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Calcium in PDB 8g3z: Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules (pdb code 8g3z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules, PDB code: 8g3z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8g3z

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Calcium binding site 1 out of 5 in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:36.6
occ:1.00
 O A:ASP293 2.5 46.8 1.0
O A:GLY346 2.5 39.8 1.0
O A:THR297 2.5 41.7 1.0
O A:GLY344 2.6 44.3 1.0
OD2 A:ASP324 2.6 49.6 1.0
CG A:ASP324 3.4 49.0 1.0
C A:ASP293 3.6 44.1 1.0
C A:THR297 3.7 42.3 1.0
C A:GLY344 3.7 45.7 1.0
C A:GLY346 3.7 38.9 1.0
CA A:GLY347 4.1 37.3 1.0
OD1 A:ASP324 4.1 48.4 1.0
CB A:ASP324 4.2 48.8 1.0
CA A:ALA298 4.3 43.1 1.0
CA A:GLY344 4.3 48.8 1.0
N A:ALA298 4.4 44.7 1.0
N A:GLY347 4.4 38.5 1.0
CA A:ASP293 4.4 41.7 1.0
CB A:ASP293 4.5 41.2 1.0
N A:ASP293 4.5 41.8 1.0
N A:ASN294 4.6 47.7 1.0
C A:SER345 4.6 45.8 1.0
CA A:ASN294 4.7 49.8 1.0
N A:THR297 4.7 43.2 1.0
N A:GLY346 4.7 43.7 1.0
O A:SER345 4.7 46.6 1.0
N A:SER345 4.8 46.9 1.0
O A:PRO326 4.8 45.7 1.0
CA A:THR297 4.8 42.5 1.0
CA A:GLY346 4.9 40.7 1.0
OD1 A:ASP293 4.9 44.6 1.0

Calcium binding site 2 out of 5 in 8g3z

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Calcium binding site 2 out of 5 in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:96.5
occ:1.00
 OE2 D:GLU168 2.6 59.2 1.0
OE1 A:GLU168 2.7 58.6 1.0
OE2 B:GLU168 2.8 67.5 1.0
OE1 C:GLU168 2.8 78.1 1.0
CD D:GLU168 3.7 58.1 1.0
CD A:GLU168 3.7 58.3 1.0
CD B:GLU168 3.7 67.4 1.0
CD C:GLU168 3.7 70.7 1.0
OE1 B:GLU168 3.9 70.1 1.0
OE2 C:GLU168 4.0 74.9 1.0
OE2 A:GLU168 4.1 63.4 1.0
OE1 D:GLU168 4.1 62.6 1.0
CG A:GLU168 4.9 51.7 1.0
CG D:GLU168 4.9 51.6 1.0
CG C:GLU168 5.0 60.4 1.0

Calcium binding site 3 out of 5 in 8g3z

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Calcium binding site 3 out of 5 in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:36.7
occ:1.00
 O B:ASP293 2.5 47.1 1.0
O B:GLY346 2.5 39.5 1.0
O B:THR297 2.6 41.9 1.0
O B:GLY344 2.6 44.6 1.0
OD2 B:ASP324 2.6 50.5 1.0
CG B:ASP324 3.4 49.8 1.0
C B:ASP293 3.6 44.5 1.0
C B:GLY344 3.7 45.7 1.0
C B:THR297 3.7 42.6 1.0
C B:GLY346 3.7 38.5 1.0
CA B:GLY347 4.1 36.5 1.0
OD1 B:ASP324 4.1 49.1 1.0
CB B:ASP324 4.2 49.8 1.0
CA B:ALA298 4.3 43.5 1.0
CA B:GLY344 4.3 49.1 1.0
N B:ALA298 4.4 45.1 1.0
N B:GLY347 4.4 38.0 1.0
CA B:ASP293 4.5 42.5 1.0
N B:ASN294 4.5 48.1 1.0
CB B:ASP293 4.6 42.1 1.0
N B:ASP293 4.6 42.2 1.0
C B:SER345 4.6 45.8 1.0
CA B:ASN294 4.7 49.5 1.0
OD1 B:ASP293 4.7 46.9 1.0
O B:SER345 4.7 46.1 1.0
N B:GLY346 4.7 43.9 1.0
N B:SER345 4.7 46.9 1.0
N B:THR297 4.8 43.1 1.0
O B:PRO326 4.8 49.0 1.0
CA B:THR297 4.8 42.1 1.0
CA B:GLY346 4.9 40.5 1.0
C B:ASN294 5.0 50.4 1.0

Calcium binding site 4 out of 5 in 8g3z

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Calcium binding site 4 out of 5 in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:36.2
occ:1.00
 O C:ASP293 2.4 48.5 1.0
O C:GLY346 2.5 41.1 1.0
O C:THR297 2.6 42.8 1.0
O C:GLY344 2.6 44.2 1.0
OD2 C:ASP324 2.6 52.0 1.0
CG C:ASP324 3.4 51.1 1.0
C C:ASP293 3.7 47.3 1.0
C C:GLY346 3.7 39.6 1.0
C C:THR297 3.7 43.9 1.0
C C:GLY344 3.7 46.5 1.0
CA C:GLY347 4.1 37.0 1.0
OD1 C:ASP324 4.1 49.3 1.0
CB C:ASP324 4.2 51.2 1.0
CA C:ALA298 4.3 44.8 1.0
CA C:GLY344 4.4 49.5 1.0
N C:GLY347 4.4 39.0 1.0
N C:ALA298 4.4 46.5 1.0
CA C:ASP293 4.5 45.7 1.0
N C:ASP293 4.5 44.9 1.0
CB C:ASP293 4.6 44.4 1.0
N C:ASN294 4.6 51.6 1.0
CA C:ASN294 4.6 53.0 1.0
C C:SER345 4.6 46.8 1.0
OD1 C:ASP293 4.7 49.7 1.0
N C:GLY346 4.7 44.7 1.0
N C:THR297 4.7 44.6 1.0
N C:SER345 4.8 48.0 1.0
O C:SER345 4.8 46.9 1.0
O C:PRO326 4.8 52.9 1.0
CA C:GLY346 4.8 41.3 1.0
CA C:THR297 4.8 44.2 1.0

Calcium binding site 5 out of 5 in 8g3z

Go back to Calcium Binding Sites List in 8g3z
Calcium binding site 5 out of 5 in the Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in Complex with 4 FNI17 Fab Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:36.5
occ:1.00
 O D:ASP293 2.5 47.2 1.0
O D:GLY346 2.5 40.5 1.0
O D:THR297 2.6 42.3 1.0
OD2 D:ASP324 2.6 49.7 1.0
O D:GLY344 2.6 44.2 1.0
CG D:ASP324 3.5 49.0 1.0
C D:ASP293 3.7 44.5 1.0
C D:THR297 3.7 43.1 1.0
C D:GLY346 3.7 39.5 1.0
C D:GLY344 3.8 46.9 1.0
CA D:GLY347 4.1 37.6 1.0
OD1 D:ASP324 4.2 48.2 1.0
CB D:ASP324 4.2 48.8 1.0
CA D:ALA298 4.2 43.4 1.0
N D:ALA298 4.4 45.2 1.0
N D:GLY347 4.4 38.8 1.0
CA D:GLY344 4.4 49.5 1.0
CA D:ASP293 4.5 42.1 1.0
CB D:ASP293 4.5 41.9 1.0
N D:ASP293 4.6 42.1 1.0
N D:ASN294 4.6 48.0 1.0
C D:SER345 4.7 47.6 1.0
CA D:ASN294 4.7 50.1 1.0
O D:SER345 4.7 48.2 1.0
N D:THR297 4.8 43.6 1.0
N D:GLY346 4.8 45.1 1.0
O D:PRO326 4.8 46.6 1.0
N D:SER345 4.8 49.0 1.0
O D:LYS343 4.8 54.4 1.0
OD1 D:ASP293 4.9 46.0 1.0
CA D:THR297 4.9 43.6 1.0
CA D:GLY346 4.9 41.9 1.0
C D:ASN294 5.0 50.7 1.0

Reference:

C.Momont, H.V.Dang, F.Zatta, K.Hauser, G.Snell, D.Corti, M.S.Pizzuto. A Pan-Influenza Antibody Inhibiting Neuraminidase Via Receptor Mimicry Nature 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06136-Y
Page generated: Fri Jul 19 09:10:03 2024

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