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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Jul 15 09:35:03 2024

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