Sodium in PDB 7l8o: Oxa-48 Bound By Compound 4.3

All present enzymatic activity of Oxa-48 Bound By Compound 4.3:
3.5.2.6;

The structure of Oxa-48 Bound By Compound 4.3, PDB code: 7l8o 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)	48.60 / 2.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	122.039, 122.039, 160.787, 90, 90, 120
R / Rfree (%)	16.8 / 21.1

The structure of Oxa-48 Bound By Compound 4.3 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Oxa-48 Bound By Compound 4.3 (pdb code 7l8o). 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 4.3, PDB code: 7l8o:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Oxa-48 Bound By Compound 4.3


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 4.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:46.9 occ:1.00 OG A:SER70 2.6 34.9 1.0 N A:TYR211 2.8 26.3 1.0 N A:SER70 2.9 25.9 1.0 CB A:SER70 2.9 30.0 1.0 O A:TYR211 3.0 30.3 1.0 C6 A:XV7403 3.1 62.0 1.0 CB A:ALA69 3.3 22.9 1.0 C5 A:XV7403 3.3 58.2 1.0 CA A:SER70 3.5 26.0 1.0 C4 A:XV7403 3.5 59.2 1.0 C A:TYR211 3.5 28.6 1.0 CA A:TYR211 3.6 27.5 1.0 C A:GLY210 3.8 25.8 1.0 CA A:GLY210 3.8 22.3 1.0 C A:ALA69 3.9 27.4 1.0 CA A:ALA69 4.1 26.1 1.0 CB A:TYR211 4.1 25.4 1.0 CD2 A:LEU158 4.3 32.9 1.0 O A:XV7403 4.4 54.5 1.0 C7 A:XV7403 4.4 63.7 1.0 C A:XV7403 4.5 57.2 1.0 OQ1 A:KCX73 4.6 35.5 1.0 N A:SER212 4.6 27.6 1.0 C A:SER70 4.7 27.4 1.0 C3 A:XV7403 4.7 58.2 1.0 O A:GLY210 4.9 29.3 1.0 O A:ALA69 5.0 27.3 1.0

Sodium binding site 2 out of 4 in the Oxa-48 Bound By Compound 4.3


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 4.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:46.3 occ:1.00 OG B:SER70 2.6 32.1 1.0 N B:TYR211 2.7 27.8 1.0 N B:SER70 2.8 28.4 1.0 CB B:SER70 2.9 28.6 1.0 O B:TYR211 3.0 26.0 1.0 CB B:ALA69 3.2 28.1 1.0 C6 B:XV7403 3.3 60.8 1.0 C5 B:XV7403 3.4 54.8 1.0 CA B:SER70 3.4 28.0 1.0 C B:TYR211 3.5 28.1 1.0 CA B:TYR211 3.5 29.3 1.0 C4 B:XV7403 3.6 57.1 1.0 C B:GLY210 3.7 28.4 1.0 CA B:GLY210 3.7 23.6 1.0 C B:ALA69 3.8 29.6 1.0 CB B:TYR211 4.0 26.4 1.0 CA B:ALA69 4.0 30.0 1.0 O2 B:XV7403 4.3 46.9 1.0 CD2 B:LEU158 4.5 29.3 1.0 N B:SER212 4.5 27.1 1.0 C7 B:XV7403 4.5 63.8 1.0 C B:XV7403 4.5 52.5 1.0 C B:SER70 4.7 29.9 1.0 OQ1 B:KCX73 4.7 35.6 1.0 C3 B:XV7403 4.8 57.6 1.0 O B:GLY210 4.8 31.7 1.0 O B:ALA69 4.9 29.9 1.0

Sodium binding site 3 out of 4 in the Oxa-48 Bound By Compound 4.3


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 4.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:42.1 occ:1.00 OE2 B:GLU227 2.6 36.9 1.0 NH2 B:ARG206 3.1 20.3 1.0 CD B:GLU227 3.6 34.4 1.0 OE1 B:GLU227 3.8 34.4 1.0 CD1 B:ILE204 3.8 24.5 1.0 CZ B:ARG206 4.0 20.0 1.0 NE B:ARG206 4.1 21.2 1.0 CG B:GLU227 5.0 30.8 1.0

Sodium binding site 4 out of 4 in the Oxa-48 Bound By Compound 4.3


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 4.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:36.5 occ:1.00 OH B:TYR144 2.7 24.4 1.0 OE1 B:GLN169 2.7 32.3 1.0 O B:THR71 2.8 30.8 1.0 C B:THR71 3.4 26.3 1.0 OG1 B:THR71 3.5 28.7 1.0 CE2 B:TYR144 3.5 27.0 1.0 CZ B:TYR144 3.5 25.6 1.0 CD B:GLN169 3.7 33.9 1.0 CB B:THR71 3.7 26.0 1.0 CD B:PRO75 3.9 23.9 1.0 NE2 B:GLN169 4.0 31.6 1.0 N B:PHE72 4.1 23.9 1.0 CA B:THR71 4.2 25.4 1.0 CA B:PHE72 4.4 25.2 1.0 CB B:ILE74 4.5 24.4 1.0 CG B:PRO75 4.5 24.3 1.0 CD2 B:PHE172 4.7 22.2 1.0 CD1 B:ILE74 4.7 20.8 1.0 CG1 B:ILE74 4.8 22.6 1.0 CD2 B:TYR144 4.8 28.4 1.0 CE2 B:PHE172 4.8 22.1 1.0 CG2 B:VAL223 4.8 23.3 1.0 CE1 B:TYR144 4.9 26.8 1.0 CD1 B:ILE164 4.9 25.4 1.0 CB B:PRO68 5.0 25.2 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