Calcium in PDB 9cyg: Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2)

All present enzymatic activity of Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2):
3.2.1.18;

The binding sites of Calcium atom in the Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) (pdb code 9cyg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2), PDB code: 9cyg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:135.8 occ:1.00 O A:GLY297 2.9 121.0 1.0 O A:ASP293 3.0 141.2 1.0 O A:GLY346 3.0 139.7 1.0 OD2 A:ASP324 3.5 108.8 1.0 C A:GLY297 3.9 118.9 1.0 N A:GLY348 4.0 119.5 1.0 C A:ASP293 4.2 136.0 1.0 CA A:GLY348 4.2 118.0 1.0 CG A:ASP324 4.2 108.7 1.0 C A:GLY346 4.2 138.7 1.0 O A:LYS344 4.4 116.7 1.0 O A:ASN294 4.5 142.5 1.0 C A:ASN294 4.5 140.3 1.0 CA A:SER298 4.6 109.2 1.0 C A:HIS347 4.6 137.2 1.0 N A:TRP295 4.6 127.2 1.0 N A:SER298 4.6 106.8 1.0 N A:GLY297 4.8 121.6 1.0 CA A:TRP295 4.8 127.1 1.0 OD1 A:ASP324 4.8 114.7 1.0 N A:GLY346 4.8 139.0 1.0 CA A:HIS347 5.0 134.4 1.0 CB A:ASP324 5.0 103.1 1.0 CA A:GLY297 5.0 120.6 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:139.8 occ:1.00 O B:GLY297 2.9 121.5 1.0 O B:ASP293 3.0 141.1 1.0 O B:GLY346 3.0 140.1 1.0 OD2 B:ASP324 3.5 111.2 1.0 C B:GLY297 3.9 118.8 1.0 N B:GLY348 4.0 119.6 1.0 C B:ASP293 4.2 136.1 1.0 CA B:GLY348 4.2 117.2 1.0 CG B:ASP324 4.2 111.0 1.0 C B:GLY346 4.3 138.5 1.0 O B:LYS344 4.4 118.7 1.0 O B:ASN294 4.5 142.6 1.0 C B:ASN294 4.5 140.2 1.0 CA B:SER298 4.6 111.4 1.0 C B:HIS347 4.6 137.8 1.0 N B:TRP295 4.6 127.8 1.0 N B:SER298 4.6 107.1 1.0 N B:GLY297 4.8 120.5 1.0 CA B:TRP295 4.8 128.4 1.0 OD1 B:ASP324 4.8 116.5 1.0 N B:GLY346 4.8 138.4 1.0 CB B:ASP324 4.9 105.0 1.0 CA B:GLY297 5.0 120.9 1.0 CA B:HIS347 5.0 134.8 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:139.5 occ:1.00 O C:GLY297 2.9 122.1 1.0 O C:ASP293 3.0 141.7 1.0 O C:GLY346 3.0 141.7 1.0 OD2 C:ASP324 3.5 109.8 1.0 C C:GLY297 3.9 119.3 1.0 N C:GLY348 4.0 119.0 1.0 C C:ASP293 4.2 137.0 1.0 CA C:GLY348 4.2 117.0 1.0 CG C:ASP324 4.2 109.5 1.0 C C:GLY346 4.3 140.6 1.0 O C:LYS344 4.4 118.5 1.0 O C:ASN294 4.5 143.4 1.0 C C:ASN294 4.5 141.1 1.0 CA C:SER298 4.6 110.8 1.0 C C:HIS347 4.6 137.6 1.0 N C:TRP295 4.6 128.4 1.0 N C:SER298 4.6 107.9 1.0 N C:GLY297 4.8 120.6 1.0 CA C:TRP295 4.8 128.2 1.0 OD1 C:ASP324 4.8 114.5 1.0 N C:GLY346 4.8 140.4 1.0 CB C:ASP324 4.9 103.5 1.0 CA C:HIS347 5.0 134.7 1.0 CA C:GLY297 5.0 121.2 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:138.6 occ:1.00 O D:GLY297 2.9 122.6 1.0 O D:ASP293 3.0 142.3 1.0 O D:GLY346 3.0 141.3 1.0 OD2 D:ASP324 3.5 110.1 1.0 C D:GLY297 3.9 120.3 1.0 N D:GLY348 4.0 119.5 1.0 C D:ASP293 4.2 137.2 1.0 CA D:GLY348 4.2 117.0 1.0 CG D:ASP324 4.2 109.5 1.0 C D:GLY346 4.3 140.6 1.0 O D:LYS344 4.4 119.0 1.0 O D:ASN294 4.5 142.4 1.0 C D:ASN294 4.5 140.3 1.0 CA D:SER298 4.6 110.6 1.0 C D:HIS347 4.6 137.5 1.0 N D:TRP295 4.6 128.1 1.0 N D:SER298 4.6 107.9 1.0 N D:GLY297 4.8 121.8 1.0 CA D:TRP295 4.8 128.6 1.0 OD1 D:ASP324 4.8 114.9 1.0 N D:GLY346 4.8 141.2 1.0 CB D:ASP324 4.9 103.3 1.0 CA D:HIS347 5.0 134.8 1.0 CA D:GLY297 5.0 122.2 1.0

G.Jo, S.Yamayoshi, K.M.Ma, O.Swanson, J.L.Torres, J.A.Ferguson, M.L.Fernandez-Quintero, J.Huang, J.Copps, A.J.Rodriguez, J.M.Steichen, Y.Kawaoka, J.Han, A.B.Ward. Structural Basis of Broad Protection Against Influenza Virus By Human Antibodies Targeting the Neuraminidase Active Site Via A Recurring Motif in Cdr H3. Nat Commun V. 16 7067 2025.
ISSN: ESSN 2041-1723
PubMed: 40750588
DOI: 10.1038/S41467-025-62174-2