Calcium in PDB 4h53: Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC

The structure of Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC, PDB code: 4h53 was solved by C.J.Vavricka, Y.Liu, H.Kiyota, N.Sriwilaijaroen, J.Qi, K.Tanaka, Y.Wu, Q.Li, Y.Li, J.Yan, Y.Suzuki, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.05 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.217, 114.831, 84.259, 90.00, 99.71, 90.00
R / Rfree (%)	14 / 16.1

The binding sites of Calcium atom in the Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC (pdb code 4h53). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC, PDB code: 4h53:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:17.2 occ:1.00 O A:GLY297 2.7 12.9 1.0 O A:GLN347 2.7 24.5 1.0 O A:ASP293 2.7 14.4 1.0 OD2 A:ASP324 2.8 12.1 1.0 O A:GLY345 2.9 33.2 1.0 O A:HOH774 2.9 20.3 1.0 C A:GLY345 3.5 28.2 1.0 C A:GLY297 3.6 11.2 1.0 C A:GLN347 3.7 26.1 1.0 CG A:ASP324 3.8 9.1 1.0 C A:ASP293 3.8 13.3 1.0 CA A:GLY345 4.0 21.9 1.0 O A:HOH613 4.1 8.5 1.0 CA A:GLY348 4.1 11.1 1.0 O A:THR346 4.2 25.8 1.0 C A:THR346 4.2 23.0 1.0 O A:ARG344 4.3 20.6 1.0 N A:SER298 4.3 10.3 1.0 CA A:ASN294 4.3 23.9 1.0 N A:GLY348 4.4 10.2 1.0 CA A:SER298 4.4 10.5 1.0 N A:GLY297 4.4 13.5 1.0 N A:THR346 4.4 24.4 1.0 CB A:ASP324 4.5 9.4 1.0 N A:GLN347 4.5 20.4 1.0 C A:ASN294 4.6 22.6 1.0 OD1 A:ASP324 4.6 12.5 1.0 CA A:GLY297 4.6 10.7 1.0 N A:ASN294 4.6 19.5 1.0 OD1 A:ASP293 4.7 15.3 1.0 CA A:THR346 4.7 21.3 1.0 CB A:ASP293 4.7 11.4 1.0 CA A:GLN347 4.8 18.5 1.0 CA A:ASP293 4.8 8.1 1.0 N A:TRP295 4.9 15.2 1.0 O A:ASN294 4.9 18.6 1.0 N A:ASP293 4.9 8.0 1.0

Calcium binding site 2 out of 3 in the Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:7.8 occ:1.00 O B:GLN347 2.5 9.5 1.0 OD2 B:ASP324 2.5 11.1 1.0 O B:ASP293 2.5 9.2 1.0 O B:GLY345 2.6 13.6 1.0 O B:GLY297 2.6 10.6 1.0 O B:HOH611 2.6 12.3 1.0 C B:GLY345 3.6 13.5 1.0 CG B:ASP324 3.6 9.9 1.0 C B:GLN347 3.6 13.8 1.0 C B:GLY297 3.7 12.1 1.0 C B:ASP293 3.7 8.2 1.0 CA B:GLY348 4.0 11.2 1.0 O B:HOH650 4.1 8.5 1.0 CA B:GLY345 4.1 11.2 1.0 CA B:ASN294 4.2 8.2 1.0 CA B:SER298 4.2 9.8 1.0 C B:THR346 4.3 11.4 1.0 N B:GLY348 4.3 8.3 1.0 O B:THR346 4.3 12.1 1.0 OD1 B:ASP324 4.3 9.3 1.0 N B:SER298 4.3 9.6 1.0 CB B:ASP324 4.4 7.5 1.0 N B:ASN294 4.4 8.5 1.0 C B:ASN294 4.5 10.8 1.0 N B:GLN347 4.5 12.6 1.0 O B:ARG344 4.5 11.7 1.0 N B:THR346 4.5 10.0 1.0 N B:GLY297 4.6 11.3 1.0 CA B:GLY297 4.7 10.1 1.0 CA B:GLN347 4.7 11.9 1.0 CA B:ASP293 4.7 7.9 1.0 CA B:THR346 4.8 13.6 1.0 N B:TRP295 4.8 9.7 1.0 OD1 B:ASP293 4.8 9.6 1.0 N B:ASP293 4.9 8.2 1.0 CB B:ASP293 4.9 7.3 1.0 O B:ASN294 4.9 10.5 1.0 CB B:SER298 4.9 9.4 1.0 O B:PRO326 5.0 9.8 1.0

Calcium binding site 3 out of 3 in the Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Influenza N2-TYR406ASP Neuraminidase in Complex with Beta-NEU5AC within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:8.8 occ:1.00 O C:ASP293 2.5 9.8 1.0 O C:GLN347 2.5 10.6 1.0 O C:GLY297 2.6 11.1 1.0 OD2 C:ASP324 2.6 10.3 1.0 O C:GLY345 2.6 13.6 1.0 O C:HOH618 2.6 13.3 1.0 C C:GLY345 3.6 13.6 1.0 C C:GLY297 3.6 10.9 1.0 CG C:ASP324 3.6 8.0 1.0 C C:GLN347 3.7 12.0 1.0 C C:ASP293 3.7 8.2 1.0 CA C:GLY348 4.1 9.5 1.0 O C:HOH625 4.1 8.2 1.0 CA C:GLY345 4.1 13.1 1.0 CA C:ASN294 4.2 9.3 1.0 CA C:SER298 4.3 8.9 1.0 O C:THR346 4.3 14.3 1.0 N C:SER298 4.3 8.8 1.0 C C:THR346 4.3 12.3 1.0 N C:GLY348 4.3 8.5 1.0 N C:ASN294 4.4 8.7 1.0 CB C:ASP324 4.4 8.1 1.0 OD1 C:ASP324 4.4 8.5 1.0 C C:ASN294 4.4 11.1 1.0 O C:ARG344 4.5 13.5 1.0 N C:GLN347 4.5 12.4 1.0 N C:GLY297 4.5 13.5 1.0 N C:THR346 4.6 14.8 1.0 CA C:GLY297 4.6 10.1 1.0 CA C:ASP293 4.7 8.0 1.0 N C:TRP295 4.7 8.7 1.0 CA C:GLN347 4.7 11.6 1.0 OD1 C:ASP293 4.8 9.9 1.0 CB C:ASP293 4.8 9.5 1.0 CA C:THR346 4.8 12.1 1.0 N C:ASP293 4.8 6.3 1.0 O C:ASN294 4.9 11.2 1.0

C.J.Vavricka, Y.Liu, H.Kiyota, N.Sriwilaijaroen, J.Qi, K.Tanaka, Y.Wu, Q.Li, Y.Li, J.Yan, Y.Suzuki, G.F.Gao. Influenza Neuraminidase Operates Via A Nucleophilic Mechanism and Can Be Targeted By Covalent Inhibitors Nat Commun V. 4 1491 2013.
ISSN: ESSN 2041-1723
PubMed: 23422659
DOI: 10.1038/NCOMMS2487