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Calcium in PDB 5nzn: Complex of H275Y/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir

Protein crystallography data

The structure of Complex of H275Y/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nzn 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) 48.31 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.778, 127.538, 96.773, 90.00, 93.24, 90.00
R / Rfree (%) 22.9 / 26.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of H275Y/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir (pdb code 5nzn). 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nzn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5nzn

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Calcium binding site 1 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:14.5
occ:1.00
 OD2 A:ASP324 2.3 11.4 1.0
O A:GLY298 2.3 14.4 1.0
O A:HOH714 2.4 14.3 1.0
O A:ASN344 2.4 14.2 0.5
O A:GLY342 2.4 15.6 1.0
O A:ASP294 2.4 11.1 1.0
O A:ASN344 2.4 14.2 0.5
CG A:ASP324 3.4 12.1 1.0
C A:GLY298 3.4 13.8 1.0
C A:GLY342 3.4 16.4 1.0
C A:ASN344 3.6 15.0 0.5
C A:ASP294 3.6 11.0 1.0
C A:ASN344 3.6 14.8 0.5
CA A:GLY345 4.0 13.1 1.0
O A:HOH777 4.0 13.8 1.0
O A:ALA343 4.1 16.4 1.0
C A:ALA343 4.1 16.3 1.0
CB A:ASP324 4.2 12.2 1.0
CA A:GLY342 4.2 16.1 1.0
N A:GLY298 4.2 15.2 1.0
N A:SER299 4.3 12.8 1.0
N A:GLY345 4.3 14.4 1.0
CA A:SER299 4.3 14.2 1.0
CA A:ASN295 4.3 12.9 1.0
OD1 A:ASP324 4.3 11.5 1.0
N A:ASN295 4.4 11.3 1.0
CA A:GLY298 4.4 13.6 1.0
N A:ASN344 4.4 16.4 0.5
N A:ALA343 4.4 14.5 1.0
N A:ASN344 4.5 16.2 0.5
CA A:ASP294 4.6 11.8 1.0
CA A:ALA343 4.6 15.7 1.0
CA A:ASN344 4.7 16.3 0.5
O A:ASN341 4.7 16.9 1.0
C A:ASN295 4.7 14.3 1.0
CA A:ASN344 4.7 15.9 0.5
CB A:ASP294 4.7 12.7 1.0
N A:ASP294 4.8 11.7 1.0
O A:PRO326 4.8 15.5 1.0
OD1 A:ASP294 5.0 13.2 1.0

Calcium binding site 2 out of 8 in 5nzn

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Calcium binding site 2 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:20.1
occ:1.00
 O A:HOH709 2.0 29.5 1.0
OD1 A:ASN378 2.2 19.4 1.0
OD1 A:ASP376 2.3 16.9 1.0
OD1 A:ASP384 2.3 21.0 1.0
O A:HOH681 2.4 29.4 1.0
O A:ASN386 2.4 19.9 1.0
OD2 A:ASP376 2.9 16.8 1.0
CG A:ASP376 2.9 16.8 1.0
CG A:ASP384 3.2 21.4 1.0
CG A:ASN378 3.4 20.2 1.0
OD2 A:ASP384 3.4 21.3 1.0
C A:ASN386 3.5 21.4 1.0
ND2 A:ASN378 3.9 21.5 1.0
O A:ASP384 4.0 18.8 1.0
N A:ASN386 4.0 21.6 1.0
CA A:ASN386 4.2 22.6 1.0
CB A:ASN386 4.2 26.8 1.0
CB A:ASP376 4.4 16.6 1.0
N A:ASN378 4.4 16.5 1.0
C A:ASN378 4.5 16.7 1.0
C A:ASP384 4.5 21.1 1.0
N A:GLY379 4.5 16.6 1.0
CB A:ASN378 4.6 18.5 1.0
CB A:ASP384 4.6 21.5 1.0
N A:PHE387 4.6 20.1 1.0
O A:HOH831 4.6 26.6 1.0
CA A:ASN378 4.7 16.7 1.0
CA A:GLY379 4.8 14.6 1.0
CA A:PHE387 4.8 20.2 1.0
O A:ASN378 4.8 18.6 1.0
CA A:ASP376 4.9 16.8 1.0
C A:ASP376 5.0 16.5 1.0
CA A:ASP384 5.0 19.8 1.0
CD A:PRO377 5.0 19.1 1.0

Calcium binding site 3 out of 8 in 5nzn

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Calcium binding site 3 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:20.8
occ:1.00
 O B:ASN344 2.2 18.5 0.5
O B:ASN344 2.2 18.7 0.5
O B:ASP294 2.3 18.2 1.0
O B:GLY298 2.3 20.0 1.0
OD2 B:ASP324 2.4 16.5 1.0
O B:GLY342 2.4 21.9 1.0
O B:HOH635 2.5 18.4 1.0
C B:ASN344 3.4 17.9 0.5
C B:GLY342 3.5 20.0 1.0
CG B:ASP324 3.5 19.6 1.0
C B:ASN344 3.5 18.0 0.5
C B:GLY298 3.5 20.9 1.0
C B:ASP294 3.5 17.4 1.0
CA B:GLY345 4.0 15.2 1.0
O B:HOH731 4.1 18.9 1.0
O B:ALA343 4.1 21.6 1.0
C B:ALA343 4.1 20.3 1.0
CA B:GLY342 4.1 20.6 1.0
N B:GLY298 4.2 21.4 1.0
N B:GLY345 4.2 16.1 1.0
CB B:ASP324 4.2 18.6 1.0
CA B:ASN295 4.2 17.2 1.0
N B:ASN295 4.3 17.2 1.0
N B:ASN344 4.3 18.0 0.5
N B:ASN344 4.3 17.9 0.5
N B:SER299 4.3 20.6 1.0
OD1 B:ASP324 4.4 18.3 1.0
CA B:GLY298 4.4 20.3 1.0
CA B:SER299 4.4 19.4 1.0
N B:ALA343 4.4 20.8 1.0
CA B:ASN344 4.6 18.6 0.5
CA B:ASP294 4.6 17.9 1.0
CA B:ASN344 4.6 18.9 0.5
CA B:ALA343 4.6 21.3 1.0
O B:ASN341 4.6 24.6 1.0
C B:ASN295 4.7 18.1 1.0
CB B:ASP294 4.8 19.8 1.0
N B:ASP294 4.8 18.4 1.0
O B:PRO326 4.9 19.4 1.0
OD1 B:ASP294 4.9 20.9 1.0

Calcium binding site 4 out of 8 in 5nzn

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Calcium binding site 4 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:26.7
occ:1.00
 OD1 B:ASN378 2.2 27.9 1.0
O B:ASN386 2.3 26.0 1.0
OD1 B:ASP376 2.3 24.8 1.0
O B:HOH617 2.3 29.1 1.0
OD1 B:ASP384 2.4 29.3 1.0
OD2 B:ASP376 2.8 21.5 1.0
CG B:ASP376 2.9 23.6 1.0
CG B:ASN378 3.3 29.6 1.0
CG B:ASP384 3.3 29.2 1.0
C B:ASN386 3.4 28.8 1.0
OD2 B:ASP384 3.6 32.6 1.0
O B:ASP384 3.8 31.9 1.0
ND2 B:ASN378 3.8 30.2 1.0
N B:ASN386 3.9 32.3 1.0
CA B:ASN386 4.1 31.6 1.0
CB B:ASP376 4.3 23.0 1.0
N B:GLY379 4.4 21.5 1.0
C B:ASP384 4.4 30.9 1.0
CB B:ASN386 4.4 37.9 1.0
N B:PHE387 4.5 25.5 1.0
C B:ASN378 4.5 24.5 1.0
N B:ASN378 4.5 22.5 1.0
CB B:ASN378 4.6 27.1 1.0
CB B:ASP384 4.6 28.9 1.0
CA B:GLY379 4.7 20.4 1.0
CA B:ASN378 4.8 24.2 1.0
CA B:PHE387 4.8 27.0 1.0
C B:ASN385 4.8 32.0 1.0
CA B:ASP376 4.9 22.8 1.0
O B:ASN378 4.9 20.2 1.0
OG B:SER319 5.0 22.4 1.0
CD1 B:ILE321 5.0 26.1 1.0

Calcium binding site 5 out of 8 in 5nzn

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Calcium binding site 5 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:15.1
occ:1.00
 OD2 C:ASP324 2.2 11.5 1.0
O C:HOH749 2.3 17.8 1.0
O C:GLY298 2.3 14.8 1.0
O C:ASP294 2.4 12.1 1.0
O C:GLY342 2.4 18.1 1.0
O C:ASN344 2.4 17.1 1.0
CG C:ASP324 3.4 12.5 1.0
C C:GLY342 3.5 20.1 1.0
C C:GLY298 3.5 14.2 1.0
C C:ASP294 3.6 12.5 1.0
C C:ASN344 3.6 18.2 1.0
CA C:GLY345 4.0 14.4 1.0
O C:HOH755 4.1 14.1 1.0
CB C:ASP324 4.1 12.8 1.0
CA C:GLY342 4.2 21.6 1.0
O C:ALA343 4.2 20.7 1.0
C C:ALA343 4.2 20.3 1.0
N C:GLY298 4.2 15.4 1.0
OD1 C:ASP324 4.3 12.3 1.0
CA C:ASN295 4.3 14.6 1.0
N C:SER299 4.3 14.7 1.0
N C:GLY345 4.3 16.3 1.0
CA C:SER299 4.3 16.0 1.0
N C:ASN295 4.3 13.0 1.0
CA C:GLY298 4.4 14.3 1.0
N C:ASN344 4.4 20.6 1.0
N C:ALA343 4.5 19.0 1.0
CA C:ASP294 4.6 13.1 1.0
CA C:ALA343 4.6 20.1 1.0
CB C:ASP294 4.7 13.2 1.0
C C:ASN295 4.7 15.9 1.0
CA C:ASN344 4.7 20.7 1.0
O C:ASN341 4.7 21.9 1.0
N C:ASP294 4.8 12.8 1.0
O C:PRO326 4.9 18.1 1.0

Calcium binding site 6 out of 8 in 5nzn

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Calcium binding site 6 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:21.3
occ:1.00
 O C:HOH678 2.0 26.5 1.0
OD1 C:ASN378 2.2 21.7 1.0
OD1 C:ASP376 2.3 16.2 1.0
O C:ASN386 2.3 24.1 1.0
OD1 C:ASP384 2.4 21.7 1.0
O C:HOH670 2.4 29.8 1.0
OD2 C:ASP376 2.9 16.6 1.0
CG C:ASP376 2.9 16.5 1.0
CG C:ASP384 3.3 21.6 1.0
CG C:ASN378 3.4 22.8 1.0
C C:ASN386 3.5 23.0 1.0
OD2 C:ASP384 3.5 22.9 1.0
ND2 C:ASN378 4.0 25.0 1.0
N C:ASN386 4.0 23.6 1.0
O C:ASP384 4.0 19.1 1.0
CA C:ASN386 4.1 25.6 1.0
CB C:ASN386 4.2 27.8 1.0
CB C:ASP376 4.4 16.9 1.0
N C:ASN378 4.4 18.4 1.0
N C:GLY379 4.4 16.2 1.0
C C:ASN378 4.4 18.6 1.0
C C:ASP384 4.5 21.3 1.0
N C:PHE387 4.5 22.5 1.0
CB C:ASN378 4.6 20.9 1.0
CB C:ASP384 4.6 22.4 1.0
O C:HOH859 4.7 25.2 1.0
CA C:ASN378 4.7 19.2 1.0
CA C:GLY379 4.7 14.2 1.0
CA C:PHE387 4.8 21.8 1.0
CD C:PRO377 4.9 19.5 1.0
CA C:ASP376 4.9 18.0 1.0
O C:ASN378 4.9 20.5 1.0
C C:ASP376 4.9 17.3 1.0
CA C:ASP384 5.0 20.7 1.0

Calcium binding site 7 out of 8 in 5nzn

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Calcium binding site 7 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:19.6
occ:1.00
 O D:ASN344 2.2 17.3 1.0
O D:ASP294 2.3 17.5 1.0
O D:GLY298 2.3 18.7 1.0
O D:GLY342 2.4 19.9 1.0
OD2 D:ASP324 2.4 15.6 1.0
O D:HOH622 2.5 17.7 1.0
C D:ASN344 3.4 17.2 1.0
C D:GLY342 3.5 21.0 1.0
C D:GLY298 3.5 20.4 1.0
CG D:ASP324 3.5 17.9 1.0
C D:ASP294 3.5 16.8 1.0
CA D:GLY345 4.0 15.2 1.0
O D:ALA343 4.0 20.8 1.0
O D:HOH718 4.1 18.3 1.0
C D:ALA343 4.1 21.1 1.0
CA D:GLY342 4.1 20.9 1.0
N D:GLY345 4.1 15.1 1.0
CB D:ASP324 4.2 17.5 1.0
N D:GLY298 4.2 21.5 1.0
CA D:ASN295 4.3 16.5 1.0
N D:ASN344 4.3 18.8 1.0
N D:SER299 4.3 21.5 1.0
N D:ASN295 4.3 16.7 1.0
OD1 D:ASP324 4.4 16.7 1.0
CA D:SER299 4.4 19.4 1.0
CA D:GLY298 4.4 20.5 1.0
N D:ALA343 4.5 21.1 1.0
CA D:ASP294 4.5 17.2 1.0
CA D:ASN344 4.5 20.3 1.0
O D:ASN341 4.6 22.0 1.0
C D:ASN295 4.7 16.9 1.0
CA D:ALA343 4.7 21.7 1.0
CB D:ASP294 4.7 18.0 1.0
N D:ASP294 4.7 17.3 1.0
O D:PRO326 4.8 18.0 1.0
OD1 D:ASP294 4.9 19.2 1.0

Calcium binding site 8 out of 8 in 5nzn

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Calcium binding site 8 out of 8 in the Complex of H275Y/S247N 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/S247N Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:25.1
occ:1.00
 OD1 D:ASN378 2.2 26.7 1.0
O D:ASN386 2.3 29.1 1.0
OD1 D:ASP376 2.3 24.8 1.0
OD1 D:ASP384 2.4 28.5 1.0
O D:HOH619 2.4 29.9 1.0
O D:HOH610 2.4 27.6 1.0
OD2 D:ASP376 2.7 22.9 1.0
CG D:ASP376 2.8 24.0 1.0
CG D:ASP384 3.3 28.1 1.0
CG D:ASN378 3.3 28.3 1.0
C D:ASN386 3.4 31.6 1.0
OD2 D:ASP384 3.5 30.2 1.0
O D:ASP384 3.8 30.7 1.0
ND2 D:ASN378 3.8 30.0 1.0
N D:ASN386 4.0 32.8 1.0
CA D:ASN386 4.1 32.8 1.0
CB D:ASP376 4.3 22.4 1.0
N D:GLY379 4.4 20.8 1.0
C D:ASP384 4.4 31.4 1.0
CB D:ASN386 4.4 38.5 1.0
C D:ASN378 4.5 23.8 1.0
N D:ASN378 4.5 21.7 1.0
N D:PHE387 4.5 28.3 1.0
O D:HOH861 4.6 24.5 1.0
CB D:ASN378 4.6 25.1 1.0
CA D:GLY379 4.6 20.5 1.0
CB D:ASP384 4.6 28.4 1.0
CA D:ASN378 4.7 24.1 1.0
CA D:PHE387 4.8 28.7 1.0
C D:ASN385 4.9 30.8 1.0
O D:ASN378 4.9 17.9 1.0
CA D:ASP376 4.9 22.6 1.0
OG D:SER319 4.9 22.6 1.0
CA D:ASP384 5.0 27.9 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 09:37:36 2024

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