Sodium in PDB 7k5v: Oxa-48 Bound By Compound 3.1

All present enzymatic activity of Oxa-48 Bound By Compound 3.1:
3.5.2.6;

The structure of Oxa-48 Bound By Compound 3.1, PDB code: 7k5v was solved by D.M.Taylor, L.Hu, B.V.V.Prasad, T.Palzkill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.922, 122.922, 161.143, 90, 90, 120
R / Rfree (%)	19.2 / 23.7

The structure of Oxa-48 Bound By Compound 3.1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Oxa-48 Bound By Compound 3.1 (pdb code 7k5v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Oxa-48 Bound By Compound 3.1, PDB code: 7k5v:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Oxa-48 Bound By Compound 3.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Oxa-48 Bound By Compound 3.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:43.2 occ:1.00 O A:ALA194 2.5 31.8 1.0 O A:ILE112 2.9 32.3 1.0 C A:ALA194 3.5 32.1 1.0 CB A:LYS116 3.5 38.0 1.0 N A:LYS116 3.7 36.0 1.0 CG2 A:ILE112 3.7 33.5 1.0 C A:ILE112 3.8 32.8 1.0 CA A:LYS116 3.9 37.1 1.0 CA A:ALA194 4.0 32.3 1.0 O A:LEU196 4.0 34.3 1.0 CA A:ILE112 4.1 32.6 1.0 CB A:MET115 4.6 34.9 1.0 C A:MET115 4.6 34.4 1.0 CB A:ILE112 4.6 33.6 1.0 CB A:ALA194 4.6 32.3 1.0 CG A:LYS116 4.6 38.6 1.0 N A:MET195 4.6 32.2 1.0 N A:LEU196 4.8 30.8 1.0 N A:THR113 4.9 34.0 1.0 CD A:LYS116 4.9 39.7 1.0 O A:GLN193 5.0 32.9 1.0 C A:MET195 5.0 30.9 1.0 CA A:MET195 5.0 31.6 1.0

Sodium binding site 2 out of 4 in the Oxa-48 Bound By Compound 3.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Oxa-48 Bound By Compound 3.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:74.2 occ:1.00 O A:LEU158 2.6 36.2 1.0 N A:ARG214 2.8 42.5 1.0 OG A:SER212 2.8 41.8 1.0 N A:THR213 3.3 42.9 1.0 N A:ILE215 3.4 41.1 1.0 CB A:ARG214 3.5 39.1 1.0 CA A:ARG214 3.5 40.9 1.0 C A:SER212 3.6 41.6 1.0 CD1 A:LEU67 3.6 35.0 1.0 CA A:SER212 3.7 39.4 1.0 C A:LEU158 3.7 35.8 1.0 CB A:SER212 3.8 40.2 1.0 C A:THR213 3.8 44.5 1.0 C A:ARG214 3.9 40.8 1.0 CG A:ARG214 4.0 37.7 1.0 CA A:THR213 4.1 44.3 1.0 CA A:LEU158 4.4 34.9 1.0 O A:SER212 4.4 41.5 1.0 O A:ILE215 4.4 41.7 1.0 CA A:ILE215 4.4 42.2 1.0 CB A:ILE215 4.5 42.0 1.0 CB A:LEU67 4.7 34.4 1.0 CG A:LEU67 4.8 34.6 1.0 N A:ASP159 4.8 36.3 1.0 CB A:LEU158 4.9 35.4 1.0 CG1 A:ILE215 4.9 42.2 1.0 CD A:ARG214 4.9 37.5 1.0 O A:THR213 4.9 46.7 1.0 C A:ILE215 4.9 42.5 1.0 CA A:ASP159 5.0 36.9 1.0

Sodium binding site 3 out of 4 in the Oxa-48 Bound By Compound 3.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Oxa-48 Bound By Compound 3.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:55.4 occ:1.00 O B:LEU81 2.6 39.1 1.0 O B:VAL86 2.8 37.0 1.0 NH2 B:ARG186 3.3 40.9 1.0 O B:LYS87 3.4 40.5 1.0 C B:LEU81 3.6 38.5 1.0 CA B:LEU81 3.9 36.6 1.0 C B:VAL86 3.9 37.1 1.0 C B:LYS87 4.0 40.7 1.0 CA B:LYS87 4.0 39.8 1.0 CD2 B:LEU81 4.1 34.8 1.0 CA B:GLY84 4.1 40.1 1.0 CZ B:ARG186 4.2 40.9 1.0 NH1 B:ARG186 4.2 41.1 1.0 N B:GLY84 4.3 40.3 1.0 CB B:LEU81 4.4 35.1 1.0 N B:LYS87 4.5 38.5 1.0 N B:ASP82 4.8 39.3 1.0 CG B:LEU81 4.9 34.6 1.0 O B:ALA80 4.9 37.5 1.0 C B:GLY84 4.9 40.7 1.0

Sodium binding site 4 out of 4 in the Oxa-48 Bound By Compound 3.1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Oxa-48 Bound By Compound 3.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:52.3 occ:1.00 O B:PRO217 2.6 49.1 1.0 OG B:SER212 2.8 50.2 1.0 O B:ILE215 2.9 48.0 1.0 CB B:SER212 3.6 48.0 1.0 C B:PRO217 3.6 51.7 1.0 CD1 B:LEU67 3.9 41.3 1.0 N B:PRO217 4.0 51.7 1.0 C B:ILE215 4.0 49.5 1.0 CG1 B:ILE219 4.1 43.8 1.0 CD B:PRO217 4.2 51.0 1.0 C B:GLU216 4.2 51.2 1.0 O B:SER212 4.4 51.9 1.0 CB B:LEU67 4.4 38.9 1.0 CA B:PRO217 4.4 53.1 1.0 O B:GLU216 4.5 50.0 1.0 N B:LYS218 4.5 53.2 1.0 N B:ILE219 4.6 46.2 1.0 CA B:LYS218 4.6 51.8 1.0 CG B:LEU67 4.7 40.2 1.0 C B:SER212 4.7 50.5 1.0 N B:LEU67 4.7 39.2 1.0 CG B:PRO217 4.7 52.0 1.0 CA B:SER212 4.8 47.6 1.0 CA B:GLU216 4.8 52.6 1.0 N B:GLU216 4.9 51.6 1.0 CD1 B:ILE219 4.9 42.6 1.0 CB B:PHE66 4.9 39.8 1.0 CA B:ILE215 4.9 49.1 1.0 CB B:ILE215 4.9 46.9 1.0 CG2 B:ILE215 5.0 47.2 1.0

D.M.Taylor, L.Hu, B.V.V.Prasad, T.Palzkill. Unique Diacidic Fragments Inhibit the Oxa-48 Carbapenemase and Enhance the Killing of Escherichia Coli Producing Oxa-48 Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
DOI: 10.1021/ACSINFECDIS.1C00501