Calcium in PDB 6eks: Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate

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

The structure of Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate, PDB code: 6eks 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)	44.33 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.758, 77.862, 163.477, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.4

The binding sites of Calcium atom in the Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate (pdb code 6eks). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate, PDB code: 6eks:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:22.4 occ:1.00 O A:HOH1258 2.3 17.9 1.0 O A:HOH1230 2.3 29.6 1.0 OD1 A:ASP312 2.4 18.1 1.0 O A:HOH1301 2.4 18.2 1.0 O A:HOH1266 2.4 21.3 1.0 O A:HOH1609 2.5 15.6 1.0 O A:HOH1682 2.6 42.8 1.0 CG A:ASP312 3.4 19.2 1.0 OD2 A:ASP312 3.7 25.3 1.0 O A:HOH1604 3.9 40.4 1.0 O A:ASN309 4.3 19.9 1.0 O A:HOH1146 4.5 14.5 1.0 OD2 A:ASP285 4.5 16.2 1.0 O A:HOH1589 4.5 24.6 1.0 CG2 A:THR283 4.6 16.0 1.0 CB A:GLU306 4.7 17.4 1.0 CB A:ASP312 4.7 17.3 1.0 OE1 A:GLU306 4.7 24.1 1.0

Calcium binding site 2 out of 4 in the Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:16.4 occ:1.00 O A:HOH1051 2.3 20.4 1.0 O A:PHE604 2.4 18.3 1.0 OD2 A:ASP346 2.4 16.2 1.0 O A:HOH1171 2.5 14.1 1.0 OD1 A:ASP346 2.5 21.2 1.0 O A:HOH1595 2.6 11.2 1.0 CG A:ASP346 2.8 17.9 1.0 C A:PHE604 3.4 17.8 1.0 CA A:PHE604 4.0 16.2 1.0 O A:HOH1219 4.3 21.1 1.0 CB A:PHE604 4.3 15.0 1.0 CB A:ASP346 4.3 15.8 1.0 OE1 A:GLU642 4.4 15.2 1.0 OE2 A:GLU642 4.5 17.8 1.0 N A:PHE605 4.6 15.1 1.0 O A:HOH1324 4.8 36.5 1.0 O A:HOH1349 4.8 23.2 1.0 CA A:PHE605 4.9 14.4 1.0 CD A:GLU642 4.9 14.6 1.0

Calcium binding site 3 out of 4 in the Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:14.0 occ:1.00 O A:HOH1321 2.3 8.5 1.0 O A:ALA709 2.3 14.3 1.0 OD1 A:ASP708 2.4 16.0 1.0 OD1 A:ASP647 2.4 16.5 1.0 OD2 A:ASP708 2.4 17.0 1.0 OD2 A:ASP647 2.4 14.4 1.0 O A:PRO574 2.5 18.9 1.0 CG A:ASP708 2.7 16.0 1.0 CG A:ASP647 2.8 16.9 1.0 C A:PRO574 3.5 14.8 1.0 C A:ALA709 3.5 13.4 1.0 CA A:GLY575 4.0 12.9 1.0 N A:ALA709 4.1 13.8 1.0 N A:GLY575 4.1 14.9 1.0 O A:HOH1306 4.2 16.5 1.0 CB A:ASP708 4.2 12.3 1.0 CB A:ASP647 4.3 12.1 1.0 CG A:PRO574 4.4 12.5 1.0 O A:HOH1122 4.4 15.0 1.0 O A:ALA646 4.4 15.0 1.0 N A:SER710 4.5 14.2 1.0 CA A:ALA709 4.5 13.6 1.0 CA A:SER710 4.5 14.3 1.0 O A:SER767 4.5 15.2 1.0 CB A:PRO574 4.5 12.8 1.0 CA A:PRO574 4.6 12.3 1.0 C A:ASP708 4.7 15.8 1.0 OD1 A:ASP768 4.8 13.5 1.0 C A:ALA646 4.8 13.1 1.0 CA A:ASP708 4.9 13.3 1.0 O A:HOH1334 4.9 13.1 1.0 NH1 A:ARG320 4.9 16.7 1.0 CB A:SER710 4.9 15.6 1.0

Calcium binding site 4 out of 4 in the Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Vibrio Cholerae Neuraminidase Complexed with Oseltamivir Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:14.6 occ:1.00 OD2 A:ASP315 2.3 16.6 1.0 O A:ALA279 2.3 14.2 1.0 O A:ASN282 2.3 15.0 1.0 OG1 A:THR339 2.4 17.5 1.0 OD1 A:ASN282 2.4 16.7 1.0 O A:THR339 2.5 15.9 1.0 OD1 A:ASP315 2.6 13.5 1.0 CG A:ASP315 2.7 16.0 1.0 C A:ASN282 3.2 13.7 1.0 C A:THR339 3.3 16.9 1.0 C A:ALA279 3.4 15.6 1.0 CB A:THR339 3.5 15.1 1.0 CA A:THR339 3.5 16.6 1.0 CG A:ASN282 3.6 16.4 1.0 N A:ALA279 3.7 15.4 1.0 CA A:ASN282 4.0 14.0 1.0 N A:ASN282 4.0 14.0 1.0 CA A:ALA279 4.1 14.7 1.0 N A:THR283 4.2 13.7 1.0 N A:GLY278 4.2 15.5 1.0 O A:HOH1029 4.2 12.6 1.0 CB A:ASP315 4.2 14.2 1.0 C A:GLY278 4.3 15.1 1.0 CA A:THR283 4.4 14.3 1.0 CB A:ASN282 4.4 13.4 1.0 N A:LEU280 4.4 15.6 1.0 CG2 A:THR339 4.5 16.2 1.0 ND2 A:ASN282 4.6 15.5 1.0 N A:ASP340 4.6 16.0 1.0 CA A:GLY278 4.6 14.7 1.0 CA A:LEU280 4.7 17.7 1.0 C A:LEU280 4.7 19.0 1.0 CB A:ALA279 4.8 15.2 1.0 O A:LEU280 4.9 17.3 1.0 N A:ASN284 4.9 15.6 1.0 N A:THR339 4.9 13.5 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