Calcium in PDB 9cyf: Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2)

All present enzymatic activity of Cryo-Em Structure of DA03E17 Fab in Complex with 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 DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) (pdb code 9cyf). 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 DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2), PDB code: 9cyf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with 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 DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:86.3 occ:1.00 O A:GLY297 2.3 75.5 1.0 O A:ASP293 2.4 70.8 1.0 O A:HIS347 2.5 71.5 1.0 OD2 A:ASP324 3.3 52.0 1.0 C A:GLY297 3.6 69.3 1.0 C A:ASP293 3.7 68.9 1.0 C A:HIS347 3.7 66.5 1.0 CG A:ASP324 3.7 54.1 1.0 O A:LYS344 3.8 63.9 1.0 CA A:GLY348 4.0 47.0 1.0 OD1 A:ASP324 4.2 59.6 1.0 CB A:ASP324 4.3 51.8 1.0 N A:GLY348 4.3 55.7 1.0 CA A:ASN294 4.3 71.5 1.0 N A:GLY297 4.4 65.5 1.0 N A:SER298 4.4 57.7 1.0 CA A:GLY345 4.4 80.9 1.0 CA A:SER298 4.4 56.0 1.0 N A:ASN294 4.4 68.0 1.0 CA A:GLY297 4.6 64.2 1.0 C A:ASN294 4.6 73.6 1.0 N A:HIS347 4.7 73.5 1.0 CA A:ASP293 4.7 68.3 1.0 CB A:ASP293 4.8 66.9 1.0 N A:TRP295 4.8 79.2 1.0 C A:LYS344 4.8 61.7 1.0 CA A:HIS347 4.9 68.6 1.0 C A:GLY345 4.9 85.7 1.0 N A:ASP293 5.0 68.4 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with 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 DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:87.5 occ:1.00 O B:GLY297 2.3 76.0 1.0 O B:ASP293 2.4 70.4 1.0 O B:HIS347 2.5 71.3 1.0 OD2 B:ASP324 3.3 51.4 1.0 C B:GLY297 3.6 69.3 1.0 C B:ASP293 3.7 68.4 1.0 C B:HIS347 3.7 66.3 1.0 CG B:ASP324 3.7 54.2 1.0 O B:LYS344 3.8 64.0 1.0 CA B:GLY348 4.0 46.0 1.0 OD1 B:ASP324 4.2 60.1 1.0 CB B:ASP324 4.3 51.8 1.0 N B:GLY348 4.3 54.8 1.0 CA B:ASN294 4.3 71.2 1.0 N B:GLY297 4.4 65.2 1.0 N B:SER298 4.4 58.0 1.0 CA B:GLY345 4.4 79.9 1.0 CA B:SER298 4.4 56.4 1.0 N B:ASN294 4.4 67.5 1.0 CA B:GLY297 4.6 63.8 1.0 C B:ASN294 4.6 73.1 1.0 N B:HIS347 4.7 72.8 1.0 CA B:ASP293 4.7 68.2 1.0 CB B:ASP293 4.8 66.8 1.0 N B:TRP295 4.8 79.9 1.0 C B:LYS344 4.9 61.2 1.0 CA B:HIS347 4.9 68.4 1.0 C B:GLY345 4.9 84.6 1.0 N B:ASP293 5.0 68.0 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with 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 DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:88.0 occ:1.00 O C:GLY297 2.3 75.8 1.0 O C:ASP293 2.4 69.5 1.0 O C:HIS347 2.5 72.0 1.0 OD2 C:ASP324 3.3 51.9 1.0 C C:GLY297 3.6 69.1 1.0 C C:ASP293 3.7 67.9 1.0 C C:HIS347 3.7 65.9 1.0 CG C:ASP324 3.7 54.9 1.0 O C:LYS344 3.8 64.5 1.0 CA C:GLY348 4.0 45.9 1.0 OD1 C:ASP324 4.2 59.9 1.0 CB C:ASP324 4.3 52.3 1.0 N C:GLY348 4.3 54.9 1.0 CA C:ASN294 4.3 71.1 1.0 N C:GLY297 4.4 65.1 1.0 N C:SER298 4.4 57.8 1.0 CA C:GLY345 4.4 80.1 1.0 CA C:SER298 4.4 56.4 1.0 N C:ASN294 4.4 67.1 1.0 CA C:GLY297 4.6 64.3 1.0 C C:ASN294 4.6 72.6 1.0 N C:HIS347 4.7 72.6 1.0 CA C:ASP293 4.7 67.6 1.0 CB C:ASP293 4.8 66.9 1.0 N C:TRP295 4.8 79.9 1.0 C C:LYS344 4.9 62.1 1.0 CA C:HIS347 4.9 67.9 1.0 C C:GLY345 4.9 84.8 1.0 N C:ASP293 5.0 67.8 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with 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 DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/Kansas/14/2017 (H3N2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:87.9 occ:1.00 O D:GLY297 2.3 76.5 1.0 O D:ASP293 2.4 70.4 1.0 O D:HIS347 2.5 71.9 1.0 OD2 D:ASP324 3.3 52.1 1.0 C D:GLY297 3.6 69.8 1.0 C D:ASP293 3.7 68.6 1.0 C D:HIS347 3.7 66.5 1.0 CG D:ASP324 3.7 54.6 1.0 O D:LYS344 3.8 63.8 1.0 CA D:GLY348 4.0 46.9 1.0 OD1 D:ASP324 4.2 59.6 1.0 CB D:ASP324 4.3 52.2 1.0 N D:GLY348 4.3 55.0 1.0 CA D:ASN294 4.3 71.2 1.0 N D:GLY297 4.4 65.4 1.0 N D:SER298 4.4 58.1 1.0 CA D:GLY345 4.4 81.0 1.0 CA D:SER298 4.4 56.0 1.0 N D:ASN294 4.4 67.4 1.0 CA D:GLY297 4.6 64.5 1.0 C D:ASN294 4.6 72.9 1.0 N D:HIS347 4.7 73.2 1.0 CA D:ASP293 4.7 68.3 1.0 CB D:ASP293 4.7 66.8 1.0 N D:TRP295 4.8 80.0 1.0 C D:LYS344 4.8 61.8 1.0 CA D:HIS347 4.9 68.6 1.0 C D:GLY345 4.9 85.6 1.0 N D:ASP293 5.0 68.2 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