Potassium in PDB 7uk2: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390, PDB code: 7uk2 was solved by F.Erdogan, H.-S.Seo, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.06 / 1.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.263, 83.135, 93.276, 90, 90, 90
R / Rfree (%)	19.9 / 22.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390 also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Fluorine	(F)	4 atoms

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390 (pdb code 7uk2). 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 Nn-390, PDB code: 7uk2:
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 Nn-390


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 Nn-390 within 5.0Å range: probe atom residue distance (Å) B Occ A:K803 b:62.5 occ:1.00 OD1 A:ASP610 2.5 7.3 1.0 OG A:SER633 2.5 9.6 1.0 O A:ASP610 2.6 8.4 1.0 O A:HIS614 2.7 7.8 1.0 O A:LEU634 2.7 9.9 1.0 O A:ASP612 2.7 5.0 1.0 CG A:ASP610 3.1 11.2 1.0 C A:ASP610 3.4 6.3 1.0 CB A:ASP610 3.7 4.7 1.0 CB A:SER633 3.7 10.0 1.0 C A:LEU634 3.7 6.5 1.0 C A:ASP612 3.7 9.3 1.0 C A:HIS614 3.8 7.9 1.0 OD2 A:ASP610 3.8 7.8 1.0 N A:ASP612 3.9 8.5 1.0 N A:LEU634 3.9 8.0 1.0 N A:TRP611 4.1 5.5 1.0 CA A:ASP610 4.1 5.0 1.0 CA A:SER633 4.1 10.6 1.0 CB A:HIS635 4.1 8.7 1.0 CA A:ASP612 4.2 9.9 1.0 C A:TRP611 4.3 7.5 1.0 CA A:HIS615 4.3 7.0 1.0 CA A:TRP611 4.3 6.4 1.0 CB A:ASP612 4.3 7.8 1.0 ND1 A:HIS635 4.3 8.1 1.0 N A:GLY616 4.3 8.0 1.0 C A:SER633 4.4 8.3 1.0 N A:HIS615 4.4 6.8 1.0 OH A:TYR631 4.5 6.7 1.0 CA A:LEU634 4.5 8.4 1.0 N A:HIS614 4.6 5.4 1.0 N A:HIS635 4.6 6.9 1.0 CA A:HIS635 4.6 7.0 1.0 CG A:HIS635 4.7 6.8 1.0 O A:HOH921 4.7 10.3 1.0 CE1 A:HIS573 4.7 10.4 1.0 C A:HIS615 4.7 8.5 1.0 ND1 A:HIS573 4.8 9.0 1.0 CA A:HIS614 4.8 9.6 1.0 N A:VAL613 4.9 7.2 1.0 C A:VAL613 4.9 12.0 1.0 O A:TRP611 5.0 8.9 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390


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 Nn-390 within 5.0Å range: probe atom residue distance (Å) B Occ A:K804 b:14.6 occ:1.00 O A:HOH1028 2.6 14.9 1.0 O A:VAL629 2.7 11.4 1.0 O A:PHE623 2.7 12.0 1.0 O A:TYR662 2.8 9.4 1.0 O A:ASP626 2.9 16.6 1.0 O A:HOH982 3.0 13.7 1.0 C A:TYR662 3.6 13.5 1.0 CB A:TYR662 3.6 10.0 1.0 C A:PHE623 3.7 12.9 1.0 CB A:PHE623 3.7 11.7 1.0 C A:VAL629 3.9 10.8 1.0 C A:ASP626 4.1 14.8 1.0 CA A:TYR662 4.2 12.7 1.0 N A:TYR631 4.3 7.8 1.0 CA A:PHE623 4.3 9.3 1.0 N A:ASN663 4.4 11.0 1.0 N A:ASP626 4.4 16.1 1.0 CA A:LEU630 4.6 10.9 1.0 N A:GLU624 4.6 12.8 1.0 CA A:GLU624 4.6 13.6 1.0 CA A:ASP626 4.6 16.5 1.0 CB A:ASP626 4.7 17.4 1.0 O A:GLU624 4.7 13.6 1.0 N A:LEU630 4.7 9.6 1.0 C A:GLU624 4.7 17.0 1.0 CA A:ASN663 4.7 10.6 1.0 CB A:ASN663 4.8 9.8 1.0 CB A:TYR631 4.8 8.8 1.0 O A:GLY659 4.8 17.1 1.0 C A:LEU630 4.9 11.1 1.0 CA A:VAL629 4.9 12.6 1.0 CG A:TYR662 4.9 12.8 1.0 OD1 A:ASN663 5.0 9.7 1.0 CG A:PHE623 5.0 11.4 1.0

H.K.Garcha, N.Nawar, H.Sorger, F.Erdogan, M.M.K.Aung, A.Sedighi, P.Manaswiyoungkul, H.S.Seo, S.Schonefeldt, D.Poloske, S.Dhe-Paganon, H.A.Neubauer, S.M.Mustjoki, M.Herling, E.D.De Araujo, R.Moriggl, P.T.Gunning. High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor Nn-429 in Natural Killer (Nk)/T-Cell Lymphoma. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 36355493
DOI: 10.3390/PH15111321