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Calcium in PDB 4cpz: Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir

Enzymatic activity of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir

All present enzymatic activity of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir:
3.2.1.18;

Protein crystallography data

The structure of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir, PDB code: 4cpz was solved by S.G.Vachieri, P.J.Collins, V.Escuret, J.S.Casalegno, N.Cattle, O.Ferraris, M.Sabatier, E.Frobert, V.Caro, J.J.Skehel, S.J.Gamblin, F.Valla, M.Valette, M.Ottmann, J.W.Mccauley, R.S.Daniels, B.Lina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.503 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.344, 163.255, 123.451, 90.00, 108.31, 90.00
R / Rfree (%) 15.33 / 19.97

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir (pdb code 4cpz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir, PDB code: 4cpz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4cpz

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Calcium binding site 1 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1466

b:28.6
occ:1.00
 O A:HOH2213 2.3 19.0 1.0
O A:ASP292 2.4 20.8 1.0
OD2 A:ASP323 2.4 24.4 1.0
O A:GLY345 2.5 22.4 1.0
O A:GLY343 2.5 20.3 1.0
O A:THR296 2.6 30.2 1.0
C A:GLY343 3.6 20.9 1.0
C A:THR296 3.6 26.4 1.0
CG A:ASP323 3.6 30.5 1.0
C A:ASP292 3.6 22.5 1.0
C A:GLY345 3.6 24.4 1.0
O A:HOH2210 3.9 19.7 1.0
CA A:GLY346 4.1 22.7 1.0
CA A:GLY343 4.2 21.4 1.0
CA A:ALA297 4.2 22.6 1.0
CA A:ASN293 4.3 22.9 1.0
N A:ALA297 4.3 28.9 1.0
N A:GLY346 4.3 24.2 1.0
CB A:ASP323 4.4 19.1 1.0
N A:ASN293 4.4 20.0 1.0
OD1 A:ASP323 4.4 25.2 1.0
C A:ASN293 4.5 23.0 1.0
N A:THR296 4.5 22.4 1.0
N A:GLY345 4.5 27.8 1.0
C A:SER344 4.5 31.6 1.0
N A:SER344 4.6 35.5 1.0
CA A:ASP292 4.6 23.9 1.0
O A:LYS342 4.6 28.3 1.0
CA A:THR296 4.6 21.7 1.0
CA A:GLY345 4.7 27.2 1.0
CB A:ASP292 4.7 26.3 1.0
N A:SER294 4.7 19.7 1.0
N A:ASP292 4.8 22.7 1.0
O A:SER344 4.8 24.5 1.0
CA A:SER344 4.9 27.9 1.0
O A:ASN293 4.9 19.6 1.0
O A:PRO325 4.9 23.5 1.0

Calcium binding site 2 out of 8 in 4cpz

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Calcium binding site 2 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1466

b:35.4
occ:1.00
 O B:ASP292 2.3 29.6 1.0
OD2 B:ASP323 2.4 39.0 1.0
O B:GLY345 2.5 33.7 1.0
O B:HOH2191 2.5 34.9 1.0
O B:GLY343 2.6 35.1 1.0
O B:THR296 2.6 28.4 1.0
C B:ASP292 3.5 29.3 1.0
C B:GLY343 3.5 40.5 1.0
C B:THR296 3.6 29.1 1.0
C B:GLY345 3.6 30.1 1.0
CG B:ASP323 3.7 37.7 1.0
O B:HOH2163 4.0 27.3 1.0
CA B:GLY346 4.1 28.2 1.0
CA B:ASN293 4.1 27.2 1.0
CA B:GLY343 4.1 36.2 1.0
N B:ALA297 4.2 30.3 1.0
CA B:ALA297 4.2 32.0 1.0
N B:ASN293 4.3 26.1 1.0
C B:ASN293 4.3 36.1 1.0
N B:GLY346 4.4 25.1 1.0
N B:THR296 4.4 31.4 1.0
OD1 B:ASP323 4.5 31.2 1.0
C B:SER344 4.5 35.9 1.0
N B:GLY345 4.5 31.1 1.0
N B:SER344 4.5 43.6 1.0
CA B:ASP292 4.6 27.0 1.0
CA B:THR296 4.6 26.3 1.0
CB B:ASP323 4.6 31.1 1.0
N B:SER294 4.6 34.9 1.0
O B:ASN293 4.7 39.0 1.0
CB B:ASP292 4.7 27.9 1.0
CA B:GLY345 4.7 28.4 1.0
O B:SER344 4.7 33.2 1.0
N B:ASP292 4.8 25.8 1.0
O B:LYS342 4.8 40.8 1.0
CA B:SER344 4.8 41.0 1.0
O B:PRO325 4.9 30.7 1.0
OD1 B:ASP292 4.9 31.4 1.0

Calcium binding site 3 out of 8 in 4cpz

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Calcium binding site 3 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1466

b:34.5
occ:1.00
 O C:ASP292 2.3 27.0 1.0
O C:GLY345 2.3 34.2 1.0
O C:HOH2175 2.4 21.4 1.0
OD2 C:ASP323 2.4 36.5 1.0
O C:GLY343 2.6 42.6 1.0
O C:THR296 2.6 29.6 1.0
C C:GLY345 3.5 32.6 1.0
C C:ASP292 3.6 28.3 1.0
CG C:ASP323 3.6 35.5 1.0
C C:GLY343 3.6 38.4 1.0
C C:THR296 3.7 33.6 1.0
O C:HOH2171 4.0 21.9 1.0
CA C:GLY346 4.0 27.4 1.0
CA C:GLY343 4.2 34.0 1.0
CA C:ASN293 4.2 28.7 1.0
N C:GLY346 4.2 32.6 1.0
CA C:ALA297 4.3 27.8 1.0
N C:ALA297 4.4 28.6 1.0
C C:ASN293 4.4 35.5 1.0
N C:ASN293 4.4 27.2 1.0
N C:GLY345 4.4 37.1 1.0
OD1 C:ASP323 4.4 33.0 1.0
CB C:ASP323 4.5 28.9 1.0
N C:THR296 4.5 29.7 1.0
C C:SER344 4.6 39.2 1.0
CA C:ASP292 4.6 26.8 1.0
CA C:GLY345 4.6 30.9 1.0
CB C:ASP292 4.6 27.6 1.0
N C:SER294 4.7 32.7 1.0
O C:LYS342 4.7 37.9 1.0
CA C:THR296 4.7 32.2 1.0
N C:SER344 4.7 41.2 1.0
N C:ASP292 4.7 31.8 1.0
O C:ASN293 4.7 40.8 1.0
O C:SER344 4.8 33.6 1.0
O C:PRO325 4.9 29.4 1.0
CA C:SER344 5.0 39.4 1.0

Calcium binding site 4 out of 8 in 4cpz

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Calcium binding site 4 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1466

b:42.4
occ:1.00
 O D:ASP292 2.3 36.9 1.0
O D:HOH2112 2.4 28.7 1.0
OD2 D:ASP323 2.4 39.8 1.0
O D:GLY345 2.5 40.6 1.0
O D:THR296 2.5 44.4 1.0
O D:GLY343 2.5 41.9 1.0
C D:GLY343 3.5 44.2 1.0
C D:ASP292 3.5 36.4 1.0
C D:THR296 3.6 49.1 1.0
CG D:ASP323 3.6 42.3 1.0
C D:GLY345 3.6 36.4 1.0
O D:HOH2110 3.8 37.4 1.0
CA D:GLY343 4.0 48.8 1.0
CA D:GLY346 4.1 39.7 1.0
CA D:ALA297 4.2 39.0 1.0
CA D:ASN293 4.2 45.2 1.0
N D:ALA297 4.3 40.0 1.0
N D:GLY346 4.3 37.4 1.0
N D:ASN293 4.3 38.8 1.0
CB D:ASP323 4.4 39.8 1.0
OD1 D:ASP323 4.4 38.0 1.0
C D:ASN293 4.4 48.9 1.0
N D:THR296 4.5 50.8 1.0
N D:GLY345 4.5 45.7 1.0
CA D:ASP292 4.5 36.2 1.0
C D:SER344 4.6 52.0 1.0
N D:SER344 4.6 46.3 1.0
N D:SER294 4.6 46.7 1.0
CB D:ASP292 4.6 37.9 1.0
CA D:THR296 4.6 50.5 1.0
CA D:GLY345 4.7 37.2 1.0
N D:ASP292 4.7 35.1 1.0
O D:LYS342 4.7 43.7 1.0
O D:PRO325 4.8 37.9 1.0
O D:SER344 4.8 50.2 1.0
CA D:SER344 4.9 50.9 1.0
O D:ASN293 5.0 49.2 1.0

Calcium binding site 5 out of 8 in 4cpz

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Calcium binding site 5 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1466

b:66.4
occ:1.00
 OD2 E:ASP323 2.4 69.3 1.0
O E:ASP292 2.5 51.5 1.0
O E:GLY345 2.6 53.9 1.0
O E:THR296 2.6 62.2 1.0
O E:GLY343 2.7 68.8 1.0
CG E:ASP323 3.5 70.3 1.0
C E:THR296 3.5 67.0 1.0
C E:GLY345 3.6 58.6 1.0
C E:GLY343 3.6 70.2 1.0
C E:ASP292 3.7 50.9 1.0
O E:HOH2074 3.9 48.9 1.0
CA E:ALA297 3.9 65.6 1.0
N E:ALA297 4.1 69.0 1.0
CA E:GLY343 4.1 73.3 1.0
CA E:GLY346 4.1 57.4 1.0
CB E:ASP323 4.3 67.1 1.0
N E:GLY346 4.3 59.2 1.0
O E:LYS342 4.3 75.4 1.0
OD1 E:ASP323 4.3 63.8 1.0
CA E:ASN293 4.4 60.4 1.0
N E:ASN293 4.5 52.6 1.0
O E:PRO325 4.5 65.1 1.0
N E:GLY345 4.6 69.8 1.0
CB E:ALA297 4.6 65.2 1.0
C E:SER344 4.6 70.2 1.0
N E:THR296 4.6 68.8 1.0
CA E:THR296 4.6 69.9 1.0
C E:ASN293 4.7 64.5 1.0
CA E:GLY345 4.7 58.7 1.0
CA E:ASP292 4.7 50.5 1.0
N E:SER344 4.7 68.0 1.0
O E:SER344 4.8 66.4 1.0
CB E:ASP292 4.9 52.0 1.0
N E:ASP292 4.9 60.3 1.0
O E:ASN293 4.9 65.5 1.0

Calcium binding site 6 out of 8 in 4cpz

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Calcium binding site 6 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1466

b:59.1
occ:1.00
 O F:GLY343 2.3 57.8 1.0
O F:ASP292 2.4 57.9 1.0
OD2 F:ASP323 2.5 62.2 1.0
O F:GLY345 2.5 61.3 1.0
O F:THR296 2.6 52.7 1.0
C F:GLY343 3.4 62.2 1.0
C F:ASP292 3.6 54.6 1.0
C F:THR296 3.6 60.4 1.0
CG F:ASP323 3.7 60.3 1.0
C F:GLY345 3.7 57.4 1.0
CA F:GLY343 4.1 66.7 1.0
CA F:ALA297 4.1 57.4 1.0
N F:ALA297 4.2 62.6 1.0
CA F:GLY346 4.3 49.8 1.0
CA F:ASN293 4.3 51.0 1.0
N F:ASN293 4.4 51.3 1.0
CB F:ASP323 4.4 59.1 1.0
C F:ASN293 4.4 56.0 1.0
N F:GLY346 4.5 52.3 1.0
C F:SER344 4.5 60.4 1.0
N F:SER344 4.5 64.0 1.0
N F:GLY345 4.5 61.4 1.0
N F:THR296 4.5 58.9 1.0
OD1 F:ASP323 4.5 55.9 1.0
CA F:ASP292 4.6 52.8 1.0
O F:PRO325 4.6 60.4 1.0
O F:SER344 4.6 59.1 1.0
CB F:ASP292 4.7 51.0 1.0
CA F:THR296 4.7 59.8 1.0
N F:SER294 4.7 51.6 1.0
CA F:GLY345 4.7 59.5 1.0
N F:ASP292 4.8 52.8 1.0
O F:LYS342 4.8 69.4 1.0
CA F:SER344 4.8 63.5 1.0
O F:ASN293 4.8 62.3 1.0
CB F:ALA297 4.9 53.4 1.0

Calcium binding site 7 out of 8 in 4cpz

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Calcium binding site 7 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1466

b:70.9
occ:1.00
 O G:ASP292 2.3 51.6 1.0
O G:HOH2047 2.4 50.1 1.0
OD2 G:ASP323 2.5 51.2 1.0
O G:GLY343 2.6 69.2 1.0
O G:GLY345 2.7 62.6 1.0
O G:THR296 2.7 55.5 1.0
CG G:ASP323 3.5 56.6 1.0
C G:ASP292 3.5 48.9 1.0
C G:GLY343 3.6 71.5 1.0
C G:THR296 3.7 61.5 1.0
C G:GLY345 3.8 59.3 1.0
CA G:ALA297 4.1 61.3 1.0
CB G:ASP323 4.2 54.6 1.0
CA G:GLY346 4.2 53.2 1.0
CA G:GLY343 4.2 72.6 1.0
N G:ALA297 4.3 62.6 1.0
CA G:ASN293 4.3 54.2 1.0
N G:ASN293 4.4 54.9 1.0
OD1 G:ASP323 4.4 50.7 1.0
N G:GLY346 4.4 56.5 1.0
C G:ASN293 4.5 60.4 1.0
CA G:ASP292 4.5 57.3 1.0
C G:SER344 4.5 69.0 1.0
CB G:ASP292 4.6 50.5 1.0
N G:THR296 4.6 68.8 1.0
N G:SER344 4.6 71.1 1.0
O G:SER344 4.6 74.9 1.0
N G:SER294 4.7 64.2 1.0
N G:GLY345 4.7 67.9 1.0
CA G:THR296 4.8 68.6 1.0
O G:LYS342 4.8 80.0 1.0
N G:ASP292 4.8 54.7 1.0
O G:PRO325 4.9 60.2 1.0
CA G:GLY345 4.9 64.3 1.0
CA G:SER344 4.9 67.0 1.0
CB G:ALA297 4.9 64.4 1.0
OD1 G:ASP292 4.9 57.7 1.0
C G:ALA297 5.0 58.6 1.0

Calcium binding site 8 out of 8 in 4cpz

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Calcium binding site 8 out of 8 in the Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Neuraminidase From the B/Lyon/Chu/15.216/2011 Virus in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1466

b:74.8
occ:1.00
 O H:ASP292 2.4 65.8 1.0
O H:GLY345 2.5 60.3 1.0
OD2 H:ASP323 2.5 68.3 1.0
O H:THR296 2.5 59.8 1.0
O H:GLY343 2.9 80.8 1.0
CG H:ASP323 3.4 68.4 1.0
C H:THR296 3.5 65.1 1.0
C H:GLY345 3.6 56.9 1.0
C H:GLY343 3.6 73.5 1.0
C H:ASP292 3.6 63.3 1.0
CA H:GLY343 4.0 70.2 1.0
O H:SER344 4.0 75.7 1.0
CA H:ALA297 4.0 59.9 1.0
OD1 H:ASP323 4.1 70.5 1.0
CA H:GLY346 4.1 55.0 1.0
N H:ALA297 4.2 61.4 1.0
O H:HOH2040 4.2 41.7 1.0
N H:GLY346 4.2 56.0 1.0
C H:SER344 4.3 72.4 1.0
CB H:ASP323 4.3 66.5 1.0
CA H:ASN293 4.4 66.9 1.0
N H:ASN293 4.5 63.7 1.0
N H:SER344 4.5 70.5 1.0
N H:GLY345 4.5 69.5 1.0
O H:PRO325 4.6 63.2 1.0
C H:ASN293 4.6 67.2 1.0
O H:LYS342 4.6 77.2 1.0
N H:THR296 4.6 70.2 1.0
CA H:ASP292 4.6 65.4 1.0
CA H:GLY345 4.6 61.0 1.0
CA H:THR296 4.6 68.1 1.0
CB H:ASP292 4.7 67.5 1.0
N H:SER294 4.7 68.8 1.0
CB H:ALA297 4.8 60.5 1.0
CA H:SER344 4.9 70.3 1.0
N H:ASP292 4.9 66.4 1.0
OD1 H:ASP292 5.0 77.1 1.0

Reference:

V.Escuret, P.J.Collins, J.Casalegno, S.G.Vachieri, N.Cattle, O.Ferraris, M.Sabatier, E.Frobert, V.Caro, J.J.Skehel, S.Gamblin, F.Valla, M.Valette, M.Ottmann, J.W.Mccauley, R.S.Daniels, B.Lina. A Novel I221 L Substitution in Neuraminidase Confers High Level Resistance to Oseltamivir in Influenza B Viruses. J.Infect.Dis. V. 210 1260 2014.
ISSN: ISSN 1537-6613
PubMed: 24795482
DOI: 10.1093/INFDIS/JIU244
Page generated: Sat Jul 13 23:13:08 2024

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