Sodium in PDB 8tmt: Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam

All present enzymatic activity of Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam:
3.5.2.6;

The structure of Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam, PDB code: 8tmt was solved by Z.Sun, T.Palzkill, L.Hu, N.Neetu, H.Lin, B.Sankaran, J.Wang, B.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.55 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.38, 72.38, 85.5, 90, 90, 120
R / Rfree (%)	16.1 / 20.1

The binding sites of Sodium atom in the Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam (pdb code 8tmt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam, PDB code: 8tmt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:40.0 occ:1.00 OE1 A:GLN191 2.7 22.9 0.5 CB A:MET49 3.3 24.1 1.0 CG A:MET49 3.4 38.7 1.0 O A:HOH953 3.5 32.5 1.0 CG2 A:THR187 3.7 14.9 1.0 CD A:GLN191 3.9 20.1 0.5 CG A:GLU188 3.9 17.1 1.0 CE2 A:TYR47 4.0 22.4 1.0 CA A:GLU188 4.1 14.6 1.0 SD A:MET49 4.2 43.3 1.0 O A:THR187 4.2 14.4 1.0 N A:GLU188 4.3 12.9 1.0 O A:HOH991 4.3 26.8 1.0 C A:THR187 4.3 13.4 1.0 CB A:GLN191 4.4 15.0 0.5 CB A:GLN191 4.4 15.1 0.5 CB A:GLU188 4.7 15.5 1.0 CB A:THR187 4.7 12.7 1.0 CD2 A:TYR47 4.7 17.9 1.0 CA A:MET49 4.7 19.7 1.0 CG A:GLN191 4.8 14.4 0.5 NE2 A:GLN191 4.8 21.6 0.5 CG A:GLN191 4.8 14.4 0.5 OH A:TYR47 4.8 26.6 1.0 CZ A:TYR47 4.9 23.5 1.0 CE A:MET49 5.0 41.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Kpc-44 Carbapenemase in Complex with Vaborbactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na806 b:39.6 occ:1.00 O A:LYS192 2.4 13.1 1.0 CD A:ARG204 2.4 25.1 1.0 O A:GLY196 2.7 17.6 1.0 C A:GLY196 3.0 13.3 1.0 CG A:ARG204 3.1 19.7 1.0 N A:LEU199 3.1 14.1 1.0 O A:LEU199 3.2 16.6 1.0 N A:ALA198 3.2 12.6 1.0 N A:SER197 3.5 12.4 1.0 C A:LYS192 3.5 13.7 1.0 N A:GLY196 3.6 12.8 1.0 C A:LEU193 3.6 13.2 1.0 O A:LEU193 3.6 14.5 1.0 NE A:ARG204 3.6 26.6 1.0 CA A:LEU193 3.7 9.9 1.0 C A:SER197 3.8 15.3 1.0 CA A:GLY196 3.8 13.6 1.0 NH1 A:ARG204 3.8 28.3 1.0 CA A:SER197 3.9 14.1 1.0 CA A:LEU199 3.9 13.7 1.0 C A:LEU199 4.0 13.8 1.0 C A:ALA198 4.0 15.6 1.0 N A:LEU193 4.1 10.6 1.0 CA A:ALA198 4.1 13.3 1.0 CB A:LEU199 4.1 14.4 1.0 N A:THR194 4.1 13.5 1.0 CZ A:ARG204 4.2 31.2 1.0 N A:LEU195 4.4 12.8 1.0 CB A:ARG204 4.5 15.7 1.0 C A:LEU195 4.5 17.9 1.0 CB A:ALA198 4.5 14.9 1.0 C A:THR194 4.6 14.4 1.0 O A:SER197 4.8 15.4 1.0 CA A:LYS192 4.8 13.2 1.0 CA A:THR194 4.8 11.7 1.0 O A:GLN191 4.9 13.9 1.0 CG A:LEU199 4.9 13.7 1.0

Z.Sun, H.Lin, L.Hu, N.Neetu, B.Sankaran, J.Wang, B.V.V.Prasad, T.Palzkill. Klebsiella Pneumoniae Carbapenemase Variant 44 (Kpc-44) Acquires Ceftazidime-Avibactam Resistance By Altering the Conformation of Active Site Loops. J.Biol.Chem. 05493 2023.
ISSN: ESSN 1083-351X
PubMed: 38000656
DOI: 10.1016/J.JBC.2023.105493