Potassium in PDB 6cgp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032, PDB code: 6cgp 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)	38.08 / 2.50
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.310, 64.950, 140.499, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.6

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032 (pdb code 6cgp). 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 Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032, PDB code: 6cgp:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032


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 Complexed with Maip-032 within 5.0Å range: probe atom residue distance (Å) B Occ A:K801 b:21.4 occ:1.00 O A:ASP612 2.6 27.9 1.0 OG A:SER633 2.8 23.8 1.0 O A:ASP610 2.8 23.9 1.0 OD1 A:ASP610 2.8 33.1 1.0 O A:HIS614 2.9 25.4 1.0 O A:LEU634 2.9 31.9 1.0 CG A:ASP610 3.1 30.1 1.0 C A:ASP610 3.4 25.0 1.0 CB A:ASP610 3.6 31.4 1.0 OD2 A:ASP610 3.6 24.8 1.0 C A:ASP612 3.7 31.0 1.0 C A:LEU634 3.7 27.6 1.0 N A:ASP612 3.7 31.8 1.0 N A:LEU634 3.8 25.5 1.0 C A:HIS614 3.9 27.9 1.0 CB A:SER633 4.0 28.4 1.0 CA A:ASP610 4.1 24.2 1.0 CA A:ASP612 4.1 29.1 1.0 N A:TRP611 4.1 26.5 1.0 CB A:HIS635 4.1 26.7 1.0 C A:TRP611 4.2 24.9 1.0 CB A:ASP612 4.2 28.4 1.0 CA A:TRP611 4.3 24.1 1.0 CA A:SER633 4.3 25.9 1.0 CA A:HIS615 4.4 26.1 1.0 CA A:LEU634 4.4 26.4 1.0 ND1 A:HIS635 4.4 28.1 1.0 C A:SER633 4.5 22.3 1.0 N A:GLY616 4.5 26.4 1.0 N A:HIS615 4.6 25.7 1.0 CA A:HIS635 4.6 28.1 1.0 N A:HIS635 4.6 24.7 1.0 O A:HOH905 4.6 27.6 1.0 N A:HIS614 4.7 26.3 1.0 CG A:HIS635 4.8 29.4 1.0 C A:HIS615 4.8 29.9 1.0 N A:VAL613 4.8 30.8 1.0 OH A:TYR631 4.9 25.1 1.0 C A:VAL613 4.9 31.3 1.0 CA A:HIS614 4.9 29.9 1.0 CE1 A:HIS573 5.0 27.4 1.0 ND1 A:HIS573 5.0 24.7 1.0 O A:TRP611 5.0 25.6 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Maip-032


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 Complexed with Maip-032 within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:43.1 occ:1.00 O A:PHE623 2.7 44.3 1.0 O A:VAL629 2.7 42.5 1.0 O A:TYR662 2.9 35.8 1.0 O A:ASP626 2.9 48.0 1.0 O A:HOH914 2.9 39.5 1.0 O A:HOH902 3.0 40.2 1.0 CB A:TYR662 3.6 43.1 1.0 C A:TYR662 3.7 35.6 1.0 C A:PHE623 3.7 43.4 1.0 CB A:PHE623 3.7 38.4 1.0 C A:VAL629 3.9 46.5 1.0 C A:ASP626 4.0 50.6 1.0 N A:TYR631 4.2 29.2 1.0 CA A:TYR662 4.3 45.3 1.0 CA A:PHE623 4.4 38.9 1.0 CA A:LEU630 4.5 33.8 1.0 N A:ASN663 4.5 34.2 1.0 CB A:TYR631 4.5 30.5 1.0 N A:ASP626 4.6 51.2 1.0 N A:LEU630 4.7 42.1 1.0 CA A:ASP626 4.7 47.5 1.0 N A:GLU624 4.7 42.9 1.0 CB A:ASP626 4.7 45.7 1.0 O A:GLY659 4.7 45.6 1.0 O A:GLU624 4.7 52.7 1.0 CB A:ASN663 4.8 31.6 1.0 C A:LEU630 4.8 33.4 1.0 CA A:ASN663 4.8 36.4 1.0 CA A:GLU624 4.8 45.6 1.0 C A:GLU624 4.8 50.3 1.0 CG A:TYR662 4.9 44.6 1.0 CG A:PHE623 4.9 42.1 1.0 CA A:VAL629 5.0 40.9 1.0

M.K.W.Mackwitz, A.Hamacher, J.D.Osko, J.Held, A.Scholer, D.W.Christianson, M.U.Kassack, F.K.Hansen. Multicomponent Synthesis and Binding Mode of Imidazo[1,2- A]Pyridine-Capped Selective HDAC6 Inhibitors. Org. Lett. V. 20 3255 2018.
ISSN: ISSN 1523-7052
PubMed: 29790770
DOI: 10.1021/ACS.ORGLETT.8B01118