Calcium in PDB 9gqq: Influenza Neuraminidase N1/19 Hybrid

All present enzymatic activity of Influenza Neuraminidase N1/19 Hybrid:
3.2.1.18;

The structure of Influenza Neuraminidase N1/19 Hybrid, PDB code: 9gqq was solved by T.A.Bowden, G.C.Paesen, P.Rijal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.69 / 1.78
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	115.412, 234.367, 115.651, 90, 90, 90
R / Rfree (%)	18.9 / 21.5

The binding sites of Calcium atom in the Influenza Neuraminidase N1/19 Hybrid (pdb code 9gqq). 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 N1/19 Hybrid, PDB code: 9gqq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Influenza Neuraminidase N1/19 Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Influenza Neuraminidase N1/19 Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:14.6 occ:1.00 OD1 A:ASP376 2.2 9.0 1.0 OD1 A:ASN378 2.2 10.8 1.0 O A:SER386 2.3 15.3 1.0 O A:HOH683 2.3 17.5 1.0 OD1 A:ASP384 2.4 15.2 1.0 OD2 A:ASP376 2.7 11.1 1.0 CG A:ASP376 2.8 10.0 1.0 CG A:ASP384 3.3 13.8 1.0 CG A:ASN378 3.3 12.8 1.0 OD2 A:ASP384 3.4 24.1 1.0 C A:SER386 3.4 18.3 1.0 ND2 A:ASN378 3.9 11.9 1.0 N A:SER386 4.0 16.1 1.0 O A:ASP384 4.0 20.8 1.0 CA A:SER386 4.2 14.2 1.0 CB A:ASP376 4.3 7.2 1.0 N A:GLY379 4.3 9.4 1.0 N A:PHE387 4.4 17.2 1.0 C A:ASN378 4.5 11.7 1.0 CB A:SER386 4.5 23.4 1.0 N A:ASN378 4.5 7.1 1.0 C A:ASP384 4.5 12.9 1.0 CA A:GLY379 4.6 6.2 1.0 O A:HOH776 4.6 22.6 1.0 CB A:ASN378 4.6 15.0 1.0 CB A:ASP384 4.6 12.9 1.0 OG A:SER319 4.7 11.7 1.0 CA A:PHE387 4.7 14.7 1.0 CA A:ASN378 4.7 12.3 1.0 C A:SER385 4.9 18.7 1.0 CA A:ASP376 4.9 8.7 1.0 O A:ASN378 4.9 15.5 1.0

Calcium binding site 2 out of 4 in the Influenza Neuraminidase N1/19 Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Influenza Neuraminidase N1/19 Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:22.3 occ:1.00 O A:ASN344 2.2 27.5 1.0 O A:GLY298 2.3 22.4 1.0 O A:GLY342 2.3 24.0 1.0 OD2 A:ASP324 2.5 15.5 1.0 O A:ASP294 2.5 22.4 1.0 C A:GLY342 3.3 21.2 1.0 C A:ASN344 3.4 24.2 1.0 C A:GLY298 3.5 19.5 1.0 CG A:ASP324 3.5 19.2 1.0 C A:ASP294 3.7 17.3 1.0 CA A:GLY345 4.0 21.4 1.0 CA A:GLY342 4.0 24.1 1.0 O A:ALA343 4.0 24.1 1.0 C A:ALA343 4.1 20.2 1.0 N A:GLY345 4.1 21.9 1.0 CB A:ASP324 4.3 16.2 1.0 N A:ASN344 4.3 29.0 1.0 N A:SER299 4.3 15.1 1.0 O A:HOH647 4.3 15.6 1.0 CA A:SER299 4.3 18.3 1.0 O A:ASN341 4.3 26.1 1.0 N A:ALA343 4.3 23.7 1.0 N A:GLY298 4.4 18.8 1.0 OD1 A:ASP324 4.4 17.6 1.0 CA A:ASN295 4.4 25.5 1.0 CA A:GLY298 4.4 12.2 1.0 CA A:ASN344 4.5 28.6 1.0 N A:ASN295 4.5 17.9 1.0 CA A:ALA343 4.6 20.4 1.0 O A:PRO326 4.7 22.8 1.0 CA A:ASP294 4.8 16.4 1.0 C A:ASN295 4.8 32.2 1.0 CB A:ASP294 4.9 17.6 1.0 N A:ASP294 5.0 15.0 1.0

Calcium binding site 3 out of 4 in the Influenza Neuraminidase N1/19 Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Influenza Neuraminidase N1/19 Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:14.2 occ:1.00 OD1 B:ASP376 2.2 13.4 1.0 OD1 B:ASN378 2.2 7.0 1.0 O B:SER386 2.3 17.6 1.0 O B:HOH604 2.3 18.3 1.0 OD1 B:ASP384 2.3 19.9 1.0 OD2 B:ASP376 2.6 13.2 1.0 CG B:ASP376 2.8 11.2 1.0 CG B:ASP384 3.2 19.4 1.0 CG B:ASN378 3.4 11.4 1.0 C B:SER386 3.4 15.0 1.0 OD2 B:ASP384 3.4 18.7 1.0 ND2 B:ASN378 3.9 14.6 1.0 N B:SER386 4.0 18.5 1.0 O B:ASP384 4.0 21.7 1.0 CA B:SER386 4.1 22.1 1.0 CB B:ASP376 4.3 6.7 1.0 N B:GLY379 4.3 10.6 1.0 CB B:SER386 4.4 30.6 1.0 N B:PHE387 4.5 20.0 1.0 C B:ASN378 4.5 14.5 1.0 C B:ASP384 4.5 18.7 1.0 N B:ASN378 4.5 7.0 1.0 CA B:GLY379 4.5 9.4 1.0 CB B:ASP384 4.6 14.1 1.0 CB B:ASN378 4.6 13.2 1.0 O B:HOH761 4.7 24.5 1.0 CA B:PHE387 4.7 10.3 1.0 OG B:SER319 4.7 14.7 1.0 CA B:ASN378 4.8 18.3 1.0 C B:SER385 4.9 22.8 1.0 O B:ASN378 4.9 16.3 1.0 CA B:ASP376 4.9 7.4 1.0

Calcium binding site 4 out of 4 in the Influenza Neuraminidase N1/19 Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Influenza Neuraminidase N1/19 Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:28.0 occ:1.00 O B:ASN344 2.1 26.8 1.0 O B:GLY298 2.3 21.7 1.0 O B:GLY342 2.3 19.7 1.0 OD2 B:ASP324 2.5 14.3 1.0 O B:ASP294 2.5 21.9 1.0 C B:ASN344 3.3 35.8 1.0 C B:GLY342 3.3 22.1 1.0 C B:GLY298 3.4 14.7 1.0 CG B:ASP324 3.5 24.4 1.0 C B:ASP294 3.7 15.3 1.0 O B:ALA343 3.9 21.6 1.0 CA B:GLY345 3.9 22.5 1.0 C B:ALA343 4.0 21.9 1.0 CA B:GLY342 4.0 17.8 1.0 N B:GLY345 4.0 26.5 1.0 O B:HOH654 4.2 10.0 1.0 N B:ASN344 4.2 28.0 1.0 N B:SER299 4.2 11.1 1.0 CB B:ASP324 4.2 19.1 1.0 CA B:SER299 4.3 16.4 1.0 N B:ALA343 4.3 30.2 1.0 OD1 B:ASP324 4.3 19.7 1.0 N B:GLY298 4.3 15.2 1.0 O B:ASN341 4.4 31.3 1.0 CA B:ASN344 4.4 28.5 1.0 CA B:GLY298 4.4 15.0 1.0 CA B:ASN295 4.4 23.7 1.0 N B:ASN295 4.5 16.4 1.0 CA B:ALA343 4.5 24.1 1.0 O B:PRO326 4.6 21.1 1.0 CA B:ASP294 4.8 13.2 1.0 C B:ASN295 4.8 24.1 1.0 CB B:ASP294 4.9 12.8 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