Sodium in PDB 7jhq: Oxa-48 Bound By Compound 2.3

All present enzymatic activity of Oxa-48 Bound By Compound 2.3:
3.5.2.6;

The structure of Oxa-48 Bound By Compound 2.3, PDB code: 7jhq 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)	34.84 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	120.68, 120.68, 159.769, 90, 90, 120
R / Rfree (%)	17 / 21.3

The structure of Oxa-48 Bound By Compound 2.3 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Oxa-48 Bound By Compound 2.3 (pdb code 7jhq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Oxa-48 Bound By Compound 2.3, PDB code: 7jhq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Oxa-48 Bound By Compound 2.3


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 2.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:49.8 occ:1.00 O3 A:VAJ301 2.4 35.7 1.0 OG A:SER118 3.0 27.6 1.0 O A:THR209 3.0 24.6 1.0 C13 A:VAJ301 3.1 34.2 1.0 OG1 A:THR209 3.1 27.0 1.0 C A:THR209 3.2 31.9 1.0 CA A:GLY210 3.3 24.5 1.0 CB A:SER70 3.3 28.2 1.0 N A:GLY210 3.4 29.9 1.0 C11 A:VAJ301 3.4 36.0 1.0 C12 A:VAJ301 3.5 39.7 1.0 CB A:SER118 3.6 25.0 1.0 NZ A:LYS208 3.6 25.8 1.0 O A:HOH422 3.8 30.1 1.0 OG A:SER70 3.8 34.2 1.0 C A:GLY210 3.8 25.5 1.0 CB A:THR209 3.8 21.0 1.0 N A:TYR211 3.8 24.6 1.0 O2 A:VAJ301 3.9 41.2 1.0 CA A:THR209 4.1 26.7 1.0 NH2 A:ARG250 4.3 26.6 1.0 O A:HOH414 4.3 27.3 1.0 C10 A:VAJ301 4.4 30.5 1.0 C7 A:VAJ301 4.5 34.8 1.0 O A:HOH416 4.6 31.1 1.0 CA A:SER70 4.6 20.6 1.0 O A:GLY210 4.6 25.3 1.0 CE A:LYS208 4.8 24.1 1.0 CB A:TYR211 4.9 22.6 1.0 N A:THR209 4.9 23.9 1.0 CA A:TYR211 5.0 25.2 1.0 C3 A:VAJ301 5.0 35.5 1.0

Sodium binding site 2 out of 3 in the Oxa-48 Bound By Compound 2.3


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 2.3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:48.4 occ:1.00 OE1 C:GLU89 2.6 31.4 1.0 NE2 C:GLN193 3.0 28.8 1.0 CE1 C:HIS90 3.4 47.4 1.0 CD C:GLU89 3.4 37.0 1.0 CG C:GLU89 3.4 30.2 1.0 NE2 C:HIS90 3.6 41.7 1.0 CD C:GLN193 3.8 35.9 1.0 OE1 C:GLN193 3.8 31.3 1.0 ND1 C:HIS90 4.4 45.1 1.0 OE2 C:GLU89 4.6 36.2 1.0 O C:HOH462 4.7 42.3 1.0 CD2 C:HIS90 4.7 41.5 1.0 CB C:GLU89 4.8 30.7 1.0

Sodium binding site 3 out of 3 in the Oxa-48 Bound By Compound 2.3


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 2.3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:60.2 occ:1.00 O D:HOH435 2.8 34.5 1.0 OE1 D:GLU227 2.8 34.0 1.0 NE D:ARG206 3.4 29.6 1.0 CD D:LYS192 3.5 31.5 1.0 CZ2 D:TRP225 3.7 32.5 1.0 CD D:ARG206 3.7 26.1 1.0 CD D:GLU227 3.9 42.6 1.0 CD1 D:TYR177 4.0 29.7 1.0 NE1 D:TRP225 4.0 27.4 1.0 CE1 D:TYR177 4.1 33.1 1.0 CB D:LYS192 4.2 27.8 1.0 CE2 D:TRP225 4.2 31.3 1.0 CZ D:ARG206 4.3 29.6 1.0 CG D:LYS192 4.3 27.8 1.0 CE D:LYS192 4.4 28.8 1.0 OE2 D:GLU227 4.5 41.6 1.0 NZ D:LYS192 4.5 30.2 1.0 NH2 D:ARG206 4.7 25.5 1.0 O D:HOH524 4.7 46.4 1.0 O D:HOH404 4.7 33.0 1.0 CH2 D:TRP225 4.7 29.4 1.0

D.M.Taylor, L.Hu, B.V.V.Prasad, T.Palzkill. Oxa-48 Bound By Compound 2.4 Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
DOI: 10.1021/ACSINFECDIS.1C00501