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Calcium in PDB 9cye: Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)

Enzymatic activity of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)

All present enzymatic activity of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1):
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 A/California/07/2009 (H1N1) (pdb code 9cye). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1), PDB code: 9cye:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 9cye

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Calcium binding site 1 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


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/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:83.7
occ:1.00
 OD2 A:ASP113 4.7 27.8 1.0
OD2 D:ASP113 4.7 27.9 1.0
OD2 B:ASP113 4.7 28.4 1.0
OD2 C:ASP113 4.7 27.8 1.0
OD1 A:ASP113 4.8 25.3 1.0
OD1 B:ASP113 4.8 25.7 1.0
OD1 C:ASP113 4.8 26.2 1.0
OD1 D:ASP113 4.8 24.8 1.0

Calcium binding site 2 out of 9 in 9cye

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Calcium binding site 2 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


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/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:16.4
occ:1.00
 O A:GLY345 2.3 14.1 1.0
OD2 A:ASP324 2.3 20.6 1.0
O A:GLY297 2.4 20.1 1.0
O A:ASN347 2.4 22.1 1.0
O A:ASP293 2.4 18.2 1.0
C A:GLY345 3.3 15.4 1.0
C A:GLY297 3.3 13.0 1.0
CG A:ASP324 3.4 16.2 1.0
C A:ASN347 3.6 11.3 1.0
C A:ASP293 3.6 15.9 1.0
CB A:ASP324 3.9 16.5 1.0
CA A:GLY345 3.9 13.9 1.0
O A:ALA346 4.0 27.0 1.0
N A:SER298 4.1 12.4 1.0
C A:ALA346 4.1 21.2 1.0
N A:GLY297 4.1 15.9 1.0
CA A:SER298 4.1 10.8 1.0
CA A:GLY348 4.2 7.1 1.0
CA A:GLY297 4.3 10.6 1.0
N A:ALA346 4.3 16.2 1.0
N A:ASN347 4.4 14.9 1.0
O A:ASN344 4.4 21.8 1.0
N A:GLY348 4.4 13.3 1.0
CA A:ASN294 4.5 10.7 1.0
N A:ASN294 4.5 12.6 1.0
OD1 A:ASP324 4.5 24.6 1.0
O A:PRO326 4.5 27.6 1.0
CA A:ALA346 4.6 12.2 1.0
CA A:ASP293 4.6 11.2 1.0
CA A:ASN347 4.6 12.4 1.0
CB A:ASP293 4.7 9.0 1.0
C A:ASN294 4.8 10.9 1.0
N A:ASP293 4.9 18.5 1.0

Calcium binding site 3 out of 9 in 9cye

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Calcium binding site 3 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


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/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:32.6
occ:1.00
 OD1 A:ASP379 2.4 26.7 1.0
OD1 A:ASN381 2.5 21.2 1.0
O A:ASN389 2.7 27.8 1.0
OD2 A:ASP387 3.0 36.4 1.0
CG A:ASP379 3.2 20.8 1.0
OD2 A:ASP379 3.2 26.5 1.0
OD1 A:ASP387 3.3 36.2 1.0
CG A:ASP387 3.4 36.0 1.0
CG A:ASN381 3.4 20.6 1.0
O A:ASP387 3.5 36.8 1.0
ND2 A:ASN381 3.7 16.6 1.0
C A:ASN389 3.8 29.5 1.0
N A:ASN389 3.9 29.6 1.0
C A:ASP387 4.2 32.5 1.0
CA A:ASN389 4.3 28.2 1.0
C A:ASN381 4.4 16.2 1.0
CB A:ASN389 4.5 29.2 1.0
N A:ASN381 4.5 16.4 1.0
CB A:ASP387 4.5 29.2 1.0
N A:GLY382 4.6 15.2 1.0
CB A:ASP379 4.6 14.2 1.0
CB A:ASN381 4.6 11.4 1.0
O A:ASN381 4.6 21.6 1.0
CA A:ASN381 4.7 11.6 1.0
CA A:GLY382 4.7 18.0 1.0
CA A:ASP387 4.8 26.3 1.0
N A:ASN388 4.9 35.4 1.0
C A:ASN388 4.9 31.9 1.0
CD A:PRO380 4.9 12.9 1.0
N A:PHE390 4.9 26.5 1.0
N A:ASP387 5.0 31.6 1.0

Calcium binding site 4 out of 9 in 9cye

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Calcium binding site 4 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


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/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:16.8
occ:1.00
 O B:GLY345 2.3 14.4 1.0
OD2 B:ASP324 2.3 21.2 1.0
O B:GLY297 2.4 19.8 1.0
O B:ASN347 2.4 22.0 1.0
O B:ASP293 2.4 18.4 1.0
C B:GLY345 3.3 15.1 1.0
C B:GLY297 3.3 13.4 1.0
CG B:ASP324 3.4 16.3 1.0
C B:ASN347 3.6 11.2 1.0
C B:ASP293 3.6 15.3 1.0
CB B:ASP324 3.9 16.6 1.0
CA B:GLY345 3.9 12.9 1.0
O B:ALA346 4.0 27.4 1.0
N B:SER298 4.1 13.0 1.0
C B:ALA346 4.1 21.2 1.0
N B:GLY297 4.1 15.9 1.0
CA B:SER298 4.1 11.0 1.0
CA B:GLY348 4.2 7.6 1.0
CA B:GLY297 4.3 11.0 1.0
N B:ALA346 4.3 16.8 1.0
N B:ASN347 4.4 15.2 1.0
O B:ASN344 4.4 23.4 1.0
N B:GLY348 4.4 13.8 1.0
CA B:ASN294 4.5 12.2 1.0
N B:ASN294 4.5 12.4 1.0
OD1 B:ASP324 4.5 25.1 1.0
O B:PRO326 4.5 27.4 1.0
CA B:ALA346 4.6 12.5 1.0
CA B:ASP293 4.6 11.5 1.0
CA B:ASN347 4.6 13.1 1.0
CB B:ASP293 4.7 9.8 1.0
C B:ASN294 4.8 11.3 1.0
N B:ASP293 4.9 18.5 1.0

Calcium binding site 5 out of 9 in 9cye

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Calcium binding site 5 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:33.4
occ:1.00
 OD1 B:ASP379 2.4 26.5 1.0
OD1 B:ASN381 2.5 21.7 1.0
O B:ASN389 2.7 27.4 1.0
OD2 B:ASP387 3.0 36.4 1.0
CG B:ASP379 3.2 20.3 1.0
OD2 B:ASP379 3.2 25.4 1.0
OD1 B:ASP387 3.3 36.2 1.0
CG B:ASP387 3.4 36.1 1.0
CG B:ASN381 3.4 21.1 1.0
O B:ASP387 3.5 36.3 1.0
ND2 B:ASN381 3.7 16.8 1.0
C B:ASN389 3.8 29.1 1.0
N B:ASN389 3.9 28.9 1.0
C B:ASP387 4.2 32.5 1.0
CA B:ASN389 4.3 27.6 1.0
C B:ASN381 4.4 15.9 1.0
CB B:ASN389 4.5 29.2 1.0
N B:ASN381 4.5 17.1 1.0
CB B:ASP387 4.5 29.4 1.0
N B:GLY382 4.6 15.0 1.0
CB B:ASP379 4.6 14.0 1.0
CB B:ASN381 4.6 11.9 1.0
O B:ASN381 4.6 22.1 1.0
CA B:ASN381 4.7 12.0 1.0
CA B:GLY382 4.7 17.7 1.0
CA B:ASP387 4.8 26.1 1.0
N B:ASN388 4.9 35.4 1.0
C B:ASN388 4.9 32.1 1.0
CD B:PRO380 4.9 13.2 1.0
N B:PHE390 4.9 26.6 1.0
N B:ASP387 5.0 31.5 1.0

Calcium binding site 6 out of 9 in 9cye

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Calcium binding site 6 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:16.6
occ:1.00
 O C:GLY345 2.3 13.9 1.0
OD2 C:ASP324 2.3 21.6 1.0
O C:GLY297 2.4 18.6 1.0
O C:ASN347 2.4 22.0 1.0
O C:ASP293 2.4 18.2 1.0
C C:GLY345 3.3 15.3 1.0
C C:GLY297 3.3 14.1 1.0
CG C:ASP324 3.4 16.3 1.0
C C:ASN347 3.6 11.8 1.0
C C:ASP293 3.6 15.4 1.0
CB C:ASP324 3.9 16.3 1.0
CA C:GLY345 3.9 13.4 1.0
O C:ALA346 4.0 27.4 1.0
N C:SER298 4.1 13.6 1.0
C C:ALA346 4.1 20.5 1.0
N C:GLY297 4.1 16.2 1.0
CA C:SER298 4.1 11.2 1.0
CA C:GLY348 4.2 7.3 1.0
CA C:GLY297 4.3 11.3 1.0
N C:ALA346 4.3 16.2 1.0
N C:ASN347 4.4 14.8 1.0
O C:ASN344 4.4 23.7 1.0
N C:GLY348 4.4 13.6 1.0
CA C:ASN294 4.5 11.6 1.0
N C:ASN294 4.5 13.2 1.0
OD1 C:ASP324 4.5 24.4 1.0
O C:PRO326 4.5 27.2 1.0
CA C:ALA346 4.6 12.0 1.0
CA C:ASP293 4.6 11.4 1.0
CA C:ASN347 4.6 12.8 1.0
CB C:ASP293 4.7 9.3 1.0
C C:ASN294 4.8 10.4 1.0
N C:ASP293 4.9 17.3 1.0

Calcium binding site 7 out of 9 in 9cye

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Calcium binding site 7 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca505

b:31.4
occ:1.00
 OD1 C:ASP379 2.4 26.2 1.0
OD1 C:ASN381 2.5 21.6 1.0
O C:ASN389 2.7 27.8 1.0
OD2 C:ASP387 3.0 35.9 1.0
CG C:ASP379 3.2 20.2 1.0
OD2 C:ASP379 3.2 24.9 1.0
OD1 C:ASP387 3.3 36.5 1.0
CG C:ASP387 3.4 35.9 1.0
CG C:ASN381 3.4 20.9 1.0
O C:ASP387 3.5 35.9 1.0
ND2 C:ASN381 3.7 16.6 1.0
C C:ASN389 3.8 29.3 1.0
N C:ASN389 3.9 29.0 1.0
C C:ASP387 4.2 32.5 1.0
CA C:ASN389 4.3 27.9 1.0
C C:ASN381 4.4 16.2 1.0
CB C:ASN389 4.5 28.9 1.0
N C:ASN381 4.5 16.1 1.0
CB C:ASP387 4.5 29.8 1.0
N C:GLY382 4.6 15.7 1.0
CB C:ASP379 4.6 14.5 1.0
CB C:ASN381 4.6 10.9 1.0
O C:ASN381 4.6 22.2 1.0
CA C:ASN381 4.7 10.5 1.0
CA C:GLY382 4.8 18.1 1.0
CA C:ASP387 4.8 26.5 1.0
N C:ASN388 4.9 35.6 1.0
C C:ASN388 4.9 31.3 1.0
CD C:PRO380 4.9 13.2 1.0
N C:PHE390 4.9 26.1 1.0
N C:ASP387 5.0 31.9 1.0

Calcium binding site 8 out of 9 in 9cye

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Calcium binding site 8 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:17.5
occ:1.00
 O D:GLY345 2.3 14.2 1.0
OD2 D:ASP324 2.3 20.8 1.0
O D:GLY297 2.4 19.1 1.0
O D:ASN347 2.4 21.1 1.0
O D:ASP293 2.4 17.4 1.0
C D:GLY345 3.3 15.4 1.0
C D:GLY297 3.3 13.2 1.0
CG D:ASP324 3.4 16.4 1.0
C D:ASN347 3.6 10.8 1.0
C D:ASP293 3.6 14.7 1.0
CB D:ASP324 3.9 17.1 1.0
CA D:GLY345 3.9 13.4 1.0
O D:ALA346 4.0 27.1 1.0
N D:SER298 4.1 12.6 1.0
C D:ALA346 4.1 21.6 1.0
N D:GLY297 4.1 16.1 1.0
CA D:SER298 4.1 10.6 1.0
CA D:GLY348 4.2 6.9 1.0
CA D:GLY297 4.3 11.4 1.0
N D:ALA346 4.3 16.1 1.0
N D:ASN347 4.4 15.7 1.0
O D:ASN344 4.4 23.1 1.0
N D:GLY348 4.4 13.7 1.0
CA D:ASN294 4.5 11.3 1.0
N D:ASN294 4.5 11.9 1.0
OD1 D:ASP324 4.5 24.7 1.0
O D:PRO326 4.5 26.9 1.0
CA D:ALA346 4.6 12.0 1.0
CA D:ASP293 4.6 11.7 1.0
CA D:ASN347 4.6 12.5 1.0
CB D:ASP293 4.7 9.7 1.0
C D:ASN294 4.8 11.2 1.0
N D:ASP293 4.9 18.1 1.0

Calcium binding site 9 out of 9 in 9cye

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Calcium binding site 9 out of 9 in the Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of DA03E17 Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca505

b:32.7
occ:1.00
 OD1 D:ASP379 2.4 26.6 1.0
OD1 D:ASN381 2.5 21.4 1.0
O D:ASN389 2.7 27.8 1.0
OD2 D:ASP387 3.0 37.1 1.0
CG D:ASP379 3.2 20.1 1.0
OD2 D:ASP379 3.2 25.3 1.0
OD1 D:ASP387 3.3 36.1 1.0
CG D:ASP387 3.4 36.5 1.0
CG D:ASN381 3.4 20.4 1.0
O D:ASP387 3.5 36.9 1.0
ND2 D:ASN381 3.7 16.4 1.0
C D:ASN389 3.8 29.4 1.0
N D:ASN389 3.9 29.6 1.0
C D:ASP387 4.2 33.0 1.0
CA D:ASN389 4.3 28.1 1.0
C D:ASN381 4.4 16.1 1.0
CB D:ASN389 4.5 29.4 1.0
N D:ASN381 4.5 16.0 1.0
CB D:ASP387 4.5 30.0 1.0
N D:GLY382 4.6 15.8 1.0
CB D:ASP379 4.6 14.6 1.0
CB D:ASN381 4.6 11.2 1.0
O D:ASN381 4.6 21.5 1.0
CA D:ASN381 4.7 11.6 1.0
CA D:GLY382 4.8 18.0 1.0
CA D:ASP387 4.8 26.8 1.0
N D:ASN388 4.9 35.7 1.0
C D:ASN388 4.9 32.1 1.0
CD D:PRO380 4.9 13.1 1.0
N D:PHE390 4.9 26.6 1.0
N D:ASP387 5.0 32.2 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 22:32:16 2025

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