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Calcium in PDB 9cyh: Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017

Enzymatic activity of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017

All present enzymatic activity of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017:
3.2.1.18;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017 (pdb code 9cyh). 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 B/Colorado/06/2017, PDB code: 9cyh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9cyh

Go back to Calcium Binding Sites List in 9cyh
Calcium binding site 1 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017


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 B/Colorado/06/2017 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:30.0
occ:1.00
 O A:GLY346 2.3 43.8 1.0
OD2 A:ASP324 2.3 43.6 1.0
O A:THR297 2.3 46.7 1.0
O A:ASP293 2.3 45.1 1.0
O A:GLY344 2.4 47.6 1.0
C A:THR297 3.4 46.7 1.0
CG A:ASP324 3.5 43.6 1.0
C A:GLY346 3.5 43.8 1.0
C A:GLY344 3.5 47.6 1.0
C A:ASP293 3.5 45.1 1.0
CA A:ALA298 4.1 46.1 1.0
CA A:GLY347 4.1 42.4 1.0
CA A:GLY344 4.1 47.6 1.0
N A:ALA298 4.1 46.1 1.0
CA A:ASN294 4.2 45.1 1.0
CB A:ASP324 4.3 43.6 1.0
N A:GLY347 4.3 42.4 1.0
N A:ASN294 4.3 45.1 1.0
C A:ASN294 4.3 45.1 1.0
OD1 A:ASP324 4.4 43.6 1.0
N A:GLY346 4.4 43.8 1.0
N A:THR297 4.5 46.7 1.0
C A:SER345 4.5 46.6 1.0
N A:ARG295 4.5 46.6 1.0
CA A:GLY346 4.5 43.8 1.0
CA A:THR297 4.6 46.7 1.0
N A:SER345 4.6 46.6 1.0
CA A:ASP293 4.6 45.1 1.0
O A:LYS343 4.6 50.6 1.0
O A:PRO326 4.7 44.5 1.0
CB A:ASP293 4.7 45.1 1.0
O A:ASN294 4.8 45.1 1.0
O A:SER345 4.8 46.6 1.0
CA A:SER345 4.9 46.6 1.0
N A:ASP293 4.9 45.1 1.0
CB A:ALA298 5.0 46.1 1.0

Calcium binding site 2 out of 4 in 9cyh

Go back to Calcium Binding Sites List in 9cyh
Calcium binding site 2 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017


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 B/Colorado/06/2017 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:30.0
occ:1.00
 O B:GLY346 2.3 43.8 1.0
OD2 B:ASP324 2.3 43.6 1.0
O B:THR297 2.3 46.7 1.0
O B:ASP293 2.3 45.1 1.0
O B:GLY344 2.4 47.6 1.0
C B:THR297 3.4 46.7 1.0
CG B:ASP324 3.5 43.6 1.0
C B:GLY346 3.5 43.8 1.0
C B:GLY344 3.5 47.6 1.0
C B:ASP293 3.5 45.1 1.0
CA B:ALA298 4.1 46.1 1.0
CA B:GLY347 4.1 42.4 1.0
CA B:GLY344 4.1 47.6 1.0
N B:ALA298 4.1 46.1 1.0
CA B:ASN294 4.2 45.1 1.0
CB B:ASP324 4.3 43.6 1.0
N B:GLY347 4.3 42.4 1.0
N B:ASN294 4.3 45.1 1.0
C B:ASN294 4.3 45.1 1.0
OD1 B:ASP324 4.4 43.6 1.0
N B:GLY346 4.4 43.8 1.0
N B:THR297 4.5 46.7 1.0
C B:SER345 4.5 46.6 1.0
N B:ARG295 4.5 46.6 1.0
CA B:GLY346 4.5 43.8 1.0
CA B:THR297 4.6 46.7 1.0
N B:SER345 4.6 46.6 1.0
CA B:ASP293 4.6 45.1 1.0
O B:LYS343 4.6 50.6 1.0
O B:PRO326 4.7 44.5 1.0
CB B:ASP293 4.7 45.1 1.0
O B:ASN294 4.7 45.1 1.0
O B:SER345 4.8 46.6 1.0
CA B:SER345 4.9 46.6 1.0
N B:ASP293 4.9 45.1 1.0
CB B:ALA298 5.0 46.1 1.0

Calcium binding site 3 out of 4 in 9cyh

Go back to Calcium Binding Sites List in 9cyh
Calcium binding site 3 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017


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 B/Colorado/06/2017 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:30.0
occ:1.00
 O C:GLY346 2.3 43.8 1.0
OD2 C:ASP324 2.3 43.6 1.0
O C:THR297 2.3 46.7 1.0
O C:ASP293 2.3 45.1 1.0
O C:GLY344 2.4 47.6 1.0
C C:THR297 3.4 46.7 1.0
CG C:ASP324 3.5 43.6 1.0
C C:GLY346 3.5 43.8 1.0
C C:GLY344 3.5 47.6 1.0
C C:ASP293 3.5 45.1 1.0
CA C:ALA298 4.1 46.1 1.0
CA C:GLY347 4.1 42.4 1.0
CA C:GLY344 4.1 47.6 1.0
N C:ALA298 4.1 46.1 1.0
CA C:ASN294 4.2 45.1 1.0
CB C:ASP324 4.3 43.6 1.0
N C:GLY347 4.3 42.4 1.0
N C:ASN294 4.3 45.1 1.0
C C:ASN294 4.3 45.1 1.0
OD1 C:ASP324 4.4 43.6 1.0
N C:GLY346 4.4 43.8 1.0
N C:THR297 4.5 46.7 1.0
C C:SER345 4.5 46.6 1.0
N C:ARG295 4.5 46.6 1.0
CA C:GLY346 4.5 43.8 1.0
CA C:THR297 4.6 46.7 1.0
N C:SER345 4.6 46.6 1.0
CA C:ASP293 4.6 45.1 1.0
O C:LYS343 4.6 50.6 1.0
O C:PRO326 4.7 44.5 1.0
CB C:ASP293 4.7 45.1 1.0
O C:ASN294 4.8 45.1 1.0
O C:SER345 4.8 46.6 1.0
CA C:SER345 4.9 46.6 1.0
N C:ASP293 4.9 45.1 1.0
CB C:ALA298 5.0 46.1 1.0

Calcium binding site 4 out of 4 in 9cyh

Go back to Calcium Binding Sites List in 9cyh
Calcium binding site 4 out of 4 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From B/Colorado/06/2017


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 B/Colorado/06/2017 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:30.0
occ:1.00
 O D:GLY346 2.3 43.8 1.0
OD2 D:ASP324 2.3 43.6 1.0
O D:THR297 2.3 46.7 1.0
O D:ASP293 2.3 45.1 1.0
O D:GLY344 2.4 47.6 1.0
C D:THR297 3.4 46.7 1.0
CG D:ASP324 3.5 43.6 1.0
C D:GLY346 3.5 43.8 1.0
C D:GLY344 3.5 47.6 1.0
C D:ASP293 3.5 45.1 1.0
CA D:ALA298 4.1 46.1 1.0
CA D:GLY347 4.1 42.4 1.0
CA D:GLY344 4.1 47.6 1.0
N D:ALA298 4.1 46.1 1.0
CA D:ASN294 4.2 45.1 1.0
CB D:ASP324 4.3 43.6 1.0
N D:GLY347 4.3 42.4 1.0
N D:ASN294 4.3 45.1 1.0
C D:ASN294 4.3 45.1 1.0
OD1 D:ASP324 4.4 43.6 1.0
N D:GLY346 4.4 43.8 1.0
N D:THR297 4.5 46.7 1.0
C D:SER345 4.5 46.6 1.0
N D:ARG295 4.5 46.6 1.0
CA D:GLY346 4.5 43.8 1.0
CA D:THR297 4.6 46.7 1.0
N D:SER345 4.6 46.6 1.0
CA D:ASP293 4.6 45.1 1.0
O D:LYS343 4.6 50.6 1.0
O D:PRO326 4.7 44.5 1.0
CB D:ASP293 4.7 45.1 1.0
O D:ASN294 4.8 45.1 1.0
O D:SER345 4.8 46.6 1.0
CA D:SER345 4.9 46.6 1.0
N D:ASP293 4.9 45.1 1.0
CB D:ALA298 5.0 46.1 1.0

Reference:

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
Page generated: Fri Aug 22 22:33:01 2025

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