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Calcium in PDB 8yvl: Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab

Enzymatic activity of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab

All present enzymatic activity of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab:
3.2.1.18;

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab (pdb code 8yvl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab, PDB code: 8yvl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 8yvl

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Calcium binding site 1 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:30.0
occ:1.00
 O A:ASP294 1.9 22.4 1.0
O A:ASN344 2.1 22.9 1.0
O A:GLY298 2.4 22.9 1.0
O A:GLY342 2.7 23.6 1.0
OD2 A:ASP324 3.0 20.6 1.0
C A:ASP294 3.1 22.4 1.0
C A:ASN344 3.3 22.9 1.0
C A:GLY298 3.5 22.9 1.0
C A:GLY342 3.7 23.6 1.0
CG A:ASP324 3.7 20.6 1.0
N A:ASN344 4.0 22.9 1.0
CA A:GLY345 4.0 19.6 1.0
N A:ASN295 4.0 22.3 1.0
CA A:ASP294 4.0 22.4 1.0
CA A:GLY342 4.1 23.6 1.0
N A:GLY345 4.1 19.6 1.0
CB A:ASP294 4.1 22.4 1.0
CA A:ASN295 4.1 22.3 1.0
N A:ASP294 4.3 22.4 1.0
N A:GLY298 4.3 22.9 1.0
OD1 A:ASP324 4.3 20.6 1.0
CA A:ASN344 4.3 22.9 1.0
N A:SER299 4.3 22.4 1.0
CA A:GLY298 4.4 22.9 1.0
CA A:SER299 4.4 22.4 1.0
CB A:ASP324 4.5 20.6 1.0
C A:ASN295 4.6 22.3 1.0
N A:ALA343 4.8 25.2 1.0
OD1 A:ASP294 4.8 22.4 1.0
CG A:ASP294 4.8 22.4 1.0
N A:TRP296 4.8 25.1 1.0
O A:ASN341 4.9 24.8 1.0

Calcium binding site 2 out of 9 in 8yvl

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Calcium binding site 2 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:30.0
occ:1.00
 OD2 A:ASP113 4.0 20.2 1.0
OD2 D:ASP113 4.0 20.3 1.0
OD2 C:ASP113 4.1 20.1 1.0
OD2 B:ASP113 4.1 20.2 1.0
OD1 A:ASP113 4.5 20.2 1.0
OD1 D:ASP113 4.5 20.3 1.0
OD1 B:ASP113 4.5 20.2 1.0
OD1 C:ASP113 4.6 20.1 1.0
CG A:ASP113 4.6 20.2 1.0
CG D:ASP113 4.6 20.3 1.0
CG B:ASP113 4.7 20.2 1.0
CG C:ASP113 4.7 20.1 1.0

Calcium binding site 3 out of 9 in 8yvl

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Calcium binding site 3 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:30.0
occ:1.00
 OD1 A:ASP376 2.2 21.2 1.0
OD1 A:ASN378 2.3 22.8 1.0
O A:ASN386 2.4 27.3 1.0
OD1 A:ASP384 2.4 28.4 1.0
CG A:ASP376 3.0 21.2 1.0
OD2 A:ASP376 3.1 21.2 1.0
CG A:ASN378 3.4 22.8 1.0
C A:ASN386 3.5 27.3 1.0
CG A:ASP384 3.5 28.4 1.0
OD2 A:ASP384 4.0 28.4 1.0
ND2 A:ASN378 4.0 22.8 1.0
O A:ASP384 4.1 28.4 1.0
N A:ASN386 4.1 27.3 1.0
CA A:ASN386 4.2 27.3 1.0
CB A:ASN386 4.3 27.3 1.0
CB A:ASP376 4.4 21.2 1.0
N A:ASN378 4.5 22.8 1.0
C A:ASN378 4.5 22.8 1.0
N A:PHE387 4.5 23.4 1.0
C A:ASP384 4.6 28.4 1.0
N A:GLY379 4.6 22.4 1.0
CB A:ASN378 4.7 22.8 1.0
CB A:ASP384 4.8 28.4 1.0
CA A:ASN378 4.8 22.8 1.0
CA A:PHE387 4.8 23.4 1.0
O A:ASN378 4.8 22.8 1.0
CA A:GLY379 4.8 22.4 1.0
CD A:PRO377 4.8 21.0 1.0
CA A:ASP376 4.9 21.2 1.0
N A:PRO377 5.0 21.0 1.0
C A:ASN385 5.0 28.5 1.0

Calcium binding site 4 out of 9 in 8yvl

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Calcium binding site 4 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:30.0
occ:1.00
 O B:ASN344 1.9 22.8 1.0
O B:ASP294 2.3 22.4 1.0
O B:GLY342 2.5 23.7 1.0
O B:GLY298 2.5 22.9 1.0
C B:ASN344 3.1 22.8 1.0
OD2 B:ASP324 3.2 20.7 1.0
C B:GLY342 3.3 23.7 1.0
C B:ASP294 3.5 22.4 1.0
C B:GLY298 3.6 22.9 1.0
N B:ASN344 3.7 22.8 1.0
CA B:GLY342 3.7 23.7 1.0
CG B:ASP324 3.8 20.7 1.0
CA B:GLY345 4.0 19.6 1.0
N B:GLY345 4.0 19.6 1.0
CA B:ASN344 4.1 22.8 1.0
N B:SER299 4.3 22.4 1.0
CA B:SER299 4.3 22.4 1.0
OD1 B:ASP324 4.3 20.7 1.0
N B:GLY298 4.4 22.9 1.0
CA B:ASN295 4.4 22.3 1.0
N B:ASN295 4.4 22.3 1.0
N B:ALA343 4.4 25.2 1.0
O B:ASN341 4.4 25.0 1.0
CA B:GLY298 4.5 22.9 1.0
CB B:ASP324 4.5 20.7 1.0
CA B:ASP294 4.5 22.4 1.0
CB B:ASP294 4.6 22.4 1.0
C B:ASN295 4.7 22.3 1.0
C B:ALA343 4.8 25.2 1.0
N B:ASP294 4.8 22.4 1.0
O B:PRO326 4.8 20.5 1.0
N B:GLY342 4.9 23.7 1.0
CA B:ALA343 4.9 25.2 1.0

Calcium binding site 5 out of 9 in 8yvl

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Calcium binding site 5 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:30.0
occ:1.00
 OD1 B:ASN378 2.1 22.7 1.0
OD1 B:ASP384 2.3 28.5 1.0
OD1 B:ASP376 2.4 21.1 1.0
O B:ASN386 2.6 27.2 1.0
CG B:ASP376 3.2 21.1 1.0
OD2 B:ASP376 3.2 21.1 1.0
CG B:ASN378 3.2 22.7 1.0
CG B:ASP384 3.4 28.5 1.0
C B:ASN386 3.7 27.2 1.0
OD2 B:ASP384 3.8 28.5 1.0
ND2 B:ASN378 3.8 22.7 1.0
O B:ASP384 4.1 28.5 1.0
N B:ASN386 4.2 27.2 1.0
CA B:ASN386 4.3 27.2 1.0
CB B:ASN386 4.4 27.2 1.0
N B:ASN378 4.4 22.7 1.0
C B:ASN378 4.5 22.7 1.0
CB B:ASN378 4.5 22.7 1.0
C B:ASP384 4.6 28.5 1.0
N B:GLY379 4.6 22.3 1.0
CB B:ASP376 4.6 21.1 1.0
CB B:ASP384 4.7 28.5 1.0
CA B:ASN378 4.7 22.7 1.0
O B:ASN378 4.7 22.7 1.0
N B:PHE387 4.7 23.2 1.0
CA B:GLY379 4.8 22.3 1.0
CD B:PRO377 4.9 21.0 1.0

Calcium binding site 6 out of 9 in 8yvl

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Calcium binding site 6 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:30.0
occ:1.00
 O C:ASN344 2.1 22.8 1.0
O C:ASP294 2.3 22.4 1.0
O C:GLY298 2.3 22.8 1.0
O C:GLY342 2.6 23.5 1.0
OD2 C:ASP324 3.1 20.6 1.0
C C:ASN344 3.3 22.8 1.0
C C:GLY298 3.4 22.8 1.0
C C:GLY342 3.4 23.5 1.0
C C:ASP294 3.5 22.4 1.0
CG C:ASP324 3.7 20.6 1.0
CA C:GLY342 3.7 23.5 1.0
N C:ASN344 3.9 22.8 1.0
CA C:GLY345 4.1 19.6 1.0
N C:SER299 4.1 22.3 1.0
CA C:SER299 4.1 22.3 1.0
N C:GLY345 4.2 19.6 1.0
N C:GLY298 4.3 22.8 1.0
CA C:ASN344 4.3 22.8 1.0
OD1 C:ASP324 4.3 20.6 1.0
CA C:GLY298 4.3 22.8 1.0
CB C:ASP324 4.4 20.6 1.0
N C:ASN295 4.4 22.3 1.0
O C:ASN341 4.4 24.7 1.0
CA C:ASP294 4.5 22.4 1.0
CA C:ASN295 4.5 22.3 1.0
CB C:ASP294 4.5 22.4 1.0
N C:ALA343 4.5 25.2 1.0
N C:ASP294 4.7 22.4 1.0
O C:PRO326 4.8 20.4 1.0
C C:ASN295 4.8 22.3 1.0
N C:GLY342 4.9 23.5 1.0
C C:ALA343 5.0 25.2 1.0

Calcium binding site 7 out of 9 in 8yvl

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Calcium binding site 7 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca505

b:30.0
occ:1.00
 OD1 C:ASP376 2.3 21.1 1.0
OD1 C:ASN378 2.3 22.8 1.0
O C:ASN386 2.4 27.2 1.0
OD1 C:ASP384 2.4 28.5 1.0
CG C:ASP376 3.1 21.1 1.0
OD2 C:ASP376 3.2 21.1 1.0
CG C:ASN378 3.4 22.8 1.0
C C:ASN386 3.5 27.2 1.0
CG C:ASP384 3.5 28.5 1.0
OD2 C:ASP384 3.9 28.5 1.0
ND2 C:ASN378 4.0 22.8 1.0
N C:ASN386 4.1 27.2 1.0
CA C:ASN386 4.1 27.2 1.0
CB C:ASN386 4.2 27.2 1.0
O C:ASP384 4.2 28.5 1.0
N C:ASN378 4.4 22.8 1.0
N C:PHE387 4.5 23.2 1.0
CB C:ASP376 4.5 21.1 1.0
C C:ASN378 4.6 22.8 1.0
CB C:ASN378 4.6 22.8 1.0
C C:ASP384 4.7 28.5 1.0
N C:GLY379 4.7 22.3 1.0
CD C:PRO377 4.7 21.0 1.0
CA C:PHE387 4.8 23.2 1.0
CB C:ASP384 4.8 28.5 1.0
CA C:ASN378 4.8 22.8 1.0
O C:ASN378 4.9 22.8 1.0
N C:PRO377 5.0 21.0 1.0
CA C:GLY379 5.0 22.3 1.0
CA C:ASP376 5.0 21.1 1.0

Calcium binding site 8 out of 9 in 8yvl

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Calcium binding site 8 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:30.0
occ:1.00
 O D:ASN344 2.0 22.9 1.0
O D:ASP294 2.4 22.5 1.0
O D:GLY298 2.5 23.0 1.0
O D:GLY342 2.6 23.7 1.0
OD2 D:ASP324 3.1 20.8 1.0
C D:ASN344 3.2 22.9 1.0
C D:GLY342 3.4 23.7 1.0
C D:GLY298 3.5 23.0 1.0
C D:ASP294 3.6 22.5 1.0
CG D:ASP324 3.7 20.8 1.0
CA D:GLY342 3.8 23.7 1.0
N D:ASN344 3.8 22.9 1.0
CA D:GLY345 4.0 19.7 1.0
N D:GLY345 4.0 19.7 1.0
CA D:ASN344 4.2 22.9 1.0
CA D:SER299 4.2 22.4 1.0
N D:SER299 4.2 22.4 1.0
OD1 D:ASP324 4.2 20.8 1.0
CB D:ASP324 4.4 20.8 1.0
O D:ASN341 4.4 25.0 1.0
N D:GLY298 4.4 23.0 1.0
N D:ASN295 4.5 22.4 1.0
N D:ALA343 4.5 25.2 1.0
CA D:GLY298 4.5 23.0 1.0
CA D:ASN295 4.5 22.4 1.0
CA D:ASP294 4.6 22.5 1.0
CB D:ASP294 4.6 22.5 1.0
O D:PRO326 4.7 20.7 1.0
N D:ASP294 4.8 22.5 1.0
C D:ASN295 4.9 22.4 1.0
C D:ALA343 4.9 25.2 1.0
O D:ASN325 4.9 20.4 1.0
N D:GLY342 5.0 23.7 1.0

Calcium binding site 9 out of 9 in 8yvl

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Calcium binding site 9 out of 9 in the Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca505

b:30.0
occ:1.00
 OD1 D:ASP376 2.2 20.9 1.0
OD1 D:ASN378 2.2 22.6 1.0
O D:ASN386 2.4 27.1 1.0
OD1 D:ASP384 2.5 28.3 1.0
CG D:ASP376 3.0 20.9 1.0
OD2 D:ASP376 3.1 20.9 1.0
CG D:ASN378 3.4 22.6 1.0
CG D:ASP384 3.5 28.3 1.0
C D:ASN386 3.6 27.1 1.0
ND2 D:ASN378 3.9 22.6 1.0
OD2 D:ASP384 3.9 28.3 1.0
O D:ASP384 4.2 28.3 1.0
N D:ASN386 4.2 27.1 1.0
CA D:ASN386 4.3 27.1 1.0
N D:ASN378 4.4 22.6 1.0
CB D:ASN386 4.4 27.1 1.0
CB D:ASP376 4.4 20.9 1.0
C D:ASN378 4.5 22.6 1.0
N D:GLY379 4.6 22.3 1.0
CB D:ASN378 4.6 22.6 1.0
N D:PHE387 4.6 23.1 1.0
C D:ASP384 4.7 28.3 1.0
CA D:ASN378 4.7 22.6 1.0
O D:ASN378 4.8 22.6 1.0
CD D:PRO377 4.8 20.8 1.0
CA D:GLY379 4.8 22.3 1.0
CB D:ASP384 4.8 28.3 1.0
CA D:PHE387 4.9 23.1 1.0
CA D:ASP376 4.9 20.9 1.0
N D:PRO377 4.9 20.8 1.0

Reference:

X.Wang, J.Ge, X.Li. Neuraminidase of A/California/04/2009 HIN1 in Complex with Cav-F34 Fab To Be Published.
Page generated: Mon Aug 4 18:46:06 2025

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