Calcium in PDB 4h52: Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC

The structure of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC, PDB code: 4h52 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)	38.82 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	114.698, 139.704, 140.070, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.5

The structure of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Calcium atom in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC (pdb code 4h52). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC, PDB code: 4h52:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:15.1 occ:1.00 O A:GLN347 2.4 15.0 1.0 OD2 A:ASP324 2.4 15.8 1.0 O A:ASP293 2.5 14.3 1.0 O A:HOH602 2.5 13.2 1.0 O A:GLY345 2.6 14.4 1.0 O A:GLY297 2.7 16.7 1.0 CG A:ASP324 3.5 18.2 1.0 C A:GLY345 3.6 18.5 1.0 C A:GLN347 3.6 16.8 1.0 C A:GLY297 3.7 18.6 1.0 C A:ASP293 3.7 13.0 1.0 CA A:GLY348 4.1 10.0 1.0 O A:HOH610 4.1 12.6 1.0 CA A:GLY345 4.2 16.1 1.0 CA A:ASN294 4.2 13.1 1.0 CA A:SER298 4.3 14.4 1.0 N A:GLY348 4.3 13.0 1.0 N A:SER298 4.3 13.5 1.0 OD1 A:ASP324 4.3 12.5 1.0 C A:THR346 4.3 18.8 1.0 O A:THR346 4.4 16.2 1.0 CB A:ASP324 4.4 14.4 1.0 N A:ASN294 4.4 13.3 1.0 C A:ASN294 4.5 14.1 1.0 O A:ARG344 4.5 16.8 1.0 N A:GLN347 4.5 17.9 1.0 N A:GLY297 4.6 15.3 1.0 N A:THR346 4.6 18.4 1.0 CA A:GLY297 4.7 15.3 1.0 OD1 A:ASP293 4.7 17.5 1.0 CA A:GLN347 4.7 20.0 1.0 N A:TRP295 4.7 12.9 1.0 CA A:ASP293 4.7 14.0 1.0 CA A:THR346 4.8 18.6 1.0 N A:ASP293 4.9 12.4 1.0 CB A:ASP293 4.9 13.6 1.0 O A:PRO326 5.0 12.8 1.0 O A:ASN294 5.0 14.6 1.0 CB A:SER298 5.0 13.1 1.0

Calcium binding site 2 out of 2 in the Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wild-Type Influenza N2 Neuraminidase Covalent Complex with 3-Fluoro- NEU5AC within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:15.3 occ:1.00 OD2 B:ASP324 2.4 16.8 1.0 O B:ASP293 2.4 14.4 1.0 O B:GLN347 2.5 14.7 1.0 O B:HOH607 2.5 15.7 1.0 O B:GLY345 2.5 14.5 1.0 O B:GLY297 2.6 16.5 1.0 CG B:ASP324 3.5 18.8 1.0 C B:GLY345 3.6 19.6 1.0 C B:GLY297 3.6 20.1 1.0 C B:ASP293 3.7 13.3 1.0 C B:GLN347 3.7 17.6 1.0 CA B:GLY348 4.1 13.4 1.0 O B:HOH609 4.1 14.0 1.0 CA B:ASN294 4.2 12.1 1.0 CA B:GLY345 4.2 19.1 1.0 CA B:SER298 4.3 14.4 1.0 N B:SER298 4.3 13.5 1.0 C B:THR346 4.3 16.4 1.0 O B:THR346 4.3 16.7 1.0 N B:GLY348 4.4 14.4 1.0 CB B:ASP324 4.4 15.1 1.0 OD1 B:ASP324 4.4 13.3 1.0 N B:ASN294 4.4 12.9 1.0 C B:ASN294 4.5 15.7 1.0 O B:ARG344 4.5 19.1 1.0 N B:GLN347 4.5 18.4 1.0 N B:GLY297 4.6 16.1 1.0 N B:THR346 4.6 17.1 1.0 CA B:GLY297 4.6 13.9 1.0 OD1 B:ASP293 4.7 17.5 1.0 CA B:ASP293 4.7 13.9 1.0 N B:TRP295 4.8 12.6 1.0 CA B:GLN347 4.8 16.5 1.0 CA B:THR346 4.8 16.4 1.0 N B:ASP293 4.8 13.1 1.0 CB B:ASP293 4.9 14.0 1.0 O B:ASN294 4.9 15.4 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