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Calcium in PDB 9kod: Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab

Enzymatic activity of Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab

All present enzymatic activity of Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab:
3.2.1.18;

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab (pdb code 9kod). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab, PDB code: 9kod:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 9kod

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Calcium binding site 1 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:30.0
occ:1.00
 O A:TYR344 1.7 27.4 1.0
O A:ASP294 2.3 21.2 1.0
O A:GLY342 2.4 27.4 1.0
O A:GLY298 2.7 24.9 1.0
C A:TYR344 3.0 27.4 1.0
OD2 A:ASP324 3.0 21.7 1.0
C A:GLY342 3.5 27.4 1.0
C A:ASP294 3.6 21.2 1.0
N A:TYR344 3.6 27.4 1.0
CG A:ASP324 3.6 21.7 1.0
C A:GLY298 3.7 24.9 1.0
CA A:GLY345 3.9 19.1 1.0
N A:GLY345 3.9 19.1 1.0
CA A:TYR344 3.9 27.4 1.0
OD1 A:ASP324 4.1 21.7 1.0
CA A:GLY342 4.1 27.4 1.0
CA A:ASN295 4.3 22.6 1.0
CB A:ASP324 4.4 21.7 1.0
N A:ASN295 4.4 22.6 1.0
CA A:SER299 4.4 26.0 1.0
N A:SER299 4.4 26.0 1.0
N A:GLY298 4.4 24.9 1.0
N A:ALA343 4.5 26.4 1.0
CA A:ASP294 4.6 21.2 1.0
C A:ALA343 4.6 26.4 1.0
CB A:ASP294 4.7 21.2 1.0
CA A:GLY298 4.7 24.9 1.0
CA A:ALA343 4.7 26.4 1.0
C A:ASN295 4.8 22.6 1.0
N A:ASP294 4.9 21.2 1.0
O A:PRO326 4.9 24.0 1.0

Calcium binding site 2 out of 8 in 9kod

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Calcium binding site 2 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:30.0
occ:1.00
 OD2 A:ASP384 1.6 49.5 1.0
OD1 A:ASP376 2.1 28.4 1.0
CG A:ASP384 2.2 49.5 1.0
OD1 A:ASP384 2.2 49.5 1.0
OD1 A:ASN378 2.2 31.4 1.0
O A:SER386 2.7 38.0 1.0
CG A:ASP376 2.7 28.4 1.0
OD2 A:ASP376 2.8 28.4 1.0
CG A:ASN378 3.3 31.4 1.0
CB A:ASP384 3.7 49.5 1.0
C A:SER386 3.8 38.0 1.0
ND2 A:ASN378 3.8 31.4 1.0
N A:SER386 4.2 38.0 1.0
CB A:ASP376 4.2 28.4 1.0
C A:ASN378 4.3 31.4 1.0
O A:ASN378 4.4 31.4 1.0
N A:ASN378 4.4 31.4 1.0
N A:GLY379 4.4 29.6 1.0
CA A:SER386 4.4 38.0 1.0
CB A:ASN378 4.5 31.4 1.0
CA A:GLY379 4.6 29.6 1.0
CA A:ASN378 4.6 31.4 1.0
N A:SER385 4.6 43.4 1.0
CB A:SER386 4.7 38.0 1.0
CA A:ASP384 4.7 49.5 1.0
N A:ASP384 4.8 49.5 1.0
CA A:ASP376 4.8 28.4 1.0
N A:PHE387 4.8 32.5 1.0
CD A:PRO377 4.9 27.0 1.0
C A:ASP376 4.9 28.4 1.0
N A:PRO377 5.0 27.0 1.0
OG A:SER386 5.0 38.0 1.0

Calcium binding site 3 out of 8 in 9kod

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Calcium binding site 3 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:30.0
occ:1.00
 O B:TYR344 1.9 37.5 1.0
O B:GLY298 2.3 34.9 1.0
O B:GLY342 2.3 37.2 1.0
O B:ASP294 2.5 30.5 1.0
OD2 B:ASP324 3.1 28.9 1.0
C B:TYR344 3.1 37.5 1.0
C B:GLY342 3.3 37.2 1.0
C B:GLY298 3.4 34.9 1.0
N B:TYR344 3.6 37.5 1.0
CG B:ASP324 3.6 28.9 1.0
C B:ASP294 3.7 30.5 1.0
CA B:GLY342 3.9 37.2 1.0
CA B:GLY345 4.0 26.8 1.0
N B:GLY345 4.0 26.8 1.0
CA B:TYR344 4.0 37.5 1.0
OD1 B:ASP324 4.2 28.9 1.0
CA B:SER299 4.2 34.3 1.0
N B:SER299 4.2 34.3 1.0
CB B:ASP324 4.3 28.9 1.0
N B:ALA343 4.4 35.1 1.0
N B:GLY298 4.4 34.9 1.0
CA B:GLY298 4.5 34.9 1.0
CA B:ASN295 4.5 30.6 1.0
N B:ASN295 4.6 30.6 1.0
C B:ALA343 4.6 35.1 1.0
CA B:ALA343 4.7 35.1 1.0
O B:PRO326 4.7 29.2 1.0
CA B:ASP294 4.7 30.5 1.0
CB B:ASP294 4.7 30.5 1.0
C B:ASN295 4.9 30.6 1.0

Calcium binding site 4 out of 8 in 9kod

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Calcium binding site 4 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:30.0
occ:1.00
 OD1 B:ASP376 2.2 35.9 1.0
OD1 B:ASN378 2.5 39.3 1.0
O B:SER386 2.6 48.8 1.0
OD2 B:ASP376 2.7 35.9 1.0
CG B:ASP376 2.8 35.9 1.0
CG B:ASN378 3.6 39.3 1.0
C B:SER386 3.7 48.8 1.0
CB B:ASP384 3.8 56.0 1.0
OG B:SER386 3.9 48.8 1.0
N B:SER386 4.0 48.8 1.0
ND2 B:ASN378 4.0 39.3 1.0
O B:ASP384 4.2 56.0 1.0
C B:ASP384 4.2 56.0 1.0
CB B:ASP376 4.3 35.9 1.0
CA B:SER386 4.4 48.8 1.0
CA B:ASP384 4.5 56.0 1.0
C B:ASN378 4.5 39.3 1.0
O B:ASN378 4.6 39.3 1.0
N B:GLY379 4.6 35.4 1.0
CA B:GLY379 4.7 35.4 1.0
N B:ASN378 4.7 39.3 1.0
N B:SER385 4.7 54.0 1.0
N B:PHE387 4.7 40.4 1.0
N B:ASP384 4.8 56.0 1.0
CB B:SER386 4.8 48.8 1.0
OD2 B:ASP384 4.8 56.0 1.0
CB B:ASN378 4.8 39.3 1.0
CG B:ASP384 4.8 56.0 1.0
C B:SER385 4.9 54.0 1.0
OG B:SER319 4.9 42.9 1.0
CA B:ASN378 4.9 39.3 1.0
CA B:ASP376 4.9 35.9 1.0

Calcium binding site 5 out of 8 in 9kod

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Calcium binding site 5 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:30.0
occ:1.00
 O C:TYR344 2.0 36.0 1.0
O C:GLY342 2.1 36.6 1.0
O C:GLY298 2.2 35.9 1.0
O C:ASP294 2.6 30.2 1.0
C C:GLY342 3.1 36.6 1.0
C C:TYR344 3.2 36.0 1.0
OD2 C:ASP324 3.2 29.4 1.0
C C:GLY298 3.3 35.9 1.0
N C:TYR344 3.6 36.0 1.0
CA C:GLY342 3.7 36.6 1.0
CG C:ASP324 3.8 29.4 1.0
C C:ASP294 3.8 30.2 1.0
CA C:TYR344 4.0 36.0 1.0
N C:SER299 4.1 36.7 1.0
CA C:SER299 4.1 36.7 1.0
N C:GLY345 4.1 27.4 1.0
CA C:GLY345 4.2 27.4 1.0
N C:ALA343 4.2 34.9 1.0
N C:GLY298 4.2 35.9 1.0
CA C:GLY298 4.3 35.9 1.0
OD1 C:ASP324 4.3 29.4 1.0
CB C:ASP324 4.4 29.4 1.0
C C:ALA343 4.5 34.9 1.0
CA C:ALA343 4.6 34.9 1.0
CA C:ASN295 4.6 30.4 1.0
N C:ASN295 4.6 30.4 1.0
O C:PRO326 4.7 32.7 1.0
CB C:ASP294 4.7 30.2 1.0
CA C:ASP294 4.8 30.2 1.0
C C:ASN295 4.9 30.4 1.0
CB C:SER299 5.0 36.7 1.0

Calcium binding site 6 out of 8 in 9kod

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Calcium binding site 6 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:30.0
occ:1.00
 OD1 C:ASN378 2.1 40.5 1.0
OD1 C:ASP376 2.2 37.7 1.0
O C:SER386 2.6 53.9 1.0
CG C:ASP376 3.0 37.7 1.0
OD2 C:ASP376 3.1 37.7 1.0
CG C:ASN378 3.1 40.5 1.0
ND2 C:ASN378 3.6 40.5 1.0
C C:SER386 3.8 53.9 1.0
OG C:SER386 3.8 53.9 1.0
CB C:ASP384 4.1 60.3 1.0
O C:ASP384 4.3 60.3 1.0
N C:SER386 4.3 53.9 1.0
N C:ASN378 4.3 40.5 1.0
C C:ASN378 4.3 40.5 1.0
CB C:ASP376 4.4 37.7 1.0
CB C:ASN378 4.4 40.5 1.0
O C:ASN378 4.5 40.5 1.0
CA C:SER386 4.5 53.9 1.0
N C:GLY379 4.6 38.3 1.0
CA C:ASN378 4.6 40.5 1.0
C C:ASP384 4.6 60.3 1.0
CD C:PRO377 4.8 39.6 1.0
CB C:SER386 4.8 53.9 1.0
N C:PHE387 4.8 43.8 1.0
CA C:GLY379 4.8 38.3 1.0
CA C:ASP376 4.9 37.7 1.0
CA C:ASP384 4.9 60.3 1.0
N C:PRO377 4.9 39.6 1.0
C C:ASP376 5.0 37.7 1.0

Calcium binding site 7 out of 8 in 9kod

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Calcium binding site 7 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:30.0
occ:1.00
 O D:TYR344 1.7 31.9 1.0
O D:GLY342 2.3 31.4 1.0
O D:ASP294 2.3 27.0 1.0
O D:GLY298 2.4 30.8 1.0
C D:TYR344 2.9 31.9 1.0
OD2 D:ASP324 3.2 23.8 1.0
C D:GLY342 3.4 31.4 1.0
N D:TYR344 3.5 31.9 1.0
C D:ASP294 3.6 27.0 1.0
C D:GLY298 3.6 30.8 1.0
CG D:ASP324 3.7 23.8 1.0
CA D:TYR344 3.8 31.9 1.0
N D:GLY345 3.9 22.5 1.0
CA D:GLY345 3.9 22.5 1.0
CA D:GLY342 4.1 31.4 1.0
OD1 D:ASP324 4.2 23.8 1.0
CA D:ASN295 4.3 28.2 1.0
N D:ALA343 4.4 30.6 1.0
N D:ASN295 4.4 28.2 1.0
N D:SER299 4.4 30.4 1.0
CA D:SER299 4.4 30.4 1.0
N D:GLY298 4.4 30.8 1.0
C D:ALA343 4.5 30.6 1.0
CB D:ASP324 4.5 23.8 1.0
CA D:GLY298 4.6 30.8 1.0
CA D:ASP294 4.6 27.0 1.0
CA D:ALA343 4.6 30.6 1.0
CB D:ASP294 4.7 27.0 1.0
C D:ASN295 4.7 28.2 1.0
O D:PRO326 4.9 23.7 1.0
N D:TRP296 4.9 28.2 1.0
N D:ASP294 4.9 27.0 1.0

Calcium binding site 8 out of 8 in 9kod

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Calcium binding site 8 out of 8 in the Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 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/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:30.0
occ:1.00
 OD1 D:ASP376 2.0 29.9 1.0
OD1 D:ASN378 2.1 34.7 1.0
CG D:ASP376 2.7 29.9 1.0
OD2 D:ASP376 2.8 29.9 1.0
O D:SER386 2.8 43.4 1.0
CG D:ASN378 3.2 34.7 1.0
ND2 D:ASN378 3.8 34.7 1.0
C D:SER386 3.9 43.4 1.0
CB D:ASP384 4.1 50.2 1.0
C D:ASN378 4.1 34.7 1.0
CB D:ASP376 4.1 29.9 1.0
OG D:SER386 4.2 43.4 1.0
N D:ASN378 4.2 34.7 1.0
N D:GLY379 4.3 31.9 1.0
O D:ASN378 4.3 34.7 1.0
CB D:ASN378 4.4 34.7 1.0
N D:SER386 4.4 43.4 1.0
CA D:GLY379 4.5 31.9 1.0
CA D:ASN378 4.5 34.7 1.0
O D:ASP384 4.6 50.2 1.0
C D:ASP384 4.7 50.2 1.0
CA D:SER386 4.7 43.4 1.0
CA D:ASP376 4.7 29.9 1.0
C D:ASP376 4.8 29.9 1.0
CA D:ASP384 4.8 50.2 1.0
CD D:PRO377 4.8 30.4 1.0
N D:PRO377 4.9 30.4 1.0
N D:PHE387 4.9 34.2 1.0
OD2 D:ASP384 4.9 50.2 1.0

Reference:

X.Wang, J.Ge, X.Li. Neuraminidase of A/Dairy Cow/Minnesota/24_016288-003/2024 (DCMN24 N1) in Complex with Cav-F6 Fab To Be Published.
Page generated: Mon Aug 4 18:54:41 2025

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