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Calcium in PDB 9o4q: Cryo-Em Structure of Z1A11-Gl Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)

Enzymatic activity of Cryo-Em Structure of Z1A11-Gl Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1)

All present enzymatic activity of Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1) (pdb code 9o4q). 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 Z1A11-Gl Fab in Complex with Influenza Virus Neuraminidase From A/California/07/2009 (H1N1), PDB code: 9o4q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 9o4q

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Calcium binding site 1 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:Ca503

b:77.1
occ:1.00
 O A:GLY345 2.2 91.6 1.0
OD2 A:ASP324 2.2 106.7 1.0
O A:ASP293 2.3 97.3 1.0
O A:GLY297 2.4 100.3 1.0
CA A:GLY348 3.3 72.8 1.0
CG A:ASP324 3.3 96.5 1.0
C A:GLY345 3.4 86.0 1.0
C A:ASP293 3.5 79.7 1.0
N A:GLY348 3.5 76.4 1.0
C A:GLY297 3.6 97.2 1.0
CB A:ASP324 4.1 88.3 1.0
CA A:GLY345 4.1 83.3 1.0
O A:ALA346 4.2 98.2 1.0
C A:ALA346 4.2 86.5 1.0
CA A:ASN294 4.3 84.1 1.0
OD1 A:ASP324 4.3 98.1 1.0
N A:ASN294 4.3 73.1 1.0
N A:ALA346 4.3 90.0 1.0
CG A:PRO326 4.4 97.2 1.0
C A:ASN347 4.4 99.7 1.0
O A:ASN344 4.5 107.5 1.0
N A:SER298 4.5 96.2 1.0
CA A:ASP293 4.5 75.9 1.0
CA A:SER298 4.5 96.7 1.0
CA A:ALA346 4.5 87.6 1.0
CA A:GLY297 4.6 93.9 1.0
N A:ASN347 4.6 85.0 1.0
O A:PRO326 4.6 96.9 1.0
N A:GLY297 4.6 97.7 1.0
CB A:ASP293 4.6 87.0 1.0
N A:ASP293 4.8 75.4 1.0
C A:ASN294 4.8 89.6 1.0
C A:GLY348 4.8 75.5 1.0
CD A:PRO326 4.9 91.7 1.0

Calcium binding site 2 out of 9 in 9o4q

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Calcium binding site 2 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:96.4
occ:1.00
 OD1 A:ASP379 2.3 94.9 1.0
OD1 A:ASN381 2.3 101.0 1.0
OD1 A:ASP387 2.3 121.7 1.0
OD2 A:ASP387 2.4 119.4 1.0
O A:ASN389 2.5 100.9 1.0
CG A:ASP387 2.6 117.4 1.0
CG A:ASP379 3.1 97.2 1.0
OD2 A:ASP379 3.1 101.5 1.0
O A:ASP387 3.2 109.1 1.0
CG A:ASN381 3.4 101.5 1.0
C A:ASN389 3.6 101.8 1.0
ND2 A:ASN381 3.8 103.4 1.0
C A:ASP387 3.9 109.2 1.0
N A:ASN389 4.0 101.2 1.0
CB A:ASP387 4.0 104.8 1.0
CA A:ASN389 4.3 99.2 1.0
CA A:ASP387 4.4 104.0 1.0
C A:ASN388 4.5 102.2 1.0
CB A:ASP379 4.5 85.0 1.0
N A:ASN381 4.5 97.3 1.0
CB A:ASN389 4.6 95.5 1.0
C A:ASN381 4.6 96.3 1.0
N A:GLY382 4.7 89.5 1.0
CB A:ASN381 4.7 95.5 1.0
N A:PHE390 4.7 91.4 1.0
N A:ASN388 4.7 105.5 1.0
N A:ASP387 4.7 110.8 1.0
CD A:PRO380 4.8 90.9 1.0
CA A:ASN381 4.9 96.2 1.0
CA A:GLY382 4.9 85.0 1.0
O A:ASN381 5.0 101.1 1.0
CA A:ASP379 5.0 73.8 1.0

Calcium binding site 3 out of 9 in 9o4q

Go back to Calcium Binding Sites List in 9o4q
Calcium binding site 3 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:88.9
occ:1.00
 OD2 C:ASP113 4.0 113.4 1.0
OD2 D:ASP113 4.0 113.4 1.0
OD2 A:ASP113 4.0 113.4 1.0
OD2 B:ASP113 4.0 113.4 1.0
OD1 B:ASP113 4.0 100.1 1.0
OD1 C:ASP113 4.0 100.1 1.0
OD1 A:ASP113 4.0 100.1 1.0
OD1 D:ASP113 4.0 100.1 1.0
CG C:ASP113 4.4 107.5 1.0
CG D:ASP113 4.4 107.5 1.0
CG A:ASP113 4.4 107.5 1.0
CG B:ASP113 4.4 107.5 1.0

Calcium binding site 4 out of 9 in 9o4q

Go back to Calcium Binding Sites List in 9o4q
Calcium binding site 4 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:Ca503

b:77.1
occ:1.00
 O B:GLY345 2.2 91.6 1.0
OD2 B:ASP324 2.2 106.7 1.0
O B:ASP293 2.3 97.3 1.0
O B:GLY297 2.4 100.3 1.0
CA B:GLY348 3.3 72.8 1.0
CG B:ASP324 3.3 96.5 1.0
C B:GLY345 3.4 86.0 1.0
C B:ASP293 3.5 79.7 1.0
N B:GLY348 3.5 76.4 1.0
C B:GLY297 3.6 97.2 1.0
CB B:ASP324 4.1 88.3 1.0
CA B:GLY345 4.1 83.3 1.0
O B:ALA346 4.2 98.2 1.0
C B:ALA346 4.2 86.5 1.0
CA B:ASN294 4.3 84.1 1.0
OD1 B:ASP324 4.3 98.1 1.0
N B:ASN294 4.3 73.1 1.0
N B:ALA346 4.3 90.0 1.0
CG B:PRO326 4.4 97.2 1.0
C B:ASN347 4.4 99.7 1.0
O B:ASN344 4.5 107.5 1.0
N B:SER298 4.5 96.2 1.0
CA B:ASP293 4.5 75.9 1.0
CA B:SER298 4.5 96.7 1.0
CA B:ALA346 4.5 87.6 1.0
CA B:GLY297 4.6 93.9 1.0
N B:ASN347 4.6 85.0 1.0
O B:PRO326 4.6 96.9 1.0
N B:GLY297 4.6 97.7 1.0
CB B:ASP293 4.6 87.0 1.0
N B:ASP293 4.8 75.4 1.0
C B:ASN294 4.8 89.6 1.0
C B:GLY348 4.8 75.5 1.0
CD B:PRO326 4.9 91.7 1.0

Calcium binding site 5 out of 9 in 9o4q

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Calcium binding site 5 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:96.4
occ:1.00
 OD1 B:ASP379 2.3 94.9 1.0
OD1 B:ASN381 2.3 101.0 1.0
OD1 B:ASP387 2.3 121.7 1.0
OD2 B:ASP387 2.4 119.4 1.0
O B:ASN389 2.5 100.9 1.0
CG B:ASP387 2.6 117.4 1.0
CG B:ASP379 3.1 97.2 1.0
OD2 B:ASP379 3.1 101.5 1.0
O B:ASP387 3.2 109.1 1.0
CG B:ASN381 3.4 101.5 1.0
C B:ASN389 3.6 101.8 1.0
ND2 B:ASN381 3.8 103.4 1.0
C B:ASP387 3.9 109.2 1.0
N B:ASN389 4.0 101.2 1.0
CB B:ASP387 4.0 104.8 1.0
CA B:ASN389 4.3 99.2 1.0
CA B:ASP387 4.4 104.0 1.0
C B:ASN388 4.5 102.2 1.0
CB B:ASP379 4.5 85.0 1.0
N B:ASN381 4.5 97.3 1.0
CB B:ASN389 4.6 95.5 1.0
C B:ASN381 4.6 96.3 1.0
N B:GLY382 4.7 89.5 1.0
CB B:ASN381 4.7 95.5 1.0
N B:PHE390 4.7 91.4 1.0
N B:ASN388 4.7 105.5 1.0
N B:ASP387 4.7 110.8 1.0
CD B:PRO380 4.8 90.9 1.0
CA B:ASN381 4.9 96.2 1.0
CA B:GLY382 4.9 85.0 1.0
O B:ASN381 5.0 101.1 1.0
CA B:ASP379 5.0 73.8 1.0

Calcium binding site 6 out of 9 in 9o4q

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Calcium binding site 6 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:Ca503

b:77.1
occ:1.00
 O C:GLY345 2.2 91.6 1.0
OD2 C:ASP324 2.2 106.7 1.0
O C:ASP293 2.3 97.3 1.0
O C:GLY297 2.4 100.3 1.0
CA C:GLY348 3.3 72.8 1.0
CG C:ASP324 3.3 96.5 1.0
C C:GLY345 3.4 86.0 1.0
C C:ASP293 3.5 79.7 1.0
N C:GLY348 3.5 76.4 1.0
C C:GLY297 3.6 97.2 1.0
CB C:ASP324 4.1 88.3 1.0
CA C:GLY345 4.1 83.3 1.0
O C:ALA346 4.2 98.2 1.0
C C:ALA346 4.2 86.5 1.0
CA C:ASN294 4.3 84.1 1.0
OD1 C:ASP324 4.3 98.1 1.0
N C:ASN294 4.3 73.1 1.0
N C:ALA346 4.3 90.0 1.0
CG C:PRO326 4.4 97.2 1.0
C C:ASN347 4.4 99.7 1.0
O C:ASN344 4.5 107.5 1.0
N C:SER298 4.5 96.2 1.0
CA C:ASP293 4.5 75.9 1.0
CA C:SER298 4.5 96.7 1.0
CA C:ALA346 4.5 87.6 1.0
CA C:GLY297 4.6 93.9 1.0
N C:ASN347 4.6 85.0 1.0
O C:PRO326 4.6 96.9 1.0
N C:GLY297 4.6 97.7 1.0
CB C:ASP293 4.6 87.0 1.0
N C:ASP293 4.8 75.4 1.0
C C:ASN294 4.8 89.6 1.0
C C:GLY348 4.8 75.5 1.0
CD C:PRO326 4.9 91.7 1.0

Calcium binding site 7 out of 9 in 9o4q

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Calcium binding site 7 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:96.4
occ:1.00
 OD1 C:ASP379 2.3 94.9 1.0
OD1 C:ASN381 2.3 101.0 1.0
OD1 C:ASP387 2.3 121.7 1.0
OD2 C:ASP387 2.4 119.4 1.0
O C:ASN389 2.5 100.9 1.0
CG C:ASP387 2.6 117.4 1.0
CG C:ASP379 3.1 97.2 1.0
OD2 C:ASP379 3.1 101.5 1.0
O C:ASP387 3.2 109.1 1.0
CG C:ASN381 3.4 101.5 1.0
C C:ASN389 3.6 101.8 1.0
ND2 C:ASN381 3.8 103.4 1.0
C C:ASP387 3.9 109.2 1.0
N C:ASN389 4.0 101.2 1.0
CB C:ASP387 4.0 104.8 1.0
CA C:ASN389 4.3 99.2 1.0
CA C:ASP387 4.4 104.0 1.0
C C:ASN388 4.5 102.2 1.0
CB C:ASP379 4.5 85.0 1.0
N C:ASN381 4.5 97.3 1.0
CB C:ASN389 4.6 95.5 1.0
C C:ASN381 4.6 96.3 1.0
N C:GLY382 4.7 89.5 1.0
CB C:ASN381 4.7 95.5 1.0
N C:PHE390 4.7 91.4 1.0
N C:ASN388 4.7 105.5 1.0
N C:ASP387 4.7 110.8 1.0
CD C:PRO380 4.8 90.9 1.0
CA C:ASN381 4.9 96.2 1.0
CA C:GLY382 4.9 85.0 1.0
O C:ASN381 5.0 101.1 1.0
CA C:ASP379 5.0 73.8 1.0

Calcium binding site 8 out of 9 in 9o4q

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Calcium binding site 8 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:Ca503

b:77.1
occ:1.00
 O D:GLY345 2.2 91.6 1.0
OD2 D:ASP324 2.2 106.7 1.0
O D:ASP293 2.3 97.3 1.0
O D:GLY297 2.4 100.3 1.0
CA D:GLY348 3.3 72.8 1.0
CG D:ASP324 3.3 96.5 1.0
C D:GLY345 3.4 86.0 1.0
C D:ASP293 3.5 79.7 1.0
N D:GLY348 3.5 76.4 1.0
C D:GLY297 3.6 97.2 1.0
CB D:ASP324 4.1 88.3 1.0
CA D:GLY345 4.1 83.3 1.0
O D:ALA346 4.2 98.2 1.0
C D:ALA346 4.2 86.5 1.0
CA D:ASN294 4.3 84.1 1.0
OD1 D:ASP324 4.3 98.1 1.0
N D:ASN294 4.3 73.1 1.0
N D:ALA346 4.3 90.0 1.0
CG D:PRO326 4.4 97.2 1.0
C D:ASN347 4.4 99.7 1.0
O D:ASN344 4.5 107.5 1.0
N D:SER298 4.5 96.2 1.0
CA D:ASP293 4.5 75.9 1.0
CA D:SER298 4.5 96.7 1.0
CA D:ALA346 4.5 87.6 1.0
CA D:GLY297 4.6 93.9 1.0
N D:ASN347 4.6 85.0 1.0
O D:PRO326 4.6 96.9 1.0
N D:GLY297 4.6 97.7 1.0
CB D:ASP293 4.6 87.0 1.0
N D:ASP293 4.8 75.4 1.0
C D:ASN294 4.8 89.6 1.0
C D:GLY348 4.8 75.5 1.0
CD D:PRO326 4.9 91.7 1.0

Calcium binding site 9 out of 9 in 9o4q

Go back to Calcium Binding Sites List in 9o4q
Calcium binding site 9 out of 9 in the Cryo-Em Structure of Z1A11-Gl 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 Z1A11-Gl 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:96.4
occ:1.00
 OD1 D:ASP379 2.3 94.9 1.0
OD1 D:ASN381 2.3 101.0 1.0
OD1 D:ASP387 2.3 121.7 1.0
OD2 D:ASP387 2.4 119.4 1.0
O D:ASN389 2.5 100.9 1.0
CG D:ASP387 2.6 117.4 1.0
CG D:ASP379 3.1 97.2 1.0
OD2 D:ASP379 3.1 101.5 1.0
O D:ASP387 3.2 109.1 1.0
CG D:ASN381 3.4 101.5 1.0
C D:ASN389 3.6 101.8 1.0
ND2 D:ASN381 3.8 103.4 1.0
C D:ASP387 3.9 109.2 1.0
N D:ASN389 4.0 101.2 1.0
CB D:ASP387 4.0 104.8 1.0
CA D:ASN389 4.3 99.2 1.0
CA D:ASP387 4.4 104.0 1.0
C D:ASN388 4.5 102.2 1.0
CB D:ASP379 4.5 85.0 1.0
N D:ASN381 4.5 97.3 1.0
CB D:ASN389 4.6 95.5 1.0
C D:ASN381 4.6 96.3 1.0
N D:GLY382 4.7 89.5 1.0
CB D:ASN381 4.7 95.5 1.0
N D:PHE390 4.7 91.4 1.0
N D:ASN388 4.7 105.5 1.0
N D:ASP387 4.7 110.8 1.0
CD D:PRO380 4.8 90.9 1.0
CA D:ASN381 4.9 96.2 1.0
CA D:GLY382 4.9 85.0 1.0
O D:ASN381 5.0 101.1 1.0
CA D:ASP379 5.0 73.8 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 22:38:57 2025

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