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

Protein crystallography data

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

Other elements in 8szu:

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

Zinc (Zn) 2 atoms
Chlorine (Cl) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii, PDB code: 8szu:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8szu

Go back to Potassium Binding Sites List in 8szu
Potassium binding site 1 out of 4 in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K404

b:13.3
occ:1.00
 O A:ASP181 2.5 11.2 1.0
O A:HIS183 2.7 13.2 1.0
OD1 A:ASP179 2.8 14.2 1.0
O A:ILE203 2.8 13.7 1.0
OG A:SER202 2.8 12.8 1.0
O A:ASP179 2.9 12.5 1.0
CG A:ASP179 3.1 13.5 1.0
OD2 A:ASP179 3.5 14.0 1.0
C A:ASP179 3.6 14.2 1.0
C A:ASP181 3.6 13.5 1.0
C A:ILE203 3.7 13.1 1.0
C A:HIS183 3.8 12.9 1.0
N A:ILE203 3.9 11.7 1.0
CB A:ASP179 3.9 11.4 1.0
CB A:HIS204 3.9 11.9 1.0
N A:ASP181 3.9 10.8 1.0
CB A:SER202 3.9 12.2 1.0
CA A:SER202 4.2 12.7 1.0
N A:GLY185 4.2 13.7 1.0
ND1 A:HIS204 4.2 13.9 1.0
CA A:ASP181 4.2 12.3 1.0
N A:TRP180 4.2 14.4 1.0
C A:TRP180 4.3 11.5 1.0
C A:SER202 4.3 14.7 1.0
CA A:TRP180 4.3 13.3 1.0
CB A:ASP181 4.3 13.1 1.0
CA A:ASP179 4.4 12.1 1.0
CA A:HIS184 4.4 13.7 1.0
N A:HIS183 4.4 11.3 1.0
CA A:ILE203 4.5 12.5 1.0
CG A:HIS204 4.5 14.5 1.0
CA A:HIS204 4.5 12.9 1.0
N A:HIS204 4.5 11.8 1.0
N A:HIS184 4.5 12.0 1.0
CE1 A:HIS143 4.5 13.2 1.0
ND1 A:HIS143 4.6 12.2 1.0
C A:HIS184 4.6 13.2 1.0
O A:HOH555 4.7 12.3 1.0
N A:VAL182 4.7 11.8 1.0
C A:VAL182 4.7 12.2 1.0
CA A:HIS183 4.8 10.1 1.0

Potassium binding site 2 out of 4 in 8szu

Go back to Potassium Binding Sites List in 8szu
Potassium binding site 2 out of 4 in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:14.9
occ:1.00
 O A:VAL198 2.6 16.2 1.0
O A:HOH521 2.7 16.5 1.0
O A:TRP192 2.7 15.2 1.0
O A:TYR227 2.8 15.2 1.0
O A:ASP195 2.9 19.4 1.0
O A:HOH591 2.9 14.3 1.0
CB A:TRP192 3.6 12.0 1.0
C A:TRP192 3.6 14.3 1.0
OG1 A:THR200 3.6 15.1 1.0
C A:TYR227 3.7 15.7 1.0
C A:VAL198 3.9 15.1 1.0
CB A:TYR227 4.0 17.1 1.0
C A:ASP195 4.0 18.1 1.0
CA A:TRP192 4.2 12.8 1.0
CG2 A:THR200 4.2 16.3 1.0
N A:THR200 4.3 12.2 1.0
N A:ASN228 4.4 15.0 1.0
CA A:TYR227 4.4 16.9 1.0
CB A:THR200 4.5 13.3 1.0
N A:TRP193 4.5 13.7 1.0
N A:ASP195 4.5 17.0 1.0
CA A:LEU199 4.6 15.2 1.0
O A:TRP193 4.7 15.4 1.0
N A:LEU199 4.7 16.4 1.0
CA A:ASP195 4.7 18.8 1.0
CA A:TRP193 4.7 15.7 1.0
C A:TRP193 4.8 16.7 1.0
CB A:ASN228 4.8 16.0 1.0
CA A:ASN228 4.8 16.1 1.0
CG A:TRP192 4.8 14.8 1.0
C A:LEU199 4.9 14.8 1.0
CA A:VAL198 4.9 14.9 1.0
O A:GLY224 4.9 15.8 1.0
CB A:ASP195 4.9 18.6 1.0
N A:VAL198 5.0 14.2 1.0
N A:SER196 5.0 17.8 1.0

Potassium binding site 3 out of 4 in 8szu

Go back to Potassium Binding Sites List in 8szu
Potassium binding site 3 out of 4 in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:14.2
occ:1.00
 O B:ASP181 2.5 12.9 1.0
O B:HIS183 2.6 13.3 1.0
OG B:SER202 2.8 16.0 1.0
O B:ILE203 2.9 14.4 1.0
OD1 B:ASP179 2.9 15.4 1.0
O B:ASP179 3.0 15.6 1.0
CG B:ASP179 3.2 14.7 1.0
C B:ASP179 3.6 15.1 1.0
OD2 B:ASP179 3.6 17.5 1.0
C B:ASP181 3.6 13.9 1.0
C B:ILE203 3.7 12.8 1.0
C B:HIS183 3.7 16.0 1.0
N B:ILE203 3.9 14.0 1.0
CB B:ASP179 3.9 14.8 1.0
CB B:HIS204 3.9 13.7 1.0
CB B:SER202 3.9 14.3 1.0
N B:ASP181 3.9 13.3 1.0
CA B:SER202 4.1 16.2 1.0
N B:GLY185 4.1 16.7 1.0
CA B:ASP181 4.2 14.2 1.0
N B:TRP180 4.2 13.5 1.0
ND1 B:HIS204 4.3 17.5 1.0
C B:TRP180 4.3 12.8 1.0
C B:SER202 4.3 14.9 1.0
CB B:ASP181 4.3 14.1 1.0
CA B:TRP180 4.3 14.4 1.0
CA B:HIS184 4.4 14.5 1.0
CA B:ASP179 4.4 14.5 1.0
N B:HIS183 4.4 13.3 1.0
CA B:HIS204 4.5 14.2 1.0
N B:HIS184 4.5 14.1 1.0
CA B:ILE203 4.5 14.9 1.0
N B:HIS204 4.5 12.6 1.0
ND1 B:HIS143 4.5 15.1 1.0
CE1 B:HIS143 4.5 17.6 1.0
CG B:HIS204 4.6 13.6 1.0
C B:HIS184 4.6 15.7 1.0
O B:HOH524 4.7 14.7 1.0
N B:VAL182 4.7 12.4 1.0
C B:VAL182 4.7 13.9 1.0
CA B:HIS183 4.7 12.3 1.0
OD1 B:ASP181 5.0 11.4 1.0

Potassium binding site 4 out of 4 in 8szu

Go back to Potassium Binding Sites List in 8szu
Potassium binding site 4 out of 4 in the Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of KDAC1-Citarinostat Complex From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:20.7
occ:1.00
 O B:TRP192 2.6 20.8 1.0
O B:VAL198 2.7 19.6 1.0
O B:HOH551 2.7 20.4 1.0
O B:HOH521 2.7 18.8 1.0
O B:ASP195 2.8 25.8 1.0
O B:TYR227 2.9 17.6 1.0
CB B:TRP192 3.5 19.4 1.0
C B:TRP192 3.6 22.3 1.0
OG1 B:THR200 3.7 19.9 1.0
C B:TYR227 3.7 21.5 1.0
C B:VAL198 3.9 14.4 1.0
CB B:TYR227 3.9 22.8 1.0
C B:ASP195 4.0 25.3 1.0
CA B:TRP192 4.1 22.7 1.0
CG2 B:THR200 4.2 16.0 1.0
N B:THR200 4.3 17.7 1.0
N B:ASN228 4.4 21.7 1.0
CA B:TYR227 4.4 20.8 1.0
CB B:THR200 4.5 17.0 1.0
N B:TRP193 4.5 18.6 1.0
N B:ASP195 4.6 21.7 1.0
CA B:LEU199 4.6 18.0 1.0
N B:LEU199 4.7 18.3 1.0
CA B:ASP195 4.7 24.1 1.0
O B:TRP193 4.7 21.2 1.0
CA B:ASN228 4.8 18.9 1.0
CA B:TRP193 4.8 18.0 1.0
CG B:TRP192 4.8 20.0 1.0
CB B:ASN228 4.8 20.2 1.0
C B:TRP193 4.8 23.9 1.0
CA B:VAL198 4.9 20.7 1.0
C B:LEU199 4.9 17.0 1.0
O B:GLY224 4.9 22.9 1.0
CB B:ASP195 4.9 26.8 1.0
N B:SER196 5.0 22.1 1.0
CB B:VAL198 5.0 20.4 1.0
N B:VAL198 5.0 21.1 1.0

Reference:

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
Page generated: Tue Aug 13 00:54:18 2024

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