Atomistry » Calcium » PDB 5npf-5odc » 5nwe
Atomistry »
  Calcium »
    PDB 5npf-5odc »
      5nwe »

Calcium in PDB 5nwe: Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir

Enzymatic activity of Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir

All present enzymatic activity of Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir:
3.2.1.18;

Protein crystallography data

The structure of Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nwe was solved by P.Pachl, J.Pokorna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.19 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.474, 126.608, 96.560, 90.00, 93.49, 90.00
R / Rfree (%) 23.5 / 27.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir (pdb code 5nwe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nwe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 1 out of 8 in the Complex of H275Y 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 H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:18.4
occ:1.00
 OD2 A:ASP324 2.3 17.8 1.0
O A:ASN344 2.3 18.2 1.0
O A:ASP294 2.4 18.9 1.0
O A:HOH658 2.4 20.1 1.0
O A:GLY342 2.4 22.2 1.0
O A:GLY298 2.4 17.9 1.0
C A:GLY342 3.4 23.8 1.0
CG A:ASP324 3.4 18.4 1.0
C A:GLY298 3.5 20.4 1.0
C A:ASN344 3.5 21.6 1.0
C A:ASP294 3.6 18.3 1.0
CA A:GLY345 4.0 18.7 1.0
CA A:GLY342 4.1 24.6 1.0
O A:ALA343 4.2 24.8 1.0
C A:ALA343 4.2 23.2 1.0
CB A:ASP324 4.2 19.3 1.0
N A:GLY345 4.2 20.1 1.0
O A:HOH727 4.2 23.0 1.0
N A:GLY298 4.2 21.0 1.0
CA A:ASN295 4.3 20.2 1.0
N A:SER299 4.3 19.9 1.0
OD1 A:ASP324 4.3 17.3 1.0
N A:ASN295 4.4 18.9 1.0
CA A:SER299 4.4 21.4 1.0
CA A:GLY298 4.4 20.1 1.0
N A:ALA343 4.4 22.0 1.0
N A:ASN344 4.5 23.2 1.0
CA A:ASP294 4.6 19.4 1.0
O A:ASN341 4.6 23.3 1.0
CA A:ALA343 4.6 22.3 1.0
CA A:ASN344 4.7 22.2 1.0
C A:ASN295 4.7 21.2 1.0
CB A:ASP294 4.8 19.6 1.0
O A:PRO326 4.8 20.6 1.0
N A:ASP294 4.8 19.4 1.0
OD1 A:ASP294 5.0 18.7 1.0

Calcium binding site 2 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 2 out of 8 in the Complex of H275Y 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 H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:36.0
occ:1.00
 O A:HOH752 2.2 26.7 1.0
OD1 A:ASN378 2.3 30.6 1.0
OD1 A:ASP384 2.3 26.9 1.0
OD1 A:ASP376 2.3 24.3 1.0
O A:HOH718 2.4 27.9 1.0
O A:ASN386 2.5 29.9 1.0
OD2 A:ASP376 3.0 23.1 1.0
CG A:ASP376 3.0 23.6 1.0
CG A:ASP384 3.2 28.1 1.0
CG A:ASN378 3.4 29.9 1.0
OD2 A:ASP384 3.5 27.3 1.0
C A:ASN386 3.6 30.6 1.0
O A:ASP384 3.8 27.8 1.0
N A:ASN386 3.9 31.1 1.0
ND2 A:ASN378 4.0 32.4 1.0
CA A:ASN386 4.1 30.3 1.0
CB A:ASN386 4.2 33.9 1.0
C A:ASP384 4.3 29.9 1.0
CB A:ASP376 4.4 23.3 1.0
N A:GLY379 4.5 25.6 1.0
CB A:ASP384 4.5 28.7 1.0
O A:HOH846 4.5 37.5 1.0
N A:ASN378 4.5 25.9 1.0
C A:ASN378 4.6 26.6 1.0
N A:PHE387 4.7 29.4 1.0
CB A:ASN378 4.7 28.6 1.0
CA A:GLY379 4.7 25.2 1.0
CA A:ASN378 4.8 27.7 1.0
CA A:ASP384 4.8 28.6 1.0
OG A:SER319 4.8 21.1 1.0
C A:ASN385 4.9 31.6 1.0
N A:ASN385 5.0 29.7 1.0
CA A:PHE387 5.0 29.2 1.0
O A:ASN378 5.0 25.3 1.0
CA A:ASP376 5.0 23.7 1.0
N A:ASP384 5.0 27.9 1.0

Calcium binding site 3 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 3 out of 8 in the Complex of H275Y 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 H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:23.2
occ:1.00
 O B:ASN344 2.2 23.6 1.0
O B:GLY342 2.2 26.1 1.0
O B:ASP294 2.3 24.2 1.0
OD2 B:ASP324 2.4 17.1 1.0
O B:GLY298 2.4 24.6 1.0
O B:HOH603 2.6 22.2 1.0
C B:GLY342 3.4 27.9 1.0
C B:ASN344 3.4 23.2 1.0
CG B:ASP324 3.5 22.6 1.0
C B:GLY298 3.5 24.1 1.0
C B:ASP294 3.5 23.2 1.0
CA B:GLY345 3.9 18.8 1.0
O B:HOH643 4.0 30.0 1.0
O B:ALA343 4.0 25.9 1.0
C B:ALA343 4.1 25.6 1.0
CA B:GLY342 4.1 28.1 1.0
N B:GLY345 4.1 21.5 1.0
N B:GLY298 4.2 25.8 1.0
CB B:ASP324 4.2 23.7 1.0
CA B:ASN295 4.2 22.8 1.0
N B:ASN344 4.3 24.6 1.0
N B:ASN295 4.3 22.7 1.0
N B:SER299 4.4 23.6 1.0
N B:ALA343 4.4 26.9 1.0
CA B:GLY298 4.4 25.0 1.0
OD1 B:ASP324 4.4 24.1 1.0
CA B:SER299 4.4 25.7 1.0
CA B:ASN344 4.5 26.4 1.0
O B:ASN341 4.5 31.3 1.0
C B:ASN295 4.6 23.1 1.0
CA B:ALA343 4.6 26.7 1.0
CA B:ASP294 4.6 22.4 1.0
O B:PRO326 4.7 27.0 1.0
CB B:ASP294 4.8 23.2 1.0
O B:ASN295 4.9 21.4 1.0
N B:ASP294 5.0 22.1 1.0
OD1 B:ASP294 5.0 21.6 1.0

Calcium binding site 4 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 4 out of 8 in the Complex of H275Y 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 H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:42.0
occ:1.00
 O B:HOH644 2.3 32.6 1.0
OD1 B:ASP384 2.3 45.9 1.0
OD1 B:ASN378 2.3 31.0 1.0
O B:ASN386 2.4 40.4 1.0
O B:HOH639 2.4 35.3 1.0
OD1 B:ASP376 2.5 31.6 1.0
OD2 B:ASP376 2.9 25.7 1.0
CG B:ASP376 3.0 29.4 1.0
CG B:ASP384 3.1 42.2 1.0
OD2 B:ASP384 3.3 44.3 1.0
CG B:ASN378 3.3 35.0 1.0
C B:ASN386 3.5 40.8 1.0
ND2 B:ASN378 3.8 36.4 1.0
O B:ASP384 3.8 38.1 1.0
N B:ASN386 3.9 41.8 1.0
CA B:ASN386 4.1 42.5 1.0
C B:ASP384 4.3 40.1 1.0
CB B:ASN386 4.3 46.2 1.0
CB B:ASP376 4.5 30.1 1.0
CB B:ASP384 4.5 41.3 1.0
C B:ASN378 4.5 32.4 1.0
N B:GLY379 4.6 29.0 1.0
N B:ASN378 4.6 32.8 1.0
N B:PHE387 4.6 37.6 1.0
CB B:ASN378 4.6 34.8 1.0
CA B:GLY379 4.8 28.1 1.0
O B:ASN378 4.8 30.0 1.0
CA B:ASN378 4.8 33.4 1.0
CA B:ASP384 4.9 37.9 1.0
C B:ASN385 4.9 42.0 1.0
O B:HOH790 4.9 37.2 1.0
N B:ASN385 5.0 41.6 1.0
CA B:PHE387 5.0 36.5 1.0

Calcium binding site 5 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 5 out of 8 in the Complex of H275Y 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 H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:17.0
occ:1.00
 OD2 C:ASP324 2.3 15.8 1.0
O C:ASN344 2.3 17.2 1.0
O C:ASP294 2.3 17.2 1.0
O C:GLY298 2.4 15.7 1.0
O C:GLY342 2.4 21.8 1.0
O C:HOH620 2.5 19.3 1.0
CG C:ASP324 3.4 16.8 1.0
C C:GLY298 3.5 17.0 1.0
C C:GLY342 3.5 22.9 1.0
C C:ASN344 3.5 20.9 1.0
C C:ASP294 3.5 17.1 1.0
CA C:GLY345 4.0 18.2 1.0
O C:HOH733 4.1 27.0 1.0
O C:ALA343 4.2 20.4 1.0
C C:ALA343 4.2 22.5 1.0
CA C:GLY342 4.2 23.9 1.0
N C:GLY298 4.2 19.1 1.0
CB C:ASP324 4.2 17.6 1.0
N C:GLY345 4.2 20.2 1.0
N C:SER299 4.3 15.8 1.0
CA C:ASN295 4.3 18.8 1.0
OD1 C:ASP324 4.3 16.2 1.0
N C:ASN295 4.3 17.4 1.0
CA C:SER299 4.4 17.8 1.0
CA C:GLY298 4.4 17.4 1.0
N C:ASN344 4.4 22.8 1.0
N C:ALA343 4.5 21.8 1.0
CA C:ASP294 4.6 17.8 1.0
CA C:ASN344 4.6 23.1 1.0
CA C:ALA343 4.7 22.3 1.0
O C:ASN341 4.7 22.7 1.0
CB C:ASP294 4.7 18.5 1.0
C C:ASN295 4.7 19.2 1.0
O C:PRO326 4.8 18.7 1.0
N C:ASP294 4.8 18.8 1.0
OD1 C:ASP294 5.0 17.8 1.0

Calcium binding site 6 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 6 out of 8 in the Complex of H275Y 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 6 of Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:31.1
occ:1.00
 O C:HOH672 2.1 24.3 1.0
OD1 C:ASN378 2.3 35.5 1.0
OD1 C:ASP384 2.3 25.3 1.0
OD1 C:ASP376 2.3 24.8 1.0
O C:ASN386 2.3 27.7 1.0
O C:HOH758 2.4 28.7 1.0
OD2 C:ASP376 2.9 22.5 1.0
CG C:ASP376 3.0 23.4 1.0
CG C:ASP384 3.2 28.3 1.0
OD2 C:ASP384 3.4 28.2 1.0
CG C:ASN378 3.4 32.6 1.0
C C:ASN386 3.5 28.5 1.0
O C:ASP384 3.9 25.8 1.0
ND2 C:ASN378 4.0 34.5 1.0
N C:ASN386 4.0 29.4 1.0
CA C:ASN386 4.1 29.5 1.0
CB C:ASN386 4.2 33.8 1.0
C C:ASP384 4.4 28.6 1.0
CB C:ASP376 4.4 22.8 1.0
N C:GLY379 4.4 23.4 1.0
N C:ASN378 4.5 25.9 1.0
C C:ASN378 4.5 26.1 1.0
CB C:ASP384 4.5 28.0 1.0
N C:PHE387 4.5 27.0 1.0
CB C:ASN378 4.7 30.2 1.0
CA C:GLY379 4.7 22.6 1.0
CA C:ASN378 4.8 26.8 1.0
O C:HOH711 4.8 27.3 1.0
CA C:PHE387 4.8 26.9 1.0
CA C:ASP384 4.9 27.8 1.0
C C:ASN385 4.9 31.6 1.0
O C:ASN378 5.0 25.8 1.0
CA C:ASP376 5.0 22.3 1.0
N C:ASN385 5.0 29.9 1.0
OG C:SER319 5.0 21.9 1.0

Calcium binding site 7 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 7 out of 8 in the Complex of H275Y 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 7 of Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:23.2
occ:1.00
 O D:ASN344 2.2 25.1 1.0
O D:ASP294 2.3 24.6 1.0
O D:GLY342 2.3 27.7 1.0
O D:GLY298 2.4 28.4 1.0
OD2 D:ASP324 2.4 16.2 1.0
O D:HOH607 2.6 20.2 1.0
C D:GLY342 3.4 28.3 1.0
C D:ASN344 3.4 23.7 1.0
C D:GLY298 3.5 27.3 1.0
CG D:ASP324 3.5 20.6 1.0
C D:ASP294 3.5 23.1 1.0
CA D:GLY345 4.0 18.6 1.0
O D:HOH653 4.0 30.7 1.0
CA D:GLY342 4.1 29.0 1.0
N D:GLY298 4.1 28.0 1.0
N D:GLY345 4.1 21.3 1.0
C D:ALA343 4.2 25.7 1.0
CB D:ASP324 4.2 22.2 1.0
O D:ALA343 4.2 25.6 1.0
CA D:ASN295 4.2 22.0 1.0
N D:ASN295 4.3 22.5 1.0
N D:SER299 4.3 26.2 1.0
N D:ASN344 4.3 24.6 1.0
CA D:GLY298 4.4 28.0 1.0
CA D:SER299 4.4 27.4 1.0
N D:ALA343 4.4 27.5 1.0
OD1 D:ASP324 4.4 20.5 1.0
CA D:ASN344 4.5 27.2 1.0
CA D:ASP294 4.6 23.3 1.0
O D:ASN341 4.6 29.1 1.0
C D:ASN295 4.6 23.0 1.0
CA D:ALA343 4.6 26.6 1.0
CB D:ASP294 4.7 24.8 1.0
O D:PRO326 4.8 26.4 1.0
O D:ASN295 4.9 20.0 1.0
N D:ASP294 4.9 23.1 1.0
OD1 D:ASP294 4.9 22.6 1.0

Calcium binding site 8 out of 8 in 5nwe

Go back to Calcium Binding Sites List in 5nwe
Calcium binding site 8 out of 8 in the Complex of H275Y 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 8 of Complex of H275Y Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:37.2
occ:1.00
 OD1 D:ASN378 2.2 31.5 1.0
O D:HOH631 2.2 30.0 1.0
O D:HOH672 2.3 30.4 1.0
OD1 D:ASP384 2.3 43.9 1.0
OD1 D:ASP376 2.4 29.0 1.0
O D:ASN386 2.4 41.2 1.0
OD2 D:ASP376 3.0 23.2 1.0
CG D:ASP376 3.0 26.4 1.0
CG D:ASP384 3.2 41.4 1.0
CG D:ASN378 3.2 32.0 1.0
OD2 D:ASP384 3.3 40.6 1.0
C D:ASN386 3.5 41.3 1.0
ND2 D:ASN378 3.7 34.6 1.0
O D:ASP384 3.9 38.4 1.0
N D:ASN386 4.0 43.1 1.0
CA D:ASN386 4.1 44.4 1.0
CB D:ASN386 4.3 47.8 1.0
N D:GLY379 4.4 27.7 1.0
C D:ASP384 4.5 41.0 1.0
C D:ASN378 4.5 29.9 1.0
N D:ASN378 4.5 27.9 1.0
CB D:ASP376 4.5 26.6 1.0
CB D:ASN378 4.5 31.4 1.0
CB D:ASP384 4.6 39.8 1.0
N D:PHE387 4.6 39.2 1.0
CA D:GLY379 4.7 26.4 1.0
CA D:ASN378 4.7 30.4 1.0
O D:ASN378 4.8 27.6 1.0
CA D:PHE387 4.9 37.3 1.0
CA D:ASP384 5.0 38.6 1.0
C D:ASN385 5.0 42.1 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: Wed Jul 9 09:09:30 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy