Zinc in PDB 8szt: Structure of KDAC1 From Acinetobacter Baumannii

The structure of Structure of KDAC1 From Acinetobacter Baumannii, PDB code: 8szt 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)	60.51 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	113.949, 181.689, 155.33, 90, 90, 90
R / Rfree (%)	20.1 / 26.2

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

Potassium	(K)	8 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Structure of KDAC1 From Acinetobacter Baumannii (pdb code 8szt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of KDAC1 From Acinetobacter Baumannii, PDB code: 8szt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of KDAC1 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 From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:70.6 occ:1.00 ND1 B:HIS183 2.4 21.9 1.0 OD1 B:ASP181 2.7 22.1 1.0 OD2 B:ASP269 2.8 16.4 1.0 CE1 B:HIS183 3.2 22.5 1.0 OD2 B:ASP181 3.3 29.2 1.0 CG B:ASP181 3.4 23.4 1.0 CG B:HIS183 3.4 18.7 1.0 CB B:HIS183 3.7 14.6 1.0 NE2 B:HIS144 3.8 19.8 1.0 NE2 B:HIS143 3.9 21.8 1.0 OH B:TYR313 3.9 26.8 1.0 CG B:ASP269 4.0 17.9 1.0 CE2 B:TYR313 4.2 18.4 1.0 CA B:GLY311 4.4 16.7 1.0 NE2 B:HIS183 4.4 19.4 1.0 CD2 B:HIS183 4.5 21.4 1.0 CD2 B:HIS144 4.5 20.8 1.0 CZ B:TYR313 4.5 21.9 1.0 N B:HIS183 4.6 14.7 1.0 CE1 B:HIS143 4.6 21.2 1.0 OD1 B:ASP269 4.7 16.2 1.0 CA B:HIS183 4.8 18.4 1.0 CE1 B:HIS144 4.8 18.9 1.0 N B:GLY311 4.8 12.9 1.0 CB B:ASP181 4.9 17.7 1.0 CD2 B:HIS143 5.0 20.1 1.0

Zinc binding site 2 out of 4 in the Structure of KDAC1 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 From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:74.8 occ:1.00 ND1 A:HIS183 2.4 18.2 1.0 OD1 A:ASP181 2.7 18.1 1.0 OD2 A:ASP269 3.0 19.3 1.0 CE1 A:HIS183 3.2 16.0 1.0 CG A:HIS183 3.4 22.7 1.0 OD2 A:ASP181 3.4 18.3 1.0 CG A:ASP181 3.5 18.1 1.0 OH A:TYR313 3.7 32.9 1.0 CB A:HIS183 3.8 14.7 1.0 NE2 A:HIS144 3.9 18.0 1.0 NE2 A:HIS143 3.9 25.9 1.0 CG A:ASP269 4.2 18.9 1.0 CE2 A:TYR313 4.3 23.8 1.0 NE2 A:HIS183 4.4 16.3 1.0 CA A:GLY311 4.4 17.3 1.0 CE1 A:HIS143 4.4 23.5 1.0 CD2 A:HIS183 4.5 28.6 1.0 CZ A:TYR313 4.5 20.3 1.0 CD2 A:HIS144 4.5 15.6 1.0 N A:HIS183 4.8 17.6 1.0 OD1 A:ASP269 4.9 16.3 1.0 CB A:ASP181 4.9 18.8 1.0 CA A:HIS183 4.9 16.5 1.0 CE1 A:HIS144 4.9 18.1 1.0 N A:GLY311 4.9 20.4 1.0

Zinc binding site 3 out of 4 in the Structure of KDAC1 From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of KDAC1 From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:65.3 occ:1.00 OD2 C:ASP269 2.3 20.6 1.0 ND1 C:HIS183 2.3 20.4 1.0 OD1 C:ASP181 2.4 17.0 1.0 CG C:ASP181 3.1 18.8 1.0 OD2 C:ASP181 3.1 20.3 1.0 CE1 C:HIS183 3.2 20.0 1.0 CG C:HIS183 3.4 22.6 1.0 CG C:ASP269 3.5 19.8 1.0 CB C:HIS183 3.8 18.3 1.0 NE2 C:HIS143 4.0 19.7 1.0 OD1 C:ASP269 4.1 17.3 1.0 OH C:TYR313 4.2 27.0 1.0 N C:HIS183 4.3 15.0 1.0 NE2 C:HIS144 4.3 19.6 1.0 NE2 C:HIS183 4.3 17.6 1.0 CA C:GLY311 4.4 17.1 1.0 CE2 C:TYR313 4.5 21.3 1.0 CD2 C:HIS183 4.5 20.3 1.0 CE1 C:HIS143 4.5 18.1 1.0 CB C:ASP181 4.5 18.4 1.0 CB C:ASP269 4.5 16.6 1.0 CA C:HIS183 4.7 14.2 1.0 CG1 C:VAL182 4.7 12.4 1.0 N C:GLY311 4.7 18.3 1.0 N C:VAL182 4.8 16.9 1.0 CZ C:TYR313 4.8 25.9 1.0

Zinc binding site 4 out of 4 in the Structure of KDAC1 From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of KDAC1 From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:80.2 occ:1.00 ND1 D:HIS183 2.3 21.1 1.0 OD2 D:ASP269 2.6 17.4 1.0 OD1 D:ASP181 2.7 19.6 1.0 CE1 D:HIS183 3.2 20.6 1.0 OD2 D:ASP181 3.3 19.1 1.0 CG D:HIS183 3.3 20.9 1.0 CG D:ASP181 3.4 18.4 1.0 CB D:HIS183 3.6 15.6 1.0 CG D:ASP269 3.8 13.0 1.0 NE2 D:HIS143 3.8 14.2 1.0 OH D:TYR313 3.8 30.7 1.0 NE2 D:HIS144 4.0 20.1 1.0 CE2 D:TYR313 4.2 22.1 1.0 OD1 D:ASP269 4.3 13.6 1.0 CE1 D:HIS143 4.3 17.4 1.0 CA D:GLY311 4.4 18.5 1.0 NE2 D:HIS183 4.4 22.3 1.0 CD2 D:HIS183 4.4 23.0 1.0 CZ D:TYR313 4.5 21.6 1.0 N D:HIS183 4.5 14.2 1.0 CA D:HIS183 4.7 13.3 1.0 CD2 D:HIS144 4.8 17.7 1.0 N D:GLY311 4.8 20.2 1.0 CB D:ASP181 4.8 13.2 1.0 CB D:ASP269 4.9 12.4 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