Zinc in PDB 8szu: Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii

The structure of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii, PDB code: 8szu was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.73 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.594, 80.594, 204.645, 90, 90, 90
R / Rfree (%)	18.3 / 21.1

The structure of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii (pdb code 8szu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii, PDB code: 8szu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:29.9 occ:1.00 OD2 A:ASP269 2.0 12.4 1.0 OD1 A:ASP181 2.1 12.4 1.0 O33 A:X4U401 2.1 13.7 1.0 O31 A:X4U401 2.2 15.5 1.0 ND1 A:HIS183 2.3 9.4 1.0 OD2 A:ASP181 2.4 13.5 1.0 CG A:ASP181 2.5 13.0 1.0 N32 A:X4U401 2.8 13.6 1.0 C30 A:X4U401 2.8 15.3 1.0 CG A:ASP269 3.0 13.3 1.0 CE1 A:HIS183 3.1 12.8 1.0 CG A:HIS183 3.3 12.9 1.0 OD1 A:ASP269 3.4 12.2 1.0 CB A:HIS183 3.7 12.6 1.0 CA A:GLY311 4.0 14.2 1.0 CB A:ASP181 4.0 13.1 1.0 N A:HIS183 4.1 11.3 1.0 NE2 A:HIS143 4.2 12.9 1.0 C29 A:X4U401 4.3 18.3 1.0 NE2 A:HIS183 4.3 11.1 1.0 CB A:ASP269 4.3 12.6 1.0 N A:GLY311 4.3 13.7 1.0 N A:VAL182 4.4 11.8 1.0 CD2 A:HIS183 4.4 11.5 1.0 CE2 A:TYR313 4.5 11.8 1.0 OH A:TYR313 4.5 15.3 1.0 CE1 A:HIS143 4.5 13.2 1.0 CG1 A:VAL182 4.5 10.8 1.0 CA A:HIS183 4.6 10.1 1.0 C A:GLY311 4.8 12.4 1.0 CA A:ASP181 4.8 12.3 1.0 C A:ASP181 4.8 13.5 1.0 NE2 A:HIS144 4.9 14.4 1.0

Zinc binding site 2 out of 2 in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:32.8 occ:1.00 OD2 B:ASP269 2.1 13.1 1.0 O33 B:X4U402 2.1 18.4 1.0 OD1 B:ASP181 2.2 11.4 1.0 O31 B:X4U402 2.2 16.2 1.0 ND1 B:HIS183 2.3 12.2 1.0 OD2 B:ASP181 2.4 14.3 1.0 CG B:ASP181 2.6 13.9 1.0 N32 B:X4U402 2.8 15.4 1.0 C30 B:X4U402 2.8 19.4 1.0 CG B:ASP269 3.0 13.6 1.0 CE1 B:HIS183 3.1 16.6 1.0 CG B:HIS183 3.4 15.1 1.0 OD1 B:ASP269 3.4 13.1 1.0 CB B:HIS183 3.7 13.8 1.0 CA B:GLY311 4.0 14.8 1.0 N B:HIS183 4.1 13.3 1.0 CB B:ASP181 4.1 14.1 1.0 NE2 B:HIS143 4.1 14.0 1.0 C29 B:X4U402 4.2 20.0 1.0 NE2 B:HIS183 4.3 15.6 1.0 CB B:ASP269 4.3 14.3 1.0 N B:GLY311 4.4 18.6 1.0 N B:VAL182 4.4 12.4 1.0 CD2 B:HIS183 4.4 13.3 1.0 CE2 B:TYR313 4.4 14.2 1.0 OH B:TYR313 4.4 18.2 1.0 CG1 B:VAL182 4.5 12.6 1.0 CE1 B:HIS143 4.5 17.6 1.0 CA B:HIS183 4.6 12.3 1.0 C B:GLY311 4.7 15.9 1.0 C B:ASP181 4.8 13.9 1.0 CA B:ASP181 4.8 14.2 1.0 N B:GLY312 4.9 14.4 1.0 CZ B:TYR313 5.0 17.6 1.0 NE2 B:HIS144 5.0 14.9 1.0 C B:VAL182 5.0 13.9 1.0

P.R.Watson, D.W.Christianson. Structure and Function of KDAC1, A Class II Deacetylase From the Multidrug-Resistant Pathogen Acinetobacter Baumannii. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37624144
DOI: 10.1021/ACS.BIOCHEM.3C00288