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Calcium in PDB 7u4e: Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2)

Enzymatic activity of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2)

All present enzymatic activity of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2):
3.2.1.18;

Protein crystallography data

The structure of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2), PDB code: 7u4e was solved by R.Lei, A.Hernandez Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.54
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.339, 137.944, 138.246, 90, 92.15, 90
R / Rfree (%) 16.6 / 18

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2) (pdb code 7u4e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2), PDB code: 7u4e:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7u4e

Go back to Calcium Binding Sites List in 7u4e
Calcium binding site 1 out of 4 in the Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:12.6
occ:1.00
 O A:ASP293 2.3 12.6 1.0
OD2 A:ASP324 2.3 13.2 1.0
O A:HIS347 2.3 13.8 1.0
O A:GLY297 2.4 13.9 1.0
O A:GLY345 2.4 14.8 1.0
O A:HOH688 2.4 13.5 1.0
C A:GLY345 3.5 15.9 1.0
C A:ASP293 3.5 12.9 1.0
CG A:ASP324 3.5 13.5 1.0
C A:GLY297 3.5 13.8 1.0
C A:HIS347 3.5 14.3 1.0
CA A:GLY348 4.0 12.8 1.0
CA A:GLY345 4.1 15.8 1.0
O A:HOH828 4.1 13.5 1.0
CA A:ASN294 4.1 13.7 1.0
CA A:SER298 4.2 13.7 1.0
N A:GLY348 4.2 13.2 1.0
N A:SER298 4.2 13.9 1.0
N A:ASN294 4.2 13.2 1.0
OD1 A:ASP324 4.3 13.2 1.0
O A:ASN346 4.3 16.3 1.0
C A:ASN346 4.3 16.4 1.0
CB A:ASP324 4.4 13.1 1.0
C A:ASN294 4.4 13.9 1.0
N A:HIS347 4.5 15.8 1.0
N A:ASN346 4.5 16.3 1.0
O A:ARG344 4.5 16.1 1.0
CA A:ASP293 4.6 12.8 1.0
N A:GLY297 4.6 14.1 1.0
CA A:GLY297 4.6 14.0 1.0
CA A:HIS347 4.6 14.8 1.0
N A:TRP295 4.7 14.4 1.0
OD1 A:ASP293 4.8 13.0 1.0
N A:ASP293 4.8 12.6 1.0
CB A:ASP293 4.8 13.0 1.0
CA A:ASN346 4.8 17.1 1.0
O A:ASN294 4.9 14.0 1.0
CB A:SER298 4.9 14.1 1.0
O A:PRO326 5.0 14.1 1.0

Calcium binding site 2 out of 4 in 7u4e

Go back to Calcium Binding Sites List in 7u4e
Calcium binding site 2 out of 4 in the Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:11.7
occ:1.00
 O B:ASP293 2.2 12.2 1.0
OD2 B:ASP324 2.3 12.0 1.0
O B:HIS347 2.3 12.9 1.0
O B:GLY345 2.4 13.6 1.0
O B:GLY297 2.4 13.4 1.0
O B:HOH718 2.4 12.5 1.0
C B:GLY345 3.4 14.4 1.0
C B:ASP293 3.5 12.2 1.0
CG B:ASP324 3.5 12.1 1.0
C B:HIS347 3.5 12.9 1.0
C B:GLY297 3.5 13.2 1.0
CA B:GLY348 4.0 11.6 1.0
CA B:GLY345 4.1 14.6 1.0
CA B:ASN294 4.1 12.6 1.0
O B:HOH852 4.1 12.6 1.0
CA B:SER298 4.2 12.7 1.0
N B:ASN294 4.2 12.5 1.0
N B:GLY348 4.2 12.1 1.0
N B:SER298 4.3 13.0 1.0
O B:ASN346 4.3 14.6 1.0
C B:ASN346 4.3 14.9 1.0
OD1 B:ASP324 4.3 11.9 1.0
CB B:ASP324 4.4 11.8 1.0
C B:ASN294 4.4 12.8 1.0
N B:HIS347 4.5 14.0 1.0
N B:ASN346 4.5 14.7 1.0
CA B:ASP293 4.5 12.3 1.0
O B:ARG344 4.6 14.9 1.0
N B:GLY297 4.6 13.4 1.0
CA B:GLY297 4.6 13.3 1.0
CA B:HIS347 4.6 13.7 1.0
N B:TRP295 4.7 13.1 1.0
OD1 B:ASP293 4.8 12.8 1.0
N B:ASP293 4.8 11.9 1.0
CA B:ASN346 4.8 15.5 1.0
CB B:ASP293 4.8 12.5 1.0
O B:ASN294 4.9 13.1 1.0
CB B:SER298 4.9 12.7 1.0
O B:PRO326 4.9 12.2 1.0

Calcium binding site 3 out of 4 in 7u4e

Go back to Calcium Binding Sites List in 7u4e
Calcium binding site 3 out of 4 in the Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:12.9
occ:1.00
 O C:ASP293 2.3 12.9 1.0
OD2 C:ASP324 2.3 13.9 1.0
O C:GLY297 2.3 14.8 1.0
O C:HIS347 2.4 14.3 1.0
O C:GLY345 2.4 15.8 1.0
O C:HOH646 2.4 14.2 1.0
C C:GLY345 3.4 16.8 1.0
C C:ASP293 3.5 13.1 1.0
CG C:ASP324 3.5 14.1 1.0
C C:GLY297 3.5 14.7 1.0
C C:HIS347 3.5 14.5 1.0
CA C:GLY348 4.0 13.2 1.0
CA C:GLY345 4.1 16.8 1.0
O C:HOH806 4.1 14.1 1.0
CA C:ASN294 4.1 13.8 1.0
CA C:SER298 4.2 14.3 1.0
N C:GLY348 4.2 13.7 1.0
N C:SER298 4.2 14.6 1.0
N C:ASN294 4.2 13.3 1.0
C C:ASN346 4.3 16.7 1.0
OD1 C:ASP324 4.3 14.0 1.0
O C:ASN346 4.3 16.4 1.0
CB C:ASP324 4.4 13.6 1.0
C C:ASN294 4.4 14.1 1.0
N C:HIS347 4.5 15.8 1.0
N C:ASN346 4.5 17.0 1.0
O C:ARG344 4.5 16.8 1.0
CA C:ASP293 4.6 13.2 1.0
N C:GLY297 4.6 14.9 1.0
CA C:GLY297 4.6 14.8 1.0
CA C:HIS347 4.7 15.2 1.0
N C:TRP295 4.7 14.4 1.0
OD1 C:ASP293 4.8 13.2 1.0
N C:ASP293 4.8 13.1 1.0
CB C:ASP293 4.8 13.1 1.0
CA C:ASN346 4.8 17.6 1.0
O C:ASN294 4.9 14.0 1.0
CB C:SER298 4.9 14.8 1.0
O C:PRO326 5.0 14.1 1.0

Calcium binding site 4 out of 4 in 7u4e

Go back to Calcium Binding Sites List in 7u4e
Calcium binding site 4 out of 4 in the Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Neuraminidase From Influenza Virus A/Bilthoven/17938/1969(H3N2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:13.5
occ:1.00
 O D:ASP293 2.2 13.5 1.0
OD2 D:ASP324 2.3 13.3 1.0
O D:HIS347 2.3 14.2 1.0
O D:GLY297 2.3 14.5 1.0
O D:GLY345 2.3 15.7 1.0
O D:HOH696 2.4 15.1 1.0
C D:GLY345 3.4 16.5 1.0
C D:ASP293 3.5 13.6 1.0
C D:GLY297 3.5 14.8 1.0
CG D:ASP324 3.5 13.4 1.0
C D:HIS347 3.5 14.4 1.0
CA D:GLY348 4.0 13.2 1.0
CA D:ASN294 4.1 13.8 1.0
CA D:GLY345 4.1 16.3 1.0
O D:HOH855 4.1 13.0 1.0
CA D:SER298 4.2 14.4 1.0
N D:GLY348 4.2 13.4 1.0
N D:ASN294 4.2 13.6 1.0
N D:SER298 4.2 14.6 1.0
O D:ASN346 4.3 16.4 1.0
C D:ASN346 4.3 16.7 1.0
OD1 D:ASP324 4.3 13.4 1.0
CB D:ASP324 4.4 13.3 1.0
C D:ASN294 4.4 14.2 1.0
N D:HIS347 4.5 15.8 1.0
N D:ASN346 4.5 16.9 1.0
CA D:ASP293 4.6 13.5 1.0
O D:ARG344 4.6 15.9 1.0
N D:GLY297 4.6 15.0 1.0
CA D:GLY297 4.6 14.8 1.0
CA D:HIS347 4.6 15.1 1.0
N D:TRP295 4.7 14.7 1.0
OD1 D:ASP293 4.8 13.7 1.0
N D:ASP293 4.8 13.3 1.0
CA D:ASN346 4.8 17.4 1.0
CB D:ASP293 4.8 13.8 1.0
O D:ASN294 4.9 14.1 1.0
CB D:SER298 4.9 14.6 1.0

Reference:

R.Lei, T.J.C.Tan, A.Hernandez Garcia, Y.Wang, M.Diefenbacher, C.Teo, G.Gopan, Z.Tavakoli Dargani, Q.W.Teo, C.S.Graham, C.B.Brooke, S.K.Nair, N.C.Wu. Prevalence and Mechanisms of Evolutionary Contingency in Human Influenza H3N2 Neuraminidase. Nat Commun V. 13 6443 2022.
ISSN: ESSN 2041-1723
PubMed: 36307418
DOI: 10.1038/S41467-022-34060-8
Page generated: Tue Apr 4 18:52:21 2023

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