Potassium in PDB 5g0h: Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A, PDB code: 5g0h was solved by Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.43 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.980, 48.230, 73.780, 90.00, 103.22, 90.00
R / Rfree (%)	15.02 / 17.41

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A (pdb code 5g0h). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A, PDB code: 5g0h:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A


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 HDAC6 CD2 in Complex with ( S)-Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:K1802 b:14.3 occ:1.00 O A:ASP612 2.5 11.7 1.0 O A:LEU634 2.7 13.4 1.0 O A:HIS614 2.7 12.5 1.0 OD1 A:ASP610 2.7 14.2 1.0 OG A:SER633 2.7 13.7 1.0 O A:ASP610 2.8 12.2 1.0 CG A:ASP610 3.3 14.0 1.0 C A:ASP610 3.5 14.1 1.0 C A:ASP612 3.6 12.4 1.0 C A:HIS614 3.7 15.1 1.0 C A:LEU634 3.7 14.4 1.0 N A:ASP612 3.8 10.5 1.0 CB A:ASP610 3.9 12.7 1.0 N A:LEU634 3.9 12.5 1.0 CB A:HIS635 3.9 11.1 1.0 CB A:SER633 3.9 11.8 1.0 OD2 A:ASP610 4.0 15.6 1.0 CA A:ASP612 4.2 10.0 1.0 CB A:ASP612 4.2 10.9 1.0 N A:TRP611 4.2 12.4 1.0 C A:TRP611 4.2 13.0 1.0 CA A:ASP610 4.3 11.2 1.0 CA A:HIS615 4.3 13.0 1.0 CA A:SER633 4.3 12.1 1.0 ND1 A:HIS635 4.3 15.2 1.0 CA A:TRP611 4.4 12.4 1.0 N A:HIS614 4.4 10.4 1.0 N A:HIS615 4.4 13.0 1.0 CA A:HIS635 4.5 11.3 1.0 O A:HOH2187 4.5 14.2 1.0 C A:SER633 4.5 14.9 1.0 CA A:LEU634 4.5 12.2 1.0 N A:GLY616 4.5 13.5 1.0 N A:HIS635 4.6 12.5 1.0 CG A:HIS635 4.6 13.6 1.0 C A:VAL613 4.6 13.1 1.0 CA A:HIS614 4.7 12.9 1.0 N A:VAL613 4.7 12.2 1.0 OH A:TYR631 4.7 13.4 1.0 CE1 A:HIS573 4.8 15.7 1.0 C A:HIS615 4.8 15.4 1.0 ND1 A:HIS573 4.9 15.7 1.0 O A:TRP611 5.0 11.3 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with ( S)-Trichostatin A


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 HDAC6 CD2 in Complex with ( S)-Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:K1803 b:14.7 occ:1.00 O A:PHE623 2.6 13.9 1.0 O A:VAL629 2.6 14.8 1.0 O A:HOH2199 2.7 13.3 1.0 O A:TYR662 2.8 14.1 1.0 O A:ASP626 2.9 18.0 1.0 O A:HOH2195 3.0 15.5 1.0 C A:PHE623 3.5 15.5 1.0 C A:TYR662 3.6 14.9 1.0 CB A:TYR662 3.6 13.2 1.0 CB A:PHE623 3.7 15.7 1.0 C A:VAL629 3.9 15.7 1.0 C A:ASP626 4.0 19.6 1.0 CA A:TYR662 4.2 13.1 1.0 CA A:PHE623 4.3 14.0 1.0 N A:TYR631 4.3 12.9 1.0 N A:GLU624 4.4 15.2 1.0 N A:ASN663 4.4 12.8 1.0 N A:ASP626 4.5 19.0 1.0 CA A:LEU630 4.5 12.0 1.0 CA A:ASP626 4.6 17.6 1.0 CA A:GLU624 4.6 14.8 1.0 CB A:ASP626 4.6 19.0 1.0 N A:LEU630 4.6 12.2 1.0 O A:GLU624 4.6 16.3 1.0 C A:GLU624 4.7 17.0 1.0 CB A:TYR631 4.7 12.7 1.0 CB A:ASN663 4.8 12.6 1.0 CA A:ASN663 4.8 13.2 1.0 C A:LEU630 4.9 15.5 1.0 O A:GLY659 4.9 16.8 1.0 CA A:VAL629 4.9 11.4 1.0 CG A:TYR662 4.9 15.4 1.0 CG A:PHE623 5.0 15.2 1.0

Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias. Structural Insights Into HDAC6 Tubulin Deacetylation and Its Selective Inhibition Nat.Chem.Biol. V. 12 748 2016.
ISSN: ISSN 1552-4450
PubMed: 27454931
DOI: 10.1038/NCHEMBIO.2140