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Calcium in PDB 6n4d: The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus.

Protein crystallography data

The structure of The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus., PDB code: 6n4d was solved by H.Yang, J.Stevens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.43 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.451, 110.562, 126.620, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus. (pdb code 6n4d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus., PDB code: 6n4d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6n4d

Go back to Calcium Binding Sites List in 6n4d
Calcium binding site 1 out of 4 in the The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:24.6
occ:1.00
 O A:ASP293 2.2 24.2 1.0
OD2 A:ASP324 2.3 21.7 1.0
O A:GLY345 2.3 26.1 1.0
O A:PRO347 2.4 28.2 1.0
O A:HOH639 2.4 23.4 1.0
O A:GLY297 2.4 26.7 1.0
C A:GLY345 3.4 26.3 1.0
C A:ASP293 3.5 24.0 1.0
CG A:ASP324 3.5 22.9 1.0
C A:PRO347 3.5 26.3 1.0
C A:GLY297 3.6 26.1 1.0
CA A:GLY348 4.0 23.4 1.0
CA A:ASN294 4.1 23.0 1.0
N A:GLY348 4.2 24.9 1.0
N A:ASN294 4.2 22.8 1.0
CA A:GLY345 4.2 27.5 1.0
CA A:SER298 4.2 23.5 1.0
N A:ASN346 4.3 25.9 1.0
CB A:ASP324 4.3 22.1 1.0
OD1 A:ASP324 4.3 20.8 1.0
N A:SER298 4.3 25.3 1.0
O A:ARG344 4.4 28.1 1.0
CA A:ASN346 4.5 28.7 1.0
C A:ASN294 4.5 23.2 1.0
N A:GLY297 4.5 27.2 1.0
CA A:ASP293 4.5 23.3 1.0
CA A:GLY297 4.6 26.1 1.0
CA A:PRO347 4.7 28.6 1.0
N A:TRP295 4.8 25.3 1.0
CB A:ASP293 4.8 23.4 1.0
OD1 A:ASP293 4.8 24.0 1.0
N A:ASP293 4.8 22.7 1.0
CB A:SER298 4.9 25.4 1.0
O A:ASN294 5.0 22.3 1.0
O A:PRO326 5.0 24.3 1.0

Calcium binding site 2 out of 4 in 6n4d

Go back to Calcium Binding Sites List in 6n4d
Calcium binding site 2 out of 4 in the The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:26.5
occ:1.00
 O B:ASP293 2.2 23.9 1.0
OD2 B:ASP324 2.3 26.8 1.0
O B:PRO347 2.3 28.1 1.0
O B:GLY345 2.4 31.4 1.0
O B:GLY297 2.4 31.4 1.0
O B:HOH615 2.5 29.0 1.0
C B:ASP293 3.4 26.4 1.0
C B:GLY345 3.4 31.2 1.0
CG B:ASP324 3.5 28.2 1.0
C B:PRO347 3.5 28.7 1.0
C B:GLY297 3.6 32.1 1.0
CA B:GLY348 3.9 24.7 1.0
CA B:ASN294 4.0 26.3 1.0
O B:HOH620 4.1 25.9 1.0
N B:ASN294 4.2 24.9 1.0
N B:GLY348 4.2 23.6 1.0
CA B:SER298 4.3 29.2 1.0
OD1 B:ASP324 4.3 28.2 1.0
CA B:GLY345 4.3 32.2 1.0
N B:ASN346 4.3 32.3 1.0
N B:SER298 4.3 30.3 1.0
CB B:ASP324 4.4 25.6 1.0
C B:ASN294 4.4 25.4 1.0
CA B:ASN346 4.5 31.3 1.0
CA B:ASP293 4.5 25.7 1.0
O B:ARG344 4.5 28.4 1.0
N B:GLY297 4.6 29.4 1.0
CA B:GLY297 4.6 30.2 1.0
CA B:PRO347 4.7 31.3 1.0
N B:ASP293 4.7 26.6 1.0
N B:TRP295 4.7 25.1 1.0
OD1 B:ASP293 4.7 26.6 1.0
CB B:ASP293 4.8 26.4 1.0
OD1 B:ASN294 4.9 30.2 1.0
O B:ASN294 4.9 27.4 1.0
CB B:SER298 5.0 31.8 1.0

Calcium binding site 3 out of 4 in 6n4d

Go back to Calcium Binding Sites List in 6n4d
Calcium binding site 3 out of 4 in the The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:26.4
occ:1.00
 O C:ASP293 2.2 24.1 1.0
OD2 C:ASP324 2.3 27.9 1.0
O C:PRO347 2.3 27.8 1.0
O C:GLY345 2.4 28.9 1.0
O C:HOH613 2.4 27.3 1.0
O C:GLY297 2.5 32.8 1.0
C C:ASP293 3.4 25.7 1.0
C C:GLY345 3.4 29.8 1.0
CG C:ASP324 3.5 27.7 1.0
C C:PRO347 3.5 28.2 1.0
C C:GLY297 3.6 32.7 1.0
CA C:GLY348 3.9 24.1 1.0
CA C:ASN294 4.0 26.1 1.0
O C:HOH632 4.1 26.1 1.0
N C:ASN294 4.2 24.4 1.0
N C:GLY348 4.2 22.2 1.0
OD1 C:ASP324 4.3 28.1 1.0
CA C:SER298 4.3 29.0 1.0
CA C:GLY345 4.3 30.0 1.0
N C:ASN346 4.3 30.7 1.0
CB C:ASP324 4.3 25.2 1.0
N C:SER298 4.4 30.6 1.0
C C:ASN294 4.4 26.1 1.0
CA C:ASN346 4.5 31.3 1.0
O C:ARG344 4.5 27.6 1.0
CA C:ASP293 4.5 26.2 1.0
N C:GLY297 4.6 32.0 1.0
CA C:GLY297 4.6 31.4 1.0
CA C:PRO347 4.7 31.7 1.0
OD1 C:ASP293 4.8 28.3 1.0
N C:TRP295 4.8 26.1 1.0
N C:ASP293 4.8 27.1 1.0
CB C:ASP293 4.8 28.0 1.0
OD1 C:ASN294 4.9 30.1 1.0
O C:ASN294 5.0 29.4 1.0

Calcium binding site 4 out of 4 in 6n4d

Go back to Calcium Binding Sites List in 6n4d
Calcium binding site 4 out of 4 in the The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of Neuramindase From A/Canine/Il/11613/2015 (H3N2) Influenza Virus. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:24.2
occ:1.00
 O D:ASP293 2.2 23.9 1.0
OD2 D:ASP324 2.3 20.1 1.0
O D:HOH625 2.3 22.9 1.0
O D:GLY345 2.3 25.3 1.0
O D:PRO347 2.4 28.1 1.0
O D:GLY297 2.4 27.6 1.0
C D:GLY345 3.4 25.8 1.0
C D:ASP293 3.5 22.7 1.0
CG D:ASP324 3.5 21.9 1.0
C D:PRO347 3.5 26.5 1.0
C D:GLY297 3.6 26.9 1.0
CA D:GLY348 3.9 23.8 1.0
CA D:ASN294 4.1 22.0 1.0
N D:GLY348 4.2 24.9 1.0
N D:ASN294 4.2 21.6 1.0
CA D:GLY345 4.2 27.2 1.0
CA D:SER298 4.2 23.7 1.0
CB D:ASP324 4.3 21.7 1.0
N D:ASN346 4.3 27.0 1.0
OD1 D:ASP324 4.3 21.0 1.0
N D:SER298 4.3 25.0 1.0
O D:ARG344 4.4 26.8 1.0
CA D:ASN346 4.5 28.9 1.0
C D:ASN294 4.5 22.5 1.0
N D:GLY297 4.6 28.0 1.0
CA D:ASP293 4.6 21.8 1.0
CA D:GLY297 4.6 26.4 1.0
CA D:PRO347 4.7 28.2 1.0
N D:TRP295 4.8 24.4 1.0
OD1 D:ASP293 4.8 23.1 1.0
CB D:ASP293 4.8 23.2 1.0
N D:ASP293 4.8 22.5 1.0
CB D:SER298 4.9 25.4 1.0
O D:PRO326 5.0 24.1 1.0

Reference:

J.A.Pulit-Penaloza, N.Simpson, H.Yang, H.M.Creager, J.Jones, P.Carney, J.A.Belser, G.Yang, J.Chang, H.Zeng, S.Thor, Y.Jang, M.L.Killian, M.Jenkins-Moore, A.Janas-Martindale, E.Dubovi, D.E.Wentworth, J.Stevens, T.M.Tumpey, C.T.Davis, T.R.Maines. Assessment of Molecular, Antigenic, and Pathological Features of Canine Influenza A(H3N2) Viruses That Emerged in the United States. J. Infect. Dis. V. 216 S499 2017.
ISSN: ESSN 1537-6613
PubMed: 28934454
DOI: 10.1093/INFDIS/JIW620
Page generated: Tue Jul 16 11:34:37 2024

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