.0 HA B:VAL613 4.9 6.4 1.0 O B:TRP611 4.9 5.0 1.0 HB2 B:LEU634 5.0 7.9 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:K803 b:7.3 occ:1.00 O B:VAL629 2.7 8.0 1.0 O B:PHE623 2.7 6.1 1.0 O B:HOH1051 2.7 6.0 1.0 O B:TYR662 2.8 6.9 1.0 O B:ASP626 2.9 8.2 0.5 O B:ASP626 2.9 8.5 0.5 O B:HOH1088 3.0 6.7 1.0 HB3 B:PHE623 3.1 6.5 1.0 HB3 B:TYR662 3.2 9.1 1.0 HB2 B:TYR662 3.4 9.1 1.0 HB2 B:PHE623 3.6 6.5 1.0 C B:TYR662 3.6 6.5 1.0 C B:PHE623 3.6 5.4 1.0 CB B:TYR662 3.7 7.6 1.0 HB3 B:ASP626 3.7 12.6 0.5 H B:TYR631 3.7 5.9 1.0 CB B:PHE623 3.7 5.4 1.0 H B:ASP626 3.7 9.0 0.5 H B:ASP626 3.8 9.6 0.5 HA B:LEU630 3.8 7.4 1.0 C B:VAL629 3.9 6.5 1.0 HB3 B:ASP626 4.0 9.0 0.5 HA B:GLU624 4.0 7.7 1.0 C B:ASP626 4.0 8.0 0.5 C B:ASP626 4.0 7.4 0.5 HB2 B:ASN663 4.1 7.8 1.0 CA B:TYR662 4.2 7.0 1.0 HB3 B:TYR631 4.3 6.3 1.0 CA B:PHE623 4.3 6.0 1.0 N B:TYR631 4.3 4.9 1.0 HB2 B:TYR631 4.4 6.3 1.0 HB B:VAL629 4.4 7.5 1.0 N B:ASN663 4.4 6.2 1.0 HA B:ASN663 4.5 7.1 1.0 N B:ASP626 4.5 7.5 0.5 N B:ASP626 4.5 8.0 0.5 CB B:ASP626 4.5 10.5 0.5 N B:GLU624 4.5 5.5 1.0 H B:VAL629 4.6 7.6 1.0 CA B:LEU630 4.6 6.1 1.0 CA B:GLU624 4.6 6.4 1.0 HA3 B:GLY659 4.6 8.4 1.0 CA B:ASP626 4.6 8.6 0.5 CA B:ASP626 4.7 7.1 0.5 N B:LEU630 4.7 6.2 1.0 HA B:ASP627 4.7 11.2 1.0 C B:GLU624 4.7 6.6 1.0 O B:GLU624 4.7 6.4 1.0 HA B:PHE623 4.7 7.2 1.0 CB B:ASP626 4.7 7.5 0.5 CB B:TYR631 4.8 5.2 1.0 CA B:ASN663 4.8 6.0 1.0 CB B:ASN663 4.8 6.5 1.0 HG12 B:VAL629 4.9 8.0 1.0 HA B:TYR662 4.9 8.4 1.0 C B:LEU630 4.9 5.5 1.0 O B:GLY659 4.9 7.6 1.0 HA2 B:GLY659 4.9 8.4 1.0 HB2 B:ASP626 4.9 12.6 0.5 CA B:VAL629 4.9 6.3 1.0 CG B:PHE623 5.0 5.3 1.0 CG B:TYR662 5.0 8.5 1.0

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367