Calcium in PDB 9gqx: Influenza Neuraminidase MSN1

All present enzymatic activity of Influenza Neuraminidase MSN1:
3.2.1.18;

The structure of Influenza Neuraminidase MSN1, PDB code: 9gqx was solved by R.Pramila, G.C.Paesen, T.A.Bowden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.17 / 1.98
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	92.165, 92.165, 147.903, 90, 90, 90
R / Rfree (%)	21.1 / 23.8

The binding sites of Calcium atom in the Influenza Neuraminidase MSN1 (pdb code 9gqx). 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 MSN1, PDB code: 9gqx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Influenza Neuraminidase MSN1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Influenza Neuraminidase MSN1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:24.9 occ:1.00 O A:TYR344 2.3 25.8 1.0 O A:GLY298 2.3 26.1 1.0 O A:GLY342 2.4 22.9 1.0 O A:ASP294 2.4 25.0 1.0 O A:HOH886 2.5 21.7 1.0 OD2 A:ASP324 2.5 21.4 1.0 C A:GLY342 3.4 21.8 1.0 C A:GLY298 3.4 27.2 1.0 C A:TYR344 3.5 17.8 1.0 CG A:ASP324 3.6 25.9 1.0 C A:ASP294 3.6 19.8 1.0 CA A:GLY345 3.9 19.2 1.0 CA A:GLY342 4.0 24.1 1.0 O A:HOH872 4.0 16.1 1.0 O A:ALA343 4.0 18.9 1.0 C A:ALA343 4.1 21.5 1.0 N A:GLY298 4.2 22.4 1.0 N A:GLY345 4.2 22.4 1.0 N A:SER299 4.2 26.2 1.0 CB A:ASP324 4.3 19.3 1.0 CA A:GLY298 4.3 21.8 1.0 CA A:SER299 4.3 20.6 1.0 CA A:ASN295 4.3 22.4 1.0 N A:ALA343 4.4 20.6 1.0 N A:ASN295 4.4 22.0 1.0 OD1 A:ASP324 4.4 23.4 1.0 N A:TYR344 4.4 22.7 1.0 CA A:ASP294 4.6 19.7 1.0 CA A:ALA343 4.6 19.7 1.0 CA A:TYR344 4.6 18.4 1.0 CB A:ASP294 4.7 20.8 1.0 C A:ASN295 4.7 25.9 1.0 N A:ASP294 4.8 26.4 1.0 O A:ASN341 4.8 25.0 1.0 O A:PRO326 4.9 21.0 1.0 OD1 A:ASP294 4.9 20.8 1.0

Calcium binding site 2 out of 4 in the Influenza Neuraminidase MSN1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Influenza Neuraminidase MSN1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:36.1 occ:1.00 OD1 A:ASN378 2.2 28.5 1.0 OD1 A:ASP376 2.3 27.4 1.0 OD1 A:ASP384 2.3 28.2 1.0 O A:SER386 2.3 24.1 1.0 O A:HOH808 2.5 21.7 1.0 O A:HOH909 2.6 19.9 1.0 OD2 A:ASP376 2.9 22.9 1.0 CG A:ASP376 2.9 24.8 1.0 CG A:ASP384 3.1 23.1 1.0 OD2 A:ASP384 3.3 21.2 1.0 CG A:ASN378 3.3 34.9 1.0 C A:SER386 3.5 27.9 1.0 O A:ASP384 3.7 24.4 1.0 ND2 A:ASN378 3.9 36.0 1.0 N A:SER386 4.0 19.6 1.0 CA A:SER386 4.2 35.1 1.0 C A:ASP384 4.3 30.3 1.0 CB A:ASP376 4.4 16.2 1.0 O A:HOH1074 4.4 24.2 1.0 CB A:ASP384 4.5 26.2 1.0 N A:GLY379 4.5 22.0 1.0 N A:PHE387 4.5 20.7 1.0 C A:ASN378 4.5 26.0 1.0 CB A:SER386 4.5 22.4 1.0 N A:ASN378 4.6 19.1 1.0 CB A:ASN378 4.6 27.9 1.0 CA A:GLY379 4.7 18.5 1.0 CA A:PHE387 4.8 29.1 1.0 CA A:ASN378 4.8 24.9 1.0 CA A:ASP384 4.8 23.9 1.0 C A:SER385 4.9 28.8 1.0 OG A:SER319 4.9 21.3 1.0 O A:ASN378 4.9 24.1 1.0 CA A:ASP376 4.9 20.1 1.0

Calcium binding site 3 out of 4 in the Influenza Neuraminidase MSN1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Influenza Neuraminidase MSN1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:36.5 occ:1.00 O B:TYR344 2.3 27.6 1.0 O B:GLY298 2.5 21.7 1.0 O B:ASP294 2.5 29.9 1.0 O B:GLY342 2.5 27.4 1.0 OD2 B:ASP324 2.6 27.0 1.0 C B:GLY342 3.4 25.3 1.0 C B:TYR344 3.5 23.0 1.0 C B:GLY298 3.5 31.9 1.0 CG B:ASP324 3.6 27.6 1.0 C B:ASP294 3.7 22.3 1.0 CA B:GLY345 3.9 20.1 1.0 O B:ALA343 4.0 28.5 1.0 CA B:GLY342 4.0 33.7 1.0 O B:HOH821 4.1 21.6 1.0 C B:ALA343 4.1 29.9 1.0 N B:GLY345 4.1 18.7 1.0 N B:GLY298 4.2 27.9 1.0 N B:SER299 4.3 26.6 1.0 CA B:SER299 4.3 26.8 1.0 CA B:ASN295 4.4 27.0 1.0 CB B:ASP324 4.4 25.4 1.0 CA B:GLY298 4.4 28.1 1.0 N B:ALA343 4.4 23.9 1.0 N B:TYR344 4.5 26.8 1.0 OD1 B:ASP324 4.5 31.2 1.0 N B:ASN295 4.5 21.6 1.0 O B:ASN341 4.5 34.6 1.0 CA B:TYR344 4.6 28.2 1.0 CA B:ALA343 4.7 25.8 1.0 CA B:ASP294 4.7 22.1 1.0 C B:ASN295 4.7 25.4 1.0 O B:PRO326 4.8 29.9 1.0 CB B:ASP294 4.9 27.4 1.0 N B:ASP294 4.9 26.0 1.0

Calcium binding site 4 out of 4 in the Influenza Neuraminidase MSN1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Influenza Neuraminidase MSN1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:49.6 occ:1.00 OD1 B:ASP376 2.3 35.7 1.0 OD1 B:ASP384 2.3 44.1 1.0 OD1 B:ASN378 2.4 40.8 1.0 O B:SER386 2.4 43.3 1.0 O B:HOH967 2.7 42.3 1.0 OD2 B:ASP376 2.8 32.6 1.0 CG B:ASP376 2.9 31.5 1.0 CG B:ASP384 3.1 39.4 1.0 OD2 B:ASP384 3.3 38.1 1.0 CG B:ASN378 3.5 39.0 1.0 O B:ASP384 3.5 36.0 1.0 C B:SER386 3.5 44.0 1.0 N B:SER386 3.9 40.6 1.0 ND2 B:ASN378 4.0 51.2 1.0 C B:ASP384 4.2 49.0 1.0 CA B:SER386 4.2 49.7 1.0 CB B:ASP376 4.4 28.6 1.0 CB B:ASP384 4.4 35.5 1.0 CB B:SER386 4.4 43.5 1.0 N B:GLY379 4.5 30.8 1.0 C B:ASN378 4.6 34.3 1.0 CA B:GLY379 4.6 25.9 1.0 N B:PHE387 4.6 38.8 1.0 N B:ASN378 4.7 31.4 1.0 CB B:ASN378 4.7 28.6 1.0 CA B:ASP384 4.7 37.0 1.0 C B:SER385 4.8 40.4 1.0 O B:HOH1017 4.8 37.7 1.0 CA B:ASN378 4.9 30.6 1.0 N B:SER385 4.9 41.0 1.0 CA B:PHE387 4.9 38.6 1.0 N B:ASP384 4.9 33.2 1.0 O B:ASN378 5.0 29.3 1.0 CA B:ASP376 5.0 28.2 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