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Calcium in PDB 5huk: The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 Influenza Virus

Enzymatic activity of The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 Influenza Virus

All present enzymatic activity of The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 Influenza Virus:
3.2.1.18;

Protein crystallography data

The structure of The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 Influenza Virus, PDB code: 5huk 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) 50.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.225, 122.789, 176.846, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 Influenza Virus (pdb code 5huk). 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/Northern Pintail/Washington/40964/2014 Influenza Virus, PDB code: 5huk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5huk

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Calcium binding site 1 out of 4 in the The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 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/Northern Pintail/Washington/40964/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:82.1
occ:1.00
 O A:GLY345 2.3 62.9 1.0
O A:ASP293 2.4 49.9 1.0
O A:HOH645 2.4 54.6 1.0
O A:GLY297 2.5 51.2 1.0
OD2 A:ASP324 2.6 49.0 1.0
C A:GLY345 3.2 59.6 1.0
CG A:ASP324 3.4 53.5 1.0
C A:GLY297 3.5 55.1 1.0
C A:ASP293 3.6 44.9 1.0
CA A:GLY348 3.7 37.9 1.0
CA A:GLY345 3.7 54.6 1.0
N A:GLY348 3.9 41.1 1.0
CA A:SER298 4.0 45.6 1.0
CB A:ASP324 4.0 49.8 1.0
O A:HOH625 4.0 38.8 1.0
N A:SER298 4.1 46.6 1.0
N A:ASN346 4.2 59.4 1.0
OD1 A:ASP324 4.3 46.6 1.0
O A:ARG344 4.4 54.4 1.0
N A:ASN294 4.5 46.7 1.0
C A:PRO347 4.5 50.4 1.0
CA A:ASN346 4.6 58.1 1.0
CA A:ASP293 4.6 44.7 1.0
N A:GLY297 4.6 55.7 1.0
CA A:GLY297 4.7 58.7 1.0
CB A:ASP293 4.7 48.4 1.0
CA A:ASN294 4.7 51.5 1.0
C A:ASN294 4.8 54.4 1.0
O A:PRO347 4.8 58.4 1.0
N A:ASP293 4.8 48.2 1.0
CB A:SER298 4.8 45.1 1.0
N A:TRP295 4.8 51.7 1.0
N A:GLY345 4.8 55.0 1.0

Calcium binding site 2 out of 4 in 5huk

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Calcium binding site 2 out of 4 in the The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 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/Northern Pintail/Washington/40964/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:78.9
occ:1.00
 O B:ASP293 2.3 52.3 1.0
O B:GLY345 2.4 57.9 1.0
OD2 B:ASP324 2.5 45.2 1.0
O B:GLY297 2.6 47.6 1.0
C B:GLY345 3.3 55.0 1.0
CG B:ASP324 3.4 45.4 1.0
C B:ASP293 3.5 46.4 1.0
CA B:GLY348 3.6 39.6 1.0
C B:GLY297 3.6 43.8 1.0
CA B:GLY345 3.9 51.5 1.0
N B:GLY348 3.9 42.8 1.0
O B:HOH608 3.9 52.8 1.0
CB B:ASP324 4.0 45.5 1.0
CA B:SER298 4.1 41.7 1.0
OD1 B:ASP324 4.2 47.4 1.0
N B:SER298 4.2 42.9 1.0
N B:ASN346 4.3 57.8 1.0
N B:ASN294 4.4 46.6 1.0
C B:PRO347 4.4 48.0 1.0
CA B:ASP293 4.5 46.9 1.0
O B:ARG344 4.5 53.4 1.0
CA B:ASN294 4.6 55.3 1.0
CB B:ASP293 4.6 49.5 1.0
N B:ASP293 4.7 41.1 1.0
C B:ASN294 4.7 55.3 1.0
O B:PRO347 4.7 52.9 1.0
N B:GLY297 4.8 45.8 1.0
CA B:ASN346 4.8 56.3 1.0
CA B:GLY297 4.8 47.1 1.0
N B:TRP295 4.8 49.8 1.0
CB B:SER298 4.9 46.2 1.0
OD1 B:ASP293 5.0 42.0 1.0

Calcium binding site 3 out of 4 in 5huk

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Calcium binding site 3 out of 4 in the The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 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/Northern Pintail/Washington/40964/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:84.4
occ:1.00
 O C:ASP293 2.3 51.9 1.0
O C:GLY297 2.4 42.6 1.0
O C:GLY345 2.4 43.1 1.0
OD2 C:ASP324 2.6 43.1 1.0
C C:GLY345 3.3 44.8 1.0
C C:GLY297 3.4 40.9 1.0
CG C:ASP324 3.4 46.4 1.0
C C:ASP293 3.5 41.0 1.0
CA C:GLY348 3.7 40.0 1.0
CA C:GLY345 3.8 43.3 1.0
O C:HOH610 3.8 35.4 1.0
CA C:SER298 4.0 40.1 1.0
CB C:ASP324 4.0 41.8 1.0
N C:GLY348 4.0 39.8 1.0
N C:SER298 4.0 38.1 1.0
OD1 C:ASP324 4.3 50.6 1.0
N C:ASN294 4.4 43.5 1.0
N C:ASN346 4.4 45.6 1.0
O C:ARG344 4.4 51.0 1.0
CA C:ASP293 4.5 43.0 1.0
CB C:ASP293 4.5 46.9 1.0
N C:GLY297 4.5 49.1 1.0
CA C:GLY297 4.5 45.5 1.0
C C:PRO347 4.5 46.6 1.0
N C:ASP293 4.7 42.9 1.0
C C:ASN294 4.8 50.2 1.0
N C:TRP295 4.8 43.0 1.0
CA C:ASN294 4.8 44.0 1.0
CA C:ASN346 4.8 43.7 1.0
O C:PRO347 4.8 41.9 1.0
CB C:SER298 4.9 42.9 1.0
OD1 C:ASP293 4.9 46.8 1.0
N C:GLY345 4.9 41.0 1.0
C C:SER298 5.0 41.7 1.0

Calcium binding site 4 out of 4 in 5huk

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Calcium binding site 4 out of 4 in the The Crystal Structure of Neuraminidase From A/Northern Pintail/Washington/40964/2014 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/Northern Pintail/Washington/40964/2014 Influenza Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:63.8
occ:1.00
 O D:ASP293 2.2 44.0 1.0
O D:GLY297 2.4 42.4 1.0
OD2 D:ASP324 2.5 42.7 1.0
O D:GLY345 2.5 44.1 1.0
O D:HOH620 2.6 45.9 1.0
C D:ASP293 3.4 39.5 1.0
CG D:ASP324 3.4 48.2 1.0
C D:GLY345 3.4 48.9 1.0
C D:GLY297 3.5 42.3 1.0
O D:HOH607 3.7 43.7 1.0
CA D:GLY348 3.7 43.1 1.0
CA D:GLY345 3.8 50.2 1.0
CB D:ASP324 4.0 43.1 1.0
CA D:SER298 4.0 38.6 1.0
N D:GLY348 4.1 44.4 1.0
N D:SER298 4.1 38.6 1.0
OD1 D:ASP324 4.2 49.6 1.0
CA D:ASP293 4.3 36.9 1.0
N D:ASN294 4.3 42.6 1.0
CB D:ASP293 4.3 38.2 1.0
N D:ASN346 4.5 47.5 1.0
N D:ASP293 4.5 42.1 1.0
N D:GLY297 4.5 47.6 1.0
CA D:GLY297 4.6 45.0 1.0
O D:ARG344 4.6 50.9 1.0
C D:PRO347 4.6 45.9 1.0
CA D:ASN294 4.7 52.4 1.0
C D:ASN294 4.8 44.9 1.0
N D:TRP295 4.8 41.0 1.0
OD1 D:ASP293 4.8 44.5 1.0
CA D:ASN346 4.8 46.4 1.0
O D:PRO347 4.9 40.4 1.0
CB D:SER298 4.9 42.1 1.0
C D:SER298 5.0 41.7 1.0
CG D:ASP293 5.0 43.5 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: Sun Jul 14 20:13:53 2024

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