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Calcium in PDB 5nz4: Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir

Protein crystallography data

The structure of Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nz4 was solved by P.Pachl, J.Pokorna, E.Karlukova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.92 / 1.36
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.458, 137.576, 118.610, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir (pdb code 5nz4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nz4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5nz4

Go back to Calcium Binding Sites List in 5nz4
Calcium binding site 1 out of 5 in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:8.9
occ:1.00
 OD2 A:ASP324 2.3 8.0 1.0
O A:ASN344 2.3 8.5 1.0
O A:ASP294 2.3 9.2 1.0
O A:GLY298 2.3 9.0 1.0
O A:GLY342 2.4 10.4 1.0
O A:HOH700 2.4 10.2 1.0
CG A:ASP324 3.5 8.4 1.0
C A:GLY342 3.5 10.0 1.0
C A:GLY298 3.5 9.3 1.0
C A:ASN344 3.5 9.0 1.0
C A:ASP294 3.5 8.4 1.0
CA A:GLY345 4.0 9.2 1.0
O A:HOH793 4.0 10.3 1.0
CA A:GLY342 4.1 11.1 1.0
O A:ALA343 4.1 10.7 1.0
C A:ALA343 4.2 11.1 1.0
N A:GLY345 4.2 9.6 1.0
CB A:ASP324 4.2 8.2 1.0
N A:GLY298 4.2 10.6 1.0
CA A:ASN295 4.3 9.5 1.0
N A:SER299 4.3 8.4 1.0
OD1 A:ASP324 4.3 9.1 1.0
N A:ASN295 4.3 8.7 1.0
CA A:SER299 4.4 9.5 1.0
N A:ASN344 4.4 10.8 1.0
CA A:GLY298 4.4 9.4 1.0
N A:ALA343 4.5 10.6 1.0
CA A:ASP294 4.6 8.2 1.0
CA A:ASN344 4.6 10.5 0.5
CA A:ASN344 4.6 10.5 0.5
O A:ASN341 4.7 12.0 1.0
C A:ASN295 4.7 9.8 1.0
CA A:ALA343 4.7 11.2 1.0
N A:ASP294 4.7 8.0 1.0
OD1 A:ASP294 4.7 9.1 1.0
CB A:ASP294 4.7 9.0 1.0
O A:PRO326 4.9 9.6 1.0

Calcium binding site 2 out of 5 in 5nz4

Go back to Calcium Binding Sites List in 5nz4
Calcium binding site 2 out of 5 in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:15.1
occ:1.00
 OD1 A:ASN378 2.3 17.1 1.0
OD1 A:ASP384 2.3 14.7 1.0
O A:HOH884 2.3 17.7 1.0
OD1 A:ASP376 2.3 12.0 1.0
O A:ASN386 2.4 16.0 1.0
O A:HOH718 2.4 15.4 1.0
OD2 A:ASP376 2.6 14.1 1.0
CG A:ASP376 2.8 11.6 1.0
CG A:ASP384 3.2 15.9 1.0
CG A:ASN378 3.5 15.2 1.0
C A:ASN386 3.5 15.8 1.0
OD2 A:ASP384 3.5 18.1 1.0
O A:ASP384 3.9 13.0 1.0
N A:ASN386 4.0 15.7 1.0
ND2 A:ASN378 4.0 20.1 1.0
CA A:ASN386 4.2 16.5 1.0
O A:HOH890 4.3 34.9 1.0
CB A:ASP376 4.3 10.4 1.0
CB A:ASN386 4.4 17.8 1.0
N A:GLY379 4.4 11.2 1.0
C A:ASP384 4.4 13.8 1.0
C A:ASN378 4.5 12.3 1.0
N A:ASN378 4.5 11.8 1.0
CA A:GLY379 4.5 11.4 1.0
N A:PHE387 4.5 15.1 1.0
CB A:ASP384 4.6 14.1 1.0
CB A:ASN378 4.7 13.1 1.0
O A:HOH918 4.7 19.1 1.0
OG A:SER319 4.7 11.5 1.0
CA A:ASN378 4.8 12.0 1.0
CA A:PHE387 4.8 12.9 1.0
O A:ASN378 4.9 12.8 1.0
CA A:ASP384 4.9 13.5 1.0
CA A:ASP376 4.9 10.3 1.0
N A:ASP384 5.0 12.1 1.0

Calcium binding site 3 out of 5 in 5nz4

Go back to Calcium Binding Sites List in 5nz4
Calcium binding site 3 out of 5 in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:10.1
occ:1.00
 O B:ASP294 2.3 9.2 1.0
OD2 B:ASP324 2.3 9.5 1.0
O B:HOH708 2.3 11.3 1.0
O B:ASN344 2.3 10.2 1.0
O B:GLY342 2.4 11.5 1.0
O B:GLY298 2.4 10.9 1.0
C B:GLY342 3.4 10.8 1.0
CG B:ASP324 3.5 10.4 1.0
C B:GLY298 3.5 11.1 1.0
C B:ASN344 3.5 9.9 1.0
C B:ASP294 3.5 8.2 1.0
CA B:GLY345 4.0 8.8 1.0
O B:HOH812 4.0 10.5 1.0
CA B:GLY342 4.1 13.0 1.0
C B:ALA343 4.1 11.5 1.0
O B:ALA343 4.2 11.8 1.0
CB B:ASP324 4.2 9.5 1.0
N B:GLY345 4.2 9.8 1.0
N B:GLY298 4.3 9.6 1.0
CA B:ASN295 4.3 9.2 1.0
OD1 B:ASP324 4.3 10.1 1.0
N B:SER299 4.3 10.8 1.0
CA B:SER299 4.3 10.7 1.0
N B:ASN295 4.4 8.4 1.0
N B:ASN344 4.4 10.1 1.0
N B:ALA343 4.4 10.2 1.0
CA B:GLY298 4.5 10.3 1.0
CA B:ASP294 4.6 8.3 1.0
CA B:ASN344 4.6 11.1 0.7
CA B:ASN344 4.6 11.0 0.3
C B:ASN295 4.7 9.8 1.0
CA B:ALA343 4.7 11.2 1.0
O B:ASN341 4.7 13.3 1.0
N B:ASP294 4.7 8.3 1.0
CB B:ASP294 4.7 8.9 1.0
OD1 B:ASP294 4.8 10.1 1.0
O B:PRO326 4.8 11.0 1.0

Calcium binding site 4 out of 5 in 5nz4

Go back to Calcium Binding Sites List in 5nz4
Calcium binding site 4 out of 5 in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:15.8
occ:1.00
 OD1 B:ASN378 2.2 16.5 1.0
OD1 B:ASP384 2.3 15.6 1.0
O B:ASN386 2.3 15.4 1.0
O B:HOH805 2.4 19.6 1.0
OD1 B:ASP376 2.4 12.3 1.0
O B:HOH747 2.5 18.2 1.0
OD2 B:ASP376 2.7 13.5 1.0
CG B:ASP376 2.8 11.7 1.0
CG B:ASP384 3.3 14.1 1.0
CG B:ASN378 3.4 15.8 1.0
C B:ASN386 3.4 16.6 1.0
OD2 B:ASP384 3.6 19.2 1.0
O B:ASP384 3.9 14.4 1.0
ND2 B:ASN378 4.0 19.1 1.0
N B:ASN386 4.0 17.3 1.0
CA B:ASN386 4.1 18.8 1.0
O B:HOH967 4.2 35.7 1.0
CB B:ASN386 4.2 20.7 1.0
CB B:ASP376 4.3 10.4 1.0
N B:GLY379 4.4 11.5 1.0
C B:ASP384 4.4 13.7 1.0
C B:ASN378 4.4 12.0 1.0
N B:PHE387 4.5 15.9 1.0
N B:ASN378 4.5 11.5 1.0
CA B:GLY379 4.6 11.4 1.0
CB B:ASP384 4.6 15.2 1.0
CB B:ASN378 4.6 14.1 1.0
CA B:ASN378 4.7 11.6 1.0
O B:HOH951 4.7 20.2 1.0
OG B:SER319 4.8 12.3 1.0
CA B:PHE387 4.8 16.2 1.0
O B:ASN378 4.9 13.1 1.0
CA B:ASP384 4.9 15.1 1.0
CA B:ASP376 4.9 10.9 1.0
C B:ASN385 4.9 17.3 1.0

Calcium binding site 5 out of 5 in 5nz4

Go back to Calcium Binding Sites List in 5nz4
Calcium binding site 5 out of 5 in the Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca510

b:19.3
occ:0.50
 O B:HOH838 2.3 25.3 1.0
OD2 B:ASP113 4.3 12.5 1.0
OD1 B:ASP113 4.5 12.4 1.0
CG B:ASP113 4.8 11.5 1.0

Reference:

J.Pokorna, P.Pachl, E.Karlukova, J.Hejdanek, P.Rezacova, A.Machara, J.Hudlicky, J.Konvalinka, M.Kozisek. Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase From the 2009 Pandemic Influenza Virus. Viruses V. 10 2018.
ISSN: ISSN 1999-4915
PubMed: 29933553
DOI: 10.3390/V10070339
Page generated: Mon Jul 15 09:37:29 2024

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