Sodium in PDB 6eku: Vibrio Cholerae Neuraminidase Complexed with Zanamivir

All present enzymatic activity of Vibrio Cholerae Neuraminidase Complexed with Zanamivir:
3.2.1.18;

The structure of Vibrio Cholerae Neuraminidase Complexed with Zanamivir, PDB code: 6eku was solved by A.Schuetz, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	190.553, 50.344, 86.087, 90.00, 107.24, 90.00
R / Rfree (%)	16.7 / 20.3

The structure of Vibrio Cholerae Neuraminidase Complexed with Zanamivir also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir (pdb code 6eku). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir, PDB code: 6eku:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vibrio Cholerae Neuraminidase Complexed with Zanamivir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:30.4 occ:1.00 O A:SER223 2.2 41.9 1.0 OD1 A:ASN221 2.3 36.0 1.0 O A:HOH1143 2.3 29.1 1.0 O A:THR226 2.5 39.6 1.0 O A:GLY96 2.7 46.0 1.0 O A:GLY99 2.7 40.2 1.0 CG A:ASN221 3.3 35.6 1.0 C A:THR226 3.3 41.4 1.0 C A:SER223 3.4 43.1 1.0 C A:GLY99 3.5 49.8 1.0 C A:GLY96 3.6 46.1 1.0 ND2 A:ASN221 3.7 34.4 1.0 CA A:ASP227 3.8 40.3 1.0 N A:ASP227 3.9 40.6 1.0 O A:SER224 3.9 56.7 1.0 C A:SER224 4.1 52.5 1.0 CA A:GLY96 4.1 43.8 1.0 N A:GLY99 4.2 50.0 1.0 N A:ARG100 4.2 40.6 1.0 N A:GLY228 4.2 36.7 1.0 CA A:ARG100 4.2 39.5 1.0 CA A:SER224 4.3 49.0 1.0 N A:SER224 4.3 45.6 1.0 N A:THR226 4.3 44.2 1.0 CA A:SER223 4.3 41.1 1.0 CA A:GLY99 4.3 44.1 1.0 C A:ASP227 4.3 37.4 1.0 OD1 A:ASP227 4.4 44.1 1.0 CA A:THR226 4.4 44.3 1.0 CB A:SER223 4.4 39.9 1.0 N A:SER223 4.5 37.8 1.0 CB A:ASN221 4.7 35.7 1.0 N A:ILE97 4.7 47.3 1.0 N A:ASN225 4.7 51.0 1.0 OG A:SER223 4.9 41.2 1.0 C A:ASN225 4.9 48.7 1.0 O A:ASN221 4.9 38.0 1.0 CB A:ASP227 5.0 42.5 1.0

Sodium binding site 2 out of 2 in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Vibrio Cholerae Neuraminidase Complexed with Zanamivir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na908 b:35.8 occ:1.00 OG1 A:THR339 2.2 40.5 1.0 O A:HOH1128 2.3 28.2 1.0 O A:ASN282 2.4 44.4 1.0 O A:ALA279 2.4 42.0 1.0 O A:THR339 2.4 36.5 1.0 OD2 A:ASP315 2.5 32.4 1.0 OD1 A:ASP315 2.9 30.1 1.0 CG A:ASP315 3.0 30.8 1.0 C A:ALA279 3.2 43.4 1.0 C A:THR339 3.2 34.0 1.0 CB A:THR339 3.3 38.9 1.0 CA A:THR339 3.3 33.3 1.0 C A:ASN282 3.4 43.7 1.0 N A:ALA279 3.5 40.1 1.0 CA A:ALA279 3.9 38.0 1.0 N A:ASN282 4.0 47.5 1.0 N A:LEU280 4.0 45.5 1.0 CA A:ASN282 4.1 46.7 1.0 CB A:ASN282 4.2 47.4 1.0 C A:GLY278 4.2 37.7 1.0 O A:HOH1082 4.2 39.6 1.0 N A:GLY278 4.3 36.2 1.0 CG2 A:THR339 4.3 36.8 1.0 CA A:LEU280 4.4 48.8 1.0 N A:THR283 4.4 40.2 1.0 CB A:ASP315 4.4 29.0 1.0 N A:ASP340 4.5 30.9 1.0 C A:LEU280 4.5 52.6 1.0 CA A:GLY278 4.6 36.3 1.0 CA A:THR283 4.6 37.3 1.0 CB A:ALA279 4.6 32.9 1.0 N A:THR339 4.7 31.7 1.0 N A:SER281 4.8 51.1 1.0 O A:HOH1387 4.8 38.6 1.0 O A:LEU280 4.9 54.9 1.0 O A:GLY278 5.0 37.0 1.0

S.Quosdorf, A.Schuetz, H.Kolodziej. Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases As Assessed in A Cell-Free Fluorescence-Based Enzyme Inhibition Assay. Molecules V. 22 2017.
ISSN: ESSN 1420-3049
PubMed: 29149072
DOI: 10.3390/MOLECULES22111989