Potassium in PDB 5wgi: Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa

The structure of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa, PDB code: 5wgi 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)	47.04 / 1.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.439, 69.639, 50.193, 90.00, 110.42, 90.00
R / Rfree (%)	10.6 / 12.6

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

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa within 5.0Å range: probe atom residue distance (Å) B Occ A:K803 b:5.7 occ:1.00 O A:ASP612 2.6 5.9 1.0 O A:LEU634 2.6 5.6 1.0 O A:HIS614 2.7 5.8 1.0 OD1 A:ASP610 2.7 6.8 1.0 OG A:SER633 2.7 6.2 1.0 HG A:SER633 2.8 7.4 1.0 O A:ASP610 2.8 5.5 1.0 HB3 A:HIS635 3.0 6.1 1.0 CG A:ASP610 3.3 6.2 1.0 C A:ASP610 3.5 4.9 1.0 HB3 A:ASP612 3.5 6.8 1.0 HB3 A:ASP610 3.5 6.8 1.0 HA A:HIS615 3.5 6.2 1.0 H A:LEU634 3.6 6.4 1.0 C A:ASP612 3.6 5.0 1.0 C A:HIS614 3.7 5.2 1.0 C A:LEU634 3.7 5.4 1.0 CB A:ASP610 3.8 5.7 1.0 H A:ASP612 3.8 7.0 1.0 N A:ASP612 3.9 5.8 1.0 HA A:SER633 3.9 7.0 1.0 HA A:TRP611 3.9 6.0 1.0 N A:LEU634 3.9 5.3 1.0 OD2 A:ASP610 3.9 6.7 1.0 CB A:HIS635 4.0 5.1 1.0 CB A:SER633 4.0 5.9 1.0 HE1 A:HIS573 4.0 8.3 1.0 H A:GLY616 4.0 6.1 1.0 CA A:ASP612 4.1 5.5 1.0 HA A:HIS635 4.2 6.6 1.0 N A:TRP611 4.2 4.9 1.0 C A:TRP611 4.2 5.8 1.0 HB2 A:SER633 4.2 7.0 1.0 CA A:ASP610 4.3 5.2 1.0 CB A:ASP612 4.3 5.7 1.0 CA A:HIS615 4.3 5.2 1.0 ND1 A:HIS635 4.3 5.9 1.0 N A:HIS615 4.3 5.2 1.0 CA A:SER633 4.3 5.8 1.0 CA A:TRP611 4.4 5.0 1.0 HD1 A:HIS573 4.4 7.7 1.0 N A:HIS614 4.4 5.3 1.0 H A:HIS614 4.4 6.4 1.0 CA A:HIS635 4.4 5.5 1.0 CA A:LEU634 4.5 5.7 1.0 HH A:TYR631 4.5 7.6 1.0 N A:HIS635 4.5 5.4 1.0 N A:GLY616 4.5 5.1 1.0 C A:SER633 4.5 5.3 1.0 O A:HOH943 4.5 7.0 1.0 HB2 A:HIS635 4.6 6.1 1.0 CG A:HIS635 4.6 5.6 1.0 C A:VAL613 4.6 5.5 1.0 HB3 A:SER633 4.7 7.0 1.0 CA A:HIS614 4.7 4.8 1.0 N A:VAL613 4.7 5.1 1.0 CE1 A:HIS573 4.7 6.9 1.0 HB2 A:ASP610 4.7 6.8 1.0 OH A:TYR631 4.7 6.3 1.0 C A:HIS615 4.8 5.4 1.0 HA A:ASP610 4.8 6.3 1.0 H A:TRP611 4.9 5.9 1.0 HB2 A:ASP612 4.9 6.8 1.0 HA A:VAL613 4.9 6.2 1.0 ND1 A:HIS573 4.9 6.4 1.0 O A:TRP611 4.9 5.7 1.0 HB2 A:LEU634 4.9 7.9 1.0

Potassium binding site 2 out of 2 in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa within 5.0Å range: probe atom residue distance (Å) B Occ A:K804 b:6.8 occ:1.00 O A:VAL629 2.6 8.0 1.0 O A:HOH1036 2.7 7.7 1.0 O A:PHE623 2.7 6.8 1.0 O A:TYR662 2.8 6.5 1.0 O A:ASP626 2.9 11.2 1.0 O A:HOH1061 2.9 7.4 1.0 HB3 A:PHE623 3.0 7.6 1.0 HB3 A:TYR662 3.1 8.9 1.0 HB2 A:TYR662 3.3 8.9 1.0 C A:TYR662 3.6 6.2 1.0 HB2 A:PHE623 3.6 7.6 1.0 C A:PHE623 3.6 6.0 1.0 CB A:TYR662 3.6 7.4 1.0 H A:TYR631 3.7 6.9 1.0 CB A:PHE623 3.7 6.3 1.0 H A:ASP626 3.7 10.4 1.0 HB3 A:ASP626 3.8 12.5 1.0 HA A:LEU630 3.8 6.7 1.0 C A:VAL629 3.9 6.1 1.0 HA A:GLU624 4.0 8.4 0.5 C A:ASP626 4.0 9.6 1.0 HB2 A:ASN663 4.0 7.9 1.0 HA A:GLU624 4.1 9.3 0.6 CA A:TYR662 4.2 7.1 1.0 HB3 A:TYR631 4.3 7.0 1.0 CA A:PHE623 4.3 6.8 1.0 N A:TYR631 4.3 5.8 1.0 HB2 A:TYR631 4.4 7.0 1.0 N A:ASN663 4.4 6.5 1.0 HB A:VAL629 4.4 7.4 1.0 HA A:ASN663 4.4 7.0 1.0 N A:ASP626 4.4 8.6 1.0 CA A:LEU630 4.5 5.6 1.0 N A:GLU624 4.5 6.6 0.5 H A:VAL629 4.5 7.6 1.0 N A:GLU624 4.5 6.9 0.6 CA A:GLU624 4.6 7.0 0.5 CB A:ASP626 4.6 10.4 1.0 CA A:ASP626 4.6 9.4 1.0 CA A:GLU624 4.6 7.8 0.6 N A:LEU630 4.6 5.7 1.0 O A:GLU624 4.7 9.2 0.5 C A:GLU624 4.7 7.5 0.5 HA3 A:GLY659 4.7 13.0 1.0 C A:GLU624 4.7 7.4 0.6 HA A:PHE623 4.7 8.1 1.0 O A:GLU624 4.7 7.9 0.6 HA A:ASP627 4.7 12.4 1.0 CB A:TYR631 4.8 5.9 1.0 CA A:ASN663 4.8 5.9 1.0 CB A:ASN663 4.8 6.6 1.0 C A:LEU630 4.8 5.5 1.0 HA A:TYR662 4.8 8.5 1.0 HG12 A:VAL629 4.9 8.8 1.0 CA A:VAL629 4.9 6.0 1.0 O A:GLY659 4.9 8.9 1.0 HA2 A:GLY659 4.9 13.0 1.0 CG A:PHE623 4.9 5.9 1.0 CG A:TYR662 5.0 8.0 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