Sodium in PDB 5bqs: S. Pneumoniae Fabh with Small Molecule Inhibitor 4

All present enzymatic activity of S. Pneumoniae Fabh with Small Molecule Inhibitor 4:
2.3.1.180;

The structure of S. Pneumoniae Fabh with Small Molecule Inhibitor 4, PDB code: 5bqs was solved by S.L.Kazmirski, D.C.Mckinney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.54 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.191, 77.734, 64.633, 90.00, 108.97, 90.00
R / Rfree (%)	21.1 / 24.9

The structure of S. Pneumoniae Fabh with Small Molecule Inhibitor 4 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the S. Pneumoniae Fabh with Small Molecule Inhibitor 4 (pdb code 5bqs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the S. Pneumoniae Fabh with Small Molecule Inhibitor 4, PDB code: 5bqs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the S. Pneumoniae Fabh with Small Molecule Inhibitor 4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S. Pneumoniae Fabh with Small Molecule Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:51.3 occ:1.00 O A:ILE238 2.3 53.4 1.0 O A:ILE233 2.5 40.2 1.0 O A:SER236 2.6 47.8 1.0 O A:ASP234 2.8 46.0 1.0 C A:ASP234 3.3 45.5 1.0 C A:ILE238 3.5 54.4 1.0 C A:ILE233 3.5 42.3 1.0 C A:SER236 3.6 48.0 1.0 CA A:ASP234 3.6 41.1 1.0 OG A:SER236 3.8 44.0 1.0 N A:SER236 3.9 42.5 1.0 N A:ILE238 4.0 50.2 1.0 N A:ASP234 4.0 40.9 1.0 O A:HOH618 4.2 54.0 1.0 N A:GLU235 4.2 42.9 1.0 CA A:SER236 4.2 41.1 1.0 CA A:ILE238 4.3 50.2 1.0 N A:GLU239 4.4 52.3 1.0 OE1 A:GLU239 4.4 82.7 1.0 C A:GLU235 4.5 47.9 1.0 C A:PRO237 4.5 54.5 1.0 CA A:GLU239 4.5 52.9 1.0 CB A:SER236 4.6 39.5 1.0 N A:PRO237 4.6 47.6 1.0 CG A:GLU239 4.7 71.7 1.0 CG2 A:ILE233 4.8 41.2 1.0 CA A:PRO237 4.8 49.6 1.0 CA A:ILE233 4.8 37.8 1.0 CA A:GLU235 4.8 42.8 1.0 CD A:GLU239 5.0 95.6 1.0

Sodium binding site 2 out of 2 in the S. Pneumoniae Fabh with Small Molecule Inhibitor 4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S. Pneumoniae Fabh with Small Molecule Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:57.0 occ:1.00 O B:ILE233 2.4 46.5 1.0 O B:SER236 2.5 51.7 1.0 O B:ILE238 2.5 43.4 1.0 O B:ASP234 2.6 51.8 1.0 C B:ASP234 3.2 51.0 1.0 C B:ILE233 3.4 46.0 1.0 CA B:ASP234 3.5 47.2 1.0 C B:SER236 3.5 51.2 1.0 C B:ILE238 3.7 46.0 1.0 OG B:SER236 3.7 48.6 1.0 N B:SER236 3.8 47.7 1.0 N B:ASP234 3.9 45.2 1.0 O B:HOH597 4.0 56.5 1.0 N B:ILE238 4.1 46.4 1.0 N B:GLU235 4.1 48.2 1.0 CA B:SER236 4.1 45.9 1.0 C B:GLU235 4.3 51.1 1.0 C B:PRO237 4.5 51.9 1.0 CA B:ILE238 4.5 45.9 1.0 CB B:SER236 4.5 46.0 1.0 N B:PRO237 4.6 48.2 1.0 O B:HOH609 4.6 60.6 1.0 N B:GLU239 4.6 43.0 1.0 CA B:GLU235 4.7 48.3 1.0 CA B:ILE233 4.7 38.6 1.0 CA B:GLU239 4.7 43.3 1.0 CA B:PRO237 4.8 49.3 1.0 CG2 B:ILE233 4.8 40.5 1.0 CB B:ASP234 4.9 50.0 1.0 CG B:GLU239 4.9 59.8 1.0 O B:GLU235 5.0 49.5 1.0

D.C.Mckinney, C.J.Eyermann, R.F.Gu, J.Hu, S.L.Kazmirski, S.D.Lahiri, A.R.Mckenzie, A.B.Shapiro, G.Breault. Antibacterial Fabh Inhibitors with Mode of Action Validated in Haemophilus Influenzae By in Vitro Resistance Mutation Mapping. Acs Infect Dis. V. 2 456 2016.
ISSN: ESSN 2373-8227
PubMed: 27626097
DOI: 10.1021/ACSINFECDIS.6B00053