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Calcium in PDB 9ejf: Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]

Enzymatic activity of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]

All present enzymatic activity of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]:
3.2.1.18;

Calcium Binding Sites:

The binding sites of Calcium atom in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] (pdb code 9ejf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction], PDB code: 9ejf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9ejf

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Calcium binding site 1 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:155.0
occ:1.00
 O D:ASN344 2.2 100.0 1.0
O D:ASP294 2.3 100.0 1.0
O D:GLY298 2.5 100.0 1.0
O D:GLY342 2.6 100.0 1.0
O D:HOH649 2.6 155.0 1.0
OD2 D:ASP324 3.1 100.0 1.0
C D:GLY342 3.5 100.0 1.0
C D:ASN344 3.5 100.0 1.0
C D:ASP294 3.5 100.0 1.0
C D:GLY298 3.5 100.0 1.0
O D:HOH658 4.0 100.0 1.0
CA D:GLY342 4.0 100.0 1.0
N D:ASN344 4.1 100.0 1.0
CA D:GLY345 4.2 100.0 1.0
CG D:ASP324 4.2 100.0 1.0
N D:GLY298 4.2 100.0 1.0
N D:SER299 4.3 100.0 1.0
CA D:SER299 4.3 100.0 1.0
CA D:ASN295 4.3 100.0 1.0
N D:GLY345 4.3 100.0 1.0
N D:ASN295 4.4 100.0 1.0
N D:ALA343 4.4 100.0 1.0
CA D:ASN344 4.4 100.0 1.0
CA D:GLY298 4.5 100.0 1.0
C D:ASN295 4.5 100.0 1.0
CA D:ASP294 4.5 100.0 1.0
OD1 D:ASP294 4.6 100.0 1.0
CB D:ASP294 4.6 100.0 1.0
O D:ASN295 4.6 100.0 1.0
CB D:ASP324 4.7 100.0 1.0
N D:ASP294 4.8 100.0 1.0
O D:ASN341 4.8 87.5 1.0
C D:ALA343 4.8 100.0 1.0
CG D:ASP294 4.9 100.0 1.0
CA D:ALA343 4.9 100.0 1.0

Calcium binding site 2 out of 8 in 9ejf

Go back to Calcium Binding Sites List in 9ejf
Calcium binding site 2 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:155.0
occ:1.00
 OD1 D:ASN378 2.2 100.0 1.0
OD1 D:ASP376 2.3 100.0 1.0
O D:ASN386 2.7 100.0 1.0
O D:HOH603 2.9 50.0 1.0
CG D:ASP376 3.1 100.0 1.0
OD2 D:ASP384 3.2 50.0 1.0
OD2 D:ASP376 3.2 100.0 1.0
CG D:ASN378 3.3 100.0 1.0
C D:ASN386 3.7 100.0 1.0
CG D:ASP384 3.8 50.0 1.0
OD1 D:ASP384 3.9 50.0 1.0
ND2 D:ASN378 4.0 100.0 1.0
N D:ASN386 4.2 100.0 1.0
CA D:ASN386 4.3 100.0 1.0
CB D:ASN386 4.3 100.0 1.0
N D:ASN378 4.4 100.0 1.0
O D:ASP384 4.4 50.0 1.0
CB D:ASN378 4.5 100.0 1.0
CB D:ASP376 4.5 100.0 1.0
C D:ASN378 4.5 100.0 1.0
N D:GLY379 4.6 100.0 1.0
N D:PHE387 4.7 100.0 1.0
CA D:ASN378 4.7 100.0 1.0
C D:ASP384 4.8 50.0 1.0
CA D:GLY379 4.8 100.0 1.0
O D:ASN378 4.9 100.0 1.0
CD D:PRO377 4.9 100.0 1.0
CA D:PHE387 4.9 100.0 1.0
N D:PRO377 5.0 100.0 1.0
CA D:ASP376 5.0 100.0 1.0

Calcium binding site 3 out of 8 in 9ejf

Go back to Calcium Binding Sites List in 9ejf
Calcium binding site 3 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca503

b:155.0
occ:1.00
 OD1 E:ASP376 2.3 100.0 1.0
O E:HOH615 2.7 50.0 1.0
O E:ASN386 2.9 100.0 1.0
CG E:ASP376 3.0 100.0 1.0
OD2 E:ASP376 3.1 100.0 1.0
OD2 E:ASP384 3.3 50.0 1.0
C E:ASN386 3.8 100.0 1.0
OD1 E:ASP384 3.8 50.0 1.0
CG E:ASP384 3.8 50.0 1.0
CB E:ASN378 4.0 100.0 1.0
O E:ASP384 4.2 50.0 1.0
N E:ASN386 4.2 100.0 1.0
N E:ASN378 4.2 100.0 1.0
CB E:ASN386 4.3 100.0 1.0
CA E:ASN386 4.3 100.0 1.0
CA E:ASN378 4.5 100.0 1.0
N E:GLY379 4.5 100.0 1.0
CB E:ASP376 4.5 100.0 1.0
C E:ASN378 4.5 100.0 1.0
OD1 E:ASN378 4.6 100.0 1.0
N E:PHE387 4.7 100.0 1.0
CA E:GLY379 4.7 100.0 1.0
C E:ASP384 4.8 50.0 1.0
CG E:ASN378 4.8 100.0 1.0
C E:ASP376 5.0 100.0 1.0
CD E:PRO377 5.0 100.0 1.0
N E:PRO377 5.0 100.0 1.0
CA E:ASP376 5.0 100.0 1.0

Calcium binding site 4 out of 8 in 9ejf

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Calcium binding site 4 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca504

b:155.0
occ:1.00
 O E:ASN344 2.3 100.0 1.0
O E:ASP294 2.4 100.0 1.0
O E:HOH651 2.5 100.0 1.0
O E:GLY342 2.6 100.0 1.0
O E:GLY298 2.6 100.0 1.0
OD2 E:ASP324 3.2 100.0 1.0
C E:GLY342 3.4 100.0 1.0
C E:ASN344 3.5 100.0 1.0
C E:GLY298 3.6 100.0 1.0
C E:ASP294 3.6 100.0 1.0
O E:HOH631 4.0 100.0 1.0
CA E:GLY342 4.0 100.0 1.0
N E:ASN344 4.1 100.0 1.0
CA E:GLY345 4.2 100.0 1.0
CG E:ASP324 4.2 100.0 1.0
N E:GLY298 4.2 100.0 1.0
CA E:SER299 4.3 100.0 1.0
N E:SER299 4.3 100.0 1.0
N E:GLY345 4.3 100.0 1.0
N E:ALA343 4.3 100.0 1.0
CA E:ASN295 4.4 100.0 1.0
CA E:ASN344 4.4 100.0 1.0
N E:ASN295 4.5 100.0 1.0
CA E:GLY298 4.5 100.0 1.0
C E:ASN295 4.6 100.0 1.0
CA E:ASP294 4.6 100.0 1.0
CB E:ASP294 4.7 100.0 1.0
O E:ASN341 4.7 87.5 1.0
CB E:ASP324 4.7 100.0 1.0
O E:ASN295 4.8 100.0 1.0
C E:ALA343 4.8 100.0 1.0
CG E:ASP294 4.8 100.0 1.0
CA E:ALA343 4.9 100.0 1.0
OD1 E:ASP294 4.9 100.0 1.0
N E:ASP294 4.9 100.0 1.0

Calcium binding site 5 out of 8 in 9ejf

Go back to Calcium Binding Sites List in 9ejf
Calcium binding site 5 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca503

b:155.0
occ:1.00
 O F:ASN344 2.3 100.0 1.0
O F:ASP294 2.3 100.0 1.0
O F:GLY298 2.7 100.0 1.0
O F:GLY342 2.7 100.0 1.0
O F:HOH638 2.7 100.0 1.0
OD2 F:ASP324 3.2 100.0 1.0
C F:ASN344 3.5 100.0 1.0
C F:GLY342 3.5 100.0 1.0
C F:ASP294 3.5 100.0 1.0
C F:GLY298 3.7 100.0 1.0
O F:HOH622 3.9 100.0 1.0
N F:ASN344 4.0 100.0 1.0
CA F:GLY345 4.2 100.0 1.0
CA F:GLY342 4.2 100.0 1.0
CG F:ASP324 4.2 100.0 1.0
N F:GLY345 4.2 100.0 1.0
N F:GLY298 4.3 100.0 1.0
N F:ALA343 4.3 100.0 1.0
CA F:ASN295 4.4 100.0 1.0
CA F:SER299 4.4 100.0 1.0
N F:ASN295 4.4 100.0 1.0
N F:SER299 4.4 100.0 1.0
CA F:ASN344 4.4 100.0 1.0
CA F:ASP294 4.5 100.0 1.0
CA F:GLY298 4.6 100.0 1.0
C F:ASN295 4.6 100.0 1.0
CB F:ASP294 4.6 100.0 1.0
OD1 F:ASP294 4.6 100.0 1.0
C F:ALA343 4.7 100.0 1.0
CB F:ASP324 4.8 100.0 1.0
O F:ASN341 4.8 87.5 1.0
N F:ASP294 4.8 100.0 1.0
O F:ASN295 4.8 100.0 1.0
CA F:ALA343 4.8 100.0 1.0
CG F:ASP294 4.9 100.0 1.0

Calcium binding site 6 out of 8 in 9ejf

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Calcium binding site 6 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca504

b:155.0
occ:1.00
 OD1 F:ASN378 2.1 100.0 1.0
OD1 F:ASP376 2.2 100.0 1.0
O F:ASN386 2.6 100.0 1.0
O F:HOH609 2.7 50.0 1.0
CG F:ASP376 3.1 100.0 1.0
OD2 F:ASP376 3.2 100.0 1.0
OD2 F:ASP384 3.2 50.0 1.0
CG F:ASN378 3.3 100.0 1.0
C F:ASN386 3.7 100.0 1.0
CG F:ASP384 3.9 50.0 1.0
ND2 F:ASN378 3.9 100.0 1.0
OD1 F:ASP384 4.0 50.0 1.0
N F:ASN386 4.2 100.0 1.0
N F:ASN378 4.3 100.0 1.0
CA F:ASN386 4.3 100.0 1.0
CB F:ASN386 4.3 100.0 1.0
O F:ASP384 4.4 50.0 1.0
CB F:ASN378 4.4 100.0 1.0
CB F:ASP376 4.5 100.0 1.0
C F:ASN378 4.5 100.0 1.0
N F:GLY379 4.6 100.0 1.0
CD F:PRO377 4.6 100.0 1.0
CA F:ASN378 4.6 100.0 1.0
N F:PHE387 4.7 100.0 1.0
CA F:GLY379 4.8 100.0 1.0
C F:ASP384 4.9 50.0 1.0
N F:PRO377 4.9 100.0 1.0
O F:ASN378 4.9 100.0 1.0
C F:ASP376 4.9 100.0 1.0
CA F:ASP376 4.9 100.0 1.0
CA F:PHE387 5.0 100.0 1.0

Calcium binding site 7 out of 8 in 9ejf

Go back to Calcium Binding Sites List in 9ejf
Calcium binding site 7 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca503

b:155.0
occ:1.00
 O K:ASN344 2.2 100.0 1.0
O K:ASP294 2.3 100.0 1.0
O K:GLY298 2.6 100.0 1.0
O K:HOH629 2.8 100.0 1.0
O K:GLY342 2.9 100.0 1.0
OD2 K:ASP324 3.2 100.0 1.0
C K:ASN344 3.5 100.0 1.0
C K:ASP294 3.5 100.0 1.0
C K:GLY298 3.6 100.0 1.0
C K:GLY342 3.6 100.0 1.0
N K:ASN344 4.0 100.0 1.0
O K:HOH643 4.1 100.0 1.0
N K:GLY298 4.2 100.0 1.0
CA K:GLY345 4.2 100.0 1.0
CA K:GLY342 4.2 100.0 1.0
CG K:ASP324 4.3 100.0 1.0
CA K:SER299 4.3 100.0 1.0
N K:SER299 4.3 100.0 1.0
N K:GLY345 4.3 100.0 1.0
CA K:ASN295 4.4 100.0 1.0
N K:ALA343 4.4 100.0 1.0
N K:ASN295 4.4 100.0 1.0
CA K:ASN344 4.4 100.0 1.0
CA K:ASP294 4.5 100.0 1.0
CA K:GLY298 4.5 100.0 1.0
C K:ASN295 4.5 100.0 1.0
CB K:ASP294 4.6 100.0 1.0
OD1 K:ASP294 4.6 100.0 1.0
O K:ASN295 4.7 100.0 1.0
O K:ASN341 4.7 87.5 1.0
N K:ASP294 4.8 100.0 1.0
CB K:ASP324 4.8 100.0 1.0
CG K:ASP294 4.9 100.0 1.0
C K:ALA343 4.9 100.0 1.0
CA K:ALA343 4.9 100.0 1.0

Calcium binding site 8 out of 8 in 9ejf

Go back to Calcium Binding Sites List in 9ejf
Calcium binding site 8 out of 8 in the Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Ncs.1.1 Fab in Complex with the Snap of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction] within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca504

b:155.0
occ:1.00
 OD1 K:ASN378 2.2 100.0 1.0
OD1 K:ASP376 2.3 100.0 1.0
O K:ASN386 2.7 100.0 1.0
CG K:ASP376 3.0 100.0 1.0
OD2 K:ASP376 3.0 100.0 1.0
OD2 K:ASP384 3.3 50.0 1.0
CG K:ASN378 3.4 100.0 1.0
C K:ASN386 3.7 100.0 1.0
OD1 K:ASP384 3.8 50.0 1.0
CG K:ASP384 3.8 50.0 1.0
O K:ASP384 3.9 50.0 1.0
ND2 K:ASN378 4.0 100.0 1.0
N K:ASN386 4.1 100.0 1.0
CA K:ASN386 4.3 100.0 1.0
N K:ASN378 4.4 100.0 1.0
CB K:ASN386 4.4 100.0 1.0
CB K:ASP376 4.4 100.0 1.0
C K:ASN378 4.5 100.0 1.0
N K:GLY379 4.5 100.0 1.0
CB K:ASN378 4.5 100.0 1.0
C K:ASP384 4.6 50.0 1.0
CA K:ASN378 4.7 100.0 1.0
CA K:GLY379 4.7 100.0 1.0
N K:PHE387 4.8 100.0 1.0
O K:ASN378 4.8 100.0 1.0
CA K:ASP376 5.0 100.0 1.0
N K:PRO377 5.0 100.0 1.0

Reference:

J.Lederhofer, A.J.Borst, L.Nguyen, R.A.Gillespie, C.J.Williams, E.L.Walker, J.E.Raab, C.Yap, D.Ellis, A.Creanga, H.X.Tan, T.H.T.Do, M.Ravichandran, A.B.Mcdermott, V.Le Sage, S.F.Andrews, B.S.Graham, A.K.Wheatley, D.S.Reed, N.P.King, M.Kanekiyo. Structural Convergence and Water-Mediated Substrate Mimicry Enable Broad Neuraminidase Inhibition By Human Antibodies. Nat Commun V. 16 7068 2025.
ISSN: ESSN 2041-1723
PubMed: 40750617
DOI: 10.1038/S41467-025-62339-Z
Page generated: Fri Aug 22 22:35:03 2025

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