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Calcium in PDB 5hum: The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 Influenza Virus

Protein crystallography data

The structure of The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 Influenza Virus, PDB code: 5hum was solved by H.Yang, P.J.Carney, Z.Guo, J.C.Chang, J.Stevens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.80 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.335, 76.277, 117.211, 90.00, 90.02, 90.00
R / Rfree (%) 19.8 / 22

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 Influenza Virus (pdb code 5hum). 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 Neuraminidase From A/Sichuan/26221/2014 Influenza Virus, PDB code: 5hum:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5hum

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Calcium binding site 1 out of 4 in the The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 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 Neuraminidase From A/Sichuan/26221/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:20.5
occ:1.00
O A:HOH866 2.2 30.8 1.0
O A:PRO269 2.2 17.8 1.0
O A:ASP215 2.3 19.4 1.0
OD2 A:ASP246 2.3 19.0 1.0
O A:GLY219 2.3 22.0 1.0
O A:HOH917 2.4 20.8 1.0
CG A:ASP246 3.4 20.7 1.0
C A:PRO269 3.4 20.1 1.0
C A:GLY219 3.5 22.5 1.0
C A:ASP215 3.5 17.9 1.0
O A:HOH767 4.0 18.8 1.0
CA A:GLY270 4.1 15.5 1.0
O A:HOH663 4.1 34.8 1.0
CB A:ASP246 4.1 17.6 1.0
CA A:ASN216 4.2 15.0 1.0
N A:GLY270 4.2 17.8 1.0
N A:ALA220 4.3 20.1 1.0
OD1 A:ASP246 4.3 19.4 1.0
N A:ASN216 4.3 16.5 1.0
CA A:ALA220 4.4 24.6 1.0
N A:GLY219 4.4 19.3 1.0
CA A:PRO269 4.5 21.5 1.0
CA A:GLY219 4.5 18.6 1.0
CA A:ASP215 4.5 15.4 1.0
C A:ASN216 4.6 19.8 1.0
N A:ASP215 4.7 14.4 1.0
CB A:ASP215 4.7 15.9 1.0
O A:HOH987 4.8 49.0 1.0
C A:LYS218 4.8 25.8 1.0
O A:LYS218 4.8 23.2 1.0
O A:HOH857 5.0 28.2 1.0
OD2 A:ASP215 5.0 18.0 1.0
O A:SER248 5.0 21.9 1.0

Calcium binding site 2 out of 4 in 5hum

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Calcium binding site 2 out of 4 in the The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 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 Neuraminidase From A/Sichuan/26221/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:23.8
occ:1.00
O B:PRO269 2.3 20.8 1.0
O B:HOH767 2.3 24.5 1.0
O B:ASP215 2.3 22.1 1.0
O B:GLY219 2.4 19.2 1.0
O B:HOH803 2.4 20.6 1.0
OD2 B:ASP246 2.4 21.0 1.0
CG B:ASP246 3.4 18.3 1.0
C B:PRO269 3.4 19.4 1.0
C B:GLY219 3.5 21.0 1.0
C B:ASP215 3.6 16.3 1.0
O B:HOH612 4.1 39.3 1.0
CA B:GLY270 4.1 16.9 1.0
O B:HOH763 4.1 27.5 1.0
CB B:ASP246 4.2 20.2 1.0
CA B:ASN216 4.3 13.7 1.0
OD1 B:ASP246 4.3 18.9 1.0
N B:GLY270 4.3 20.0 1.0
N B:ALA220 4.3 22.0 1.0
N B:ASN216 4.4 18.9 1.0
CA B:ALA220 4.4 22.5 1.0
CA B:PRO269 4.4 24.3 1.0
N B:GLY219 4.5 17.9 1.0
CA B:GLY219 4.5 17.9 1.0
CA B:ASP215 4.6 20.3 1.0
C B:ASN216 4.7 18.7 1.0
N B:ASP215 4.7 16.2 1.0
O B:HOH995 4.8 37.4 1.0
CB B:ASP215 4.8 17.3 1.0
C B:LYS218 4.8 28.8 1.0
O B:LYS218 4.9 28.0 1.0
O B:SER248 4.9 22.5 1.0
OD2 B:ASP215 5.0 21.7 1.0
CB B:PRO269 5.0 21.8 1.0

Calcium binding site 3 out of 4 in 5hum

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Calcium binding site 3 out of 4 in the The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 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 Neuraminidase From A/Sichuan/26221/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:27.2
occ:1.00
O C:GLY219 2.3 30.6 1.0
OD2 C:ASP246 2.3 20.5 1.0
O C:ASP215 2.3 22.9 1.0
O C:PRO269 2.4 22.5 1.0
O C:HOH680 2.5 23.9 1.0
O C:HOH861 2.5 37.5 1.0
C C:GLY219 3.4 34.4 1.0
CG C:ASP246 3.4 21.7 1.0
C C:ASP215 3.5 24.6 1.0
C C:PRO269 3.6 24.9 1.0
O C:HOH826 3.9 25.9 1.0
CA C:GLY270 4.1 23.9 1.0
N C:ALA220 4.2 23.9 1.0
CB C:ASP246 4.2 24.6 1.0
O C:HOH632 4.2 36.0 1.0
CA C:ASN216 4.3 27.1 1.0
OD1 C:ASP246 4.3 20.4 1.0
CA C:ALA220 4.3 22.7 1.0
N C:ASN216 4.4 22.6 1.0
N C:GLY270 4.4 27.4 1.0
N C:GLY219 4.4 28.7 1.0
CA C:GLY219 4.4 29.1 1.0
CA C:ASP215 4.5 19.4 1.0
CA C:PRO269 4.6 25.3 1.0
N C:ASP215 4.6 24.4 1.0
CB C:ASP215 4.7 20.8 1.0
C C:ASN216 4.7 25.8 1.0
O C:HOH928 4.7 44.0 1.0
C C:LYS218 4.8 29.9 1.0
OD2 C:ASP215 4.9 26.7 1.0
O C:LYS218 4.9 29.6 1.0

Calcium binding site 4 out of 4 in 5hum

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Calcium binding site 4 out of 4 in the The Crystal Structure of Neuraminidase From A/Sichuan/26221/2014 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 Neuraminidase From A/Sichuan/26221/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:22.7
occ:1.00
O D:GLY219 2.2 22.8 1.0
OD2 D:ASP246 2.3 21.2 1.0
O D:ASP215 2.3 23.1 1.0
O D:PRO269 2.4 25.9 1.0
O D:HOH902 2.4 36.3 1.0
O D:HOH642 2.5 23.4 1.0
C D:GLY219 3.4 28.9 1.0
CG D:ASP246 3.4 21.6 1.0
C D:PRO269 3.5 20.5 1.0
C D:ASP215 3.5 19.6 1.0
O D:HOH788 4.0 18.6 1.0
O D:HOH658 4.1 37.0 1.0
CA D:GLY270 4.1 22.5 1.0
CB D:ASP246 4.2 20.8 1.0
N D:ALA220 4.2 24.2 1.0
OD1 D:ASP246 4.3 21.5 1.0
CA D:ASN216 4.3 21.6 1.0
N D:GLY270 4.3 23.5 1.0
CA D:ALA220 4.3 22.3 1.0
N D:GLY219 4.4 25.0 1.0
N D:ASN216 4.4 19.3 1.0
CA D:GLY219 4.4 26.7 1.0
CA D:ASP215 4.5 20.3 1.0
CA D:PRO269 4.5 21.3 1.0
O D:HOH971 4.6 40.9 1.0
N D:ASP215 4.6 19.4 1.0
C D:ASN216 4.7 23.0 1.0
CB D:ASP215 4.7 22.0 1.0
C D:LYS218 4.8 30.5 1.0
O D:LYS218 4.9 31.1 1.0
OD2 D:ASP215 4.9 22.0 1.0
O D:HOH904 4.9 41.2 1.0
O D:SER248 4.9 23.9 1.0

Reference:

H.Yang, P.J.Carney, V.P.Mishin, Z.Guo, J.C.Chang, D.E.Wentworth, L.V.Gubareva, J.Stevens. Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase From Recent H5NX Avian Influenza Viruses. J.Virol. V. 90 5770 2016.
ISSN: ESSN 1098-5514
PubMed: 27053557
DOI: 10.1128/JVI.00180-16
Page generated: Sat Dec 12 05:29:21 2020

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