Calcium in PDB 9gqt: Influenza Neuraminidase Hybrid N1/09

All present enzymatic activity of Influenza Neuraminidase Hybrid N1/09:
3.2.1.18;

The structure of Influenza Neuraminidase Hybrid N1/09, PDB code: 9gqt was solved by T.A.Bowden, G.C.Paesen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.12 / 1.94
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	92.089, 92.089, 146.804, 90, 90, 90
R / Rfree (%)	18.3 / 21.2

The binding sites of Calcium atom in the Influenza Neuraminidase Hybrid N1/09 (pdb code 9gqt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Influenza Neuraminidase Hybrid N1/09, PDB code: 9gqt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Influenza Neuraminidase Hybrid N1/09


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Influenza Neuraminidase Hybrid N1/09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:29.7 occ:1.00 O A:SER386 2.3 23.1 1.0 OD1 A:ASP376 2.3 21.7 1.0 OD1 A:ASN378 2.3 21.3 1.0 OD1 A:ASP384 2.4 22.7 1.0 CG A:ASP376 3.0 30.2 1.0 OD2 A:ASP376 3.0 22.3 1.0 CG A:ASP384 3.1 20.3 1.0 OD2 A:ASP384 3.2 21.5 1.0 CG A:ASN378 3.4 25.4 1.0 C A:SER386 3.5 24.2 1.0 ND2 A:ASN378 3.9 22.0 1.0 O A:ASP384 4.0 19.1 1.0 N A:SER386 4.0 19.8 1.0 CA A:SER386 4.2 24.9 1.0 CB A:ASP376 4.4 14.8 1.0 C A:ASP384 4.5 27.6 1.0 N A:ASN378 4.5 17.7 1.0 N A:GLY379 4.5 17.7 1.0 N A:PHE387 4.5 22.8 1.0 CB A:SER386 4.5 20.6 1.0 CB A:ASP384 4.5 21.4 1.0 O A:HOH898 4.6 30.4 1.0 C A:ASN378 4.6 23.5 1.0 CA A:GLY379 4.6 16.9 1.0 CB A:ASN378 4.7 15.8 1.0 CA A:PHE387 4.8 24.6 1.0 CA A:ASN378 4.8 21.5 1.0 CA A:ASP376 4.9 21.0 1.0 C A:ASP376 5.0 19.7 1.0 C A:SER385 5.0 23.9 1.0 O A:ASN378 5.0 19.3 1.0 CA A:ASP384 5.0 23.4 1.0

Calcium binding site 2 out of 4 in the Influenza Neuraminidase Hybrid N1/09


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Influenza Neuraminidase Hybrid N1/09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:19.4 occ:1.00 O A:ASP294 2.3 19.5 1.0 O A:GLY298 2.4 19.0 1.0 O A:ASN344 2.4 21.5 1.0 O A:GLY342 2.4 17.6 1.0 OD2 A:ASP324 2.4 16.4 1.0 C A:GLY342 3.4 18.1 1.0 C A:GLY298 3.5 25.6 1.0 CG A:ASP324 3.5 22.0 1.0 C A:ASN344 3.5 12.2 1.0 C A:ASP294 3.6 17.0 1.0 O A:HOH642 3.9 16.4 1.0 CA A:GLY345 3.9 18.3 1.0 O A:ALA343 4.0 15.8 1.0 CA A:GLY342 4.1 16.1 1.0 C A:ALA343 4.1 19.3 1.0 N A:GLY345 4.2 13.9 1.0 N A:GLY298 4.3 17.0 1.0 CB A:ASP324 4.3 22.4 1.0 N A:ALA343 4.3 12.6 1.0 OD1 A:ASP324 4.3 20.4 1.0 CA A:ASN295 4.3 13.6 1.0 N A:SER299 4.3 16.6 1.0 CA A:GLY298 4.4 17.1 1.0 N A:ASN295 4.4 14.0 1.0 N A:ASN344 4.5 16.1 1.0 CA A:SER299 4.5 15.2 1.0 CA A:ALA343 4.5 14.9 1.0 CA A:ASP294 4.5 13.8 1.0 CB A:ASP294 4.6 15.2 1.0 N A:ASP294 4.7 17.5 1.0 CA A:ASN344 4.7 17.9 1.0 O A:ASN341 4.7 22.4 1.0 C A:ASN295 4.8 22.1 1.0 OD1 A:ASP294 4.8 18.2 1.0 O A:PRO326 4.9 14.7 1.0

Calcium binding site 3 out of 4 in the Influenza Neuraminidase Hybrid N1/09


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Influenza Neuraminidase Hybrid N1/09 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:39.0 occ:1.00 O B:SER386 2.3 33.7 1.0 OD1 B:ASN378 2.3 24.1 1.0 OD1 B:ASP376 2.4 25.6 1.0 OD1 B:ASP384 2.5 42.6 1.0 OD2 B:ASP376 3.0 19.2 1.0 CG B:ASP376 3.0 30.2 1.0 CG B:ASP384 3.3 33.8 1.0 OD2 B:ASP384 3.4 34.4 1.0 CG B:ASN378 3.4 32.8 1.0 C B:SER386 3.4 31.6 1.0 O B:ASP384 3.8 23.8 1.0 N B:SER386 3.8 27.9 1.0 ND2 B:ASN378 3.9 29.4 1.0 CA B:SER386 4.1 35.5 1.0 C B:ASP384 4.3 31.5 1.0 CB B:SER386 4.4 28.4 1.0 CB B:ASP376 4.5 19.7 1.0 N B:PHE387 4.5 27.2 1.0 N B:GLY379 4.6 28.6 1.0 N B:ASN378 4.6 17.2 1.0 CB B:ASP384 4.6 24.9 1.0 C B:ASN378 4.7 29.5 1.0 CA B:GLY379 4.7 19.7 1.0 CB B:ASN378 4.7 22.1 1.0 C B:SER385 4.7 24.3 1.0 CA B:PHE387 4.8 30.0 1.0 N B:SER385 4.9 30.3 1.0 CA B:ASN378 4.9 24.0 1.0 CA B:ASP384 5.0 22.7 1.0 CA B:ASP376 5.0 19.6 1.0

Calcium binding site 4 out of 4 in the Influenza Neuraminidase Hybrid N1/09


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Influenza Neuraminidase Hybrid N1/09 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:22.8 occ:1.00 O B:ASN344 2.3 17.8 1.0 O B:ASP294 2.4 21.5 1.0 OD2 B:ASP324 2.4 24.5 1.0 O B:GLY298 2.5 22.2 1.0 O B:HOH660 2.5 20.1 1.0 O B:GLY342 2.5 18.8 1.0 CG B:ASP324 3.5 20.2 1.0 C B:GLY298 3.5 19.6 1.0 C B:GLY342 3.5 20.4 1.0 C B:ASN344 3.5 18.5 1.0 C B:ASP294 3.6 15.8 1.0 O B:HOH638 4.0 15.7 1.0 CA B:GLY345 4.0 14.7 1.0 C B:ALA343 4.2 21.9 1.0 CA B:GLY342 4.2 16.8 1.0 N B:GLY298 4.2 22.0 1.0 O B:ALA343 4.2 16.9 1.0 N B:GLY345 4.3 16.4 1.0 CB B:ASP324 4.3 21.0 1.0 CA B:ASN295 4.3 19.8 1.0 OD1 B:ASP324 4.3 15.4 1.0 N B:SER299 4.3 20.6 1.0 CA B:GLY298 4.4 16.7 1.0 N B:ASN295 4.4 16.2 1.0 N B:ASN344 4.5 17.9 1.0 CA B:SER299 4.5 17.8 1.0 N B:ALA343 4.5 19.2 1.0 CA B:ASP294 4.6 16.9 1.0 CA B:ASN344 4.6 21.1 1.0 CA B:ALA343 4.7 22.4 1.0 C B:ASN295 4.7 21.0 1.0 O B:ASN341 4.7 20.2 1.0 CB B:ASP294 4.7 14.1 1.0 N B:ASP294 4.8 18.1 1.0 OD1 B:ASP294 4.9 21.5 1.0 O B:PRO326 4.9 14.3 1.0 O B:ASN295 4.9 22.1 1.0

P.Rijal, L.Wei, G.C.Paesen, D.I.Stuart, M.R.Howarth, K.Y.A.Huang, T.A.Bowden, A.R.Townsend. Structure-Guided Loop Grafting Improves Expression and Stability of Influenza Neuraminidase For Vaccine Development Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.105317.2