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Calcium in PDB 5nzf: Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir

Protein crystallography data

The structure of Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nzf 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) 45.18 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.654, 127.217, 96.786, 90.00, 92.93, 90.00
R / Rfree (%) 21.4 / 25.5

Other elements in 5nzf:

The structure of Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir (pdb code 5nzf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir, PDB code: 5nzf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5nzf

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Calcium binding site 1 out of 9 in the Complex of H275Y/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 H275Y/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:14.6
occ:1.00
 OD2 A:ASP324 2.3 14.3 1.0
O A:GLY298 2.3 15.9 1.0
O A:ASP294 2.3 12.4 1.0
O A:ASN344 2.4 15.6 1.0
O A:GLY342 2.4 18.0 1.0
O A:HOH649 2.4 17.0 1.0
C A:GLY298 3.4 14.8 1.0
CG A:ASP324 3.4 14.3 1.0
C A:GLY342 3.5 18.3 1.0
C A:ASP294 3.5 12.4 1.0
C A:ASN344 3.6 16.8 1.0
O A:HOH772 4.0 15.2 1.0
CA A:GLY345 4.1 13.4 1.0
CA A:GLY342 4.1 17.4 1.0
CB A:ASP324 4.1 14.2 1.0
O A:ALA343 4.2 17.1 1.0
C A:ALA343 4.2 19.9 1.0
N A:GLY298 4.2 16.3 1.0
N A:SER299 4.3 14.2 1.0
N A:GLY345 4.3 14.8 1.0
OD1 A:ASP324 4.3 13.8 1.0
CA A:ASN295 4.3 13.9 1.0
N A:ASN295 4.4 12.6 1.0
CA A:SER299 4.4 15.2 1.0
CA A:GLY298 4.4 15.4 1.0
N A:ALA343 4.5 18.8 1.0
N A:ASN344 4.5 20.0 1.0
CA A:ASP294 4.6 12.8 1.0
CB A:ASP294 4.7 13.2 1.0
CA A:ALA343 4.7 18.9 1.0
O A:ASN341 4.7 16.8 1.0
CA A:ASN344 4.7 19.8 1.0
C A:ASN295 4.7 14.8 1.0
O A:PRO326 4.8 16.3 1.0
N A:ASP294 4.8 13.6 1.0

Calcium binding site 2 out of 9 in 5nzf

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Calcium binding site 2 out of 9 in the Complex of H275Y/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 H275Y/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:24.1
occ:1.00
 O A:HOH685 2.1 26.5 1.0
OD1 A:ASN378 2.2 23.5 1.0
OD1 A:ASP376 2.3 17.1 1.0
O A:HOH677 2.3 34.7 1.0
OD1 A:ASP384 2.4 23.7 1.0
O A:ASN386 2.4 22.7 1.0
OD2 A:ASP376 3.0 17.7 1.0
CG A:ASP376 3.0 18.0 1.0
CG A:ASP384 3.2 24.5 1.0
CG A:ASN378 3.4 24.5 1.0
OD2 A:ASP384 3.4 24.4 1.0
C A:ASN386 3.6 24.8 1.0
ND2 A:ASN378 3.9 26.9 1.0
N A:ASN386 4.0 24.5 1.0
O A:ASP384 4.1 20.1 1.0
CA A:ASN386 4.2 26.1 1.0
CB A:ASN386 4.3 28.3 1.0
CB A:ASP376 4.4 17.9 1.0
N A:ASN378 4.4 19.1 1.0
C A:ASN378 4.5 17.7 1.0
C A:ASP384 4.5 23.4 1.0
N A:GLY379 4.5 16.9 1.0
CB A:ASP384 4.6 23.5 1.0
CB A:ASN378 4.6 21.9 1.0
N A:PHE387 4.6 22.6 1.0
O A:HOH805 4.6 29.8 1.0
CA A:ASN378 4.7 19.4 1.0
CA A:GLY379 4.7 15.3 1.0
CA A:PHE387 4.9 23.4 1.0
CD A:PRO377 4.9 20.3 1.0
CA A:ASP376 4.9 17.6 1.0
O A:ASN378 4.9 18.1 1.0
C A:ASP376 5.0 17.7 1.0
CA A:ASP384 5.0 22.2 1.0

Calcium binding site 3 out of 9 in 5nzf

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Calcium binding site 3 out of 9 in the Complex of H275Y/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 H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:21.1
occ:1.00
 O C:HOH939 2.2 25.7 1.0
O D:HOH811 2.3 32.7 1.0
O B:HOH685 2.4 31.7 1.0
O C:HOH602 2.7 34.1 1.0
O A:HOH905 4.0 34.9 1.0
OD2 A:ASP113 4.3 16.1 1.0
OD2 C:ASP113 4.3 15.4 1.0
OD2 B:ASP113 4.5 12.3 1.0
OD1 C:ASP113 4.5 16.0 1.0
OD1 A:ASP113 4.5 16.4 1.0
OD2 D:ASP113 4.5 11.9 1.0
OD1 B:ASP113 4.6 11.0 1.0
OD1 D:ASP113 4.6 12.2 1.0
O A:HOH793 4.8 29.7 1.0
CG C:ASP113 4.8 14.5 1.0
CG A:ASP113 4.8 14.6 1.0
O C:HOH828 4.9 26.6 1.0
CG B:ASP113 4.9 12.9 1.0
CG D:ASP113 4.9 12.2 1.0

Calcium binding site 4 out of 9 in 5nzf

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Calcium binding site 4 out of 9 in the Complex of H275Y/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 H275Y/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:22.3
occ:1.00
 O B:ASN344 2.2 18.4 1.0
O B:ASP294 2.3 19.4 1.0
OD2 B:ASP324 2.4 18.1 1.0
O B:GLY342 2.4 22.2 1.0
O B:GLY298 2.4 22.4 1.0
O B:HOH621 2.5 22.0 1.0
C B:ASN344 3.4 18.1 1.0
C B:GLY342 3.4 23.4 1.0
CG B:ASP324 3.5 20.0 1.0
C B:ASP294 3.5 18.6 1.0
C B:GLY298 3.6 23.4 1.0
CA B:GLY345 4.0 16.0 1.0
C B:ALA343 4.1 23.2 1.0
CA B:GLY342 4.1 24.1 1.0
N B:GLY345 4.2 15.6 1.0
O B:ALA343 4.2 23.4 1.0
O B:HOH722 4.2 20.3 1.0
CA B:ASN295 4.2 18.6 1.0
CB B:ASP324 4.2 19.7 1.0
N B:GLY298 4.2 23.9 1.0
N B:ASN344 4.3 20.2 1.0
N B:ASN295 4.3 19.0 1.0
OD1 B:ASP324 4.4 19.1 1.0
N B:ALA343 4.4 23.3 1.0
N B:SER299 4.4 22.6 1.0
CA B:GLY298 4.4 23.3 1.0
CA B:ASN344 4.5 21.3 1.0
CA B:SER299 4.5 21.5 1.0
CA B:ASP294 4.6 19.2 1.0
C B:ASN295 4.6 19.3 1.0
O B:ASN341 4.6 25.6 1.0
CA B:ALA343 4.7 23.8 1.0
CB B:ASP294 4.7 19.7 1.0
N B:ASP294 4.8 19.6 1.0
O B:PRO326 4.8 19.6 1.0
OD1 B:ASP294 4.9 19.4 1.0
O B:ASN295 4.9 18.4 1.0

Calcium binding site 5 out of 9 in 5nzf

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Calcium binding site 5 out of 9 in the Complex of H275Y/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 H275Y/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:28.9
occ:1.00
 OD1 B:ASN378 2.2 30.5 1.0
O B:HOH614 2.3 28.4 1.0
O B:HOH602 2.3 33.2 1.0
OD1 B:ASP376 2.4 25.5 1.0
O B:ASN386 2.4 31.8 1.0
OD1 B:ASP384 2.4 34.8 1.0
OD2 B:ASP376 2.7 22.4 1.0
CG B:ASP376 2.8 25.7 1.0
CG B:ASN378 3.3 31.4 1.0
CG B:ASP384 3.3 33.6 1.0
OD2 B:ASP384 3.5 33.9 1.0
C B:ASN386 3.5 34.3 1.0
ND2 B:ASN378 3.7 34.0 1.0
O B:ASP384 3.8 34.0 1.0
N B:ASN386 4.0 34.0 1.0
CA B:ASN386 4.2 36.6 1.0
N B:GLY379 4.3 22.9 1.0
CB B:ASP376 4.3 23.9 1.0
C B:ASN378 4.4 25.8 1.0
N B:ASN378 4.4 22.9 1.0
C B:ASP384 4.5 34.2 1.0
CB B:ASN386 4.5 41.2 1.0
CB B:ASN378 4.5 27.6 1.0
N B:PHE387 4.6 32.1 1.0
CA B:GLY379 4.6 22.3 1.0
CA B:ASN378 4.7 26.0 1.0
CB B:ASP384 4.7 32.0 1.0
O B:ASN378 4.9 21.6 1.0
OG B:SER319 4.9 22.8 1.0
CA B:ASP376 4.9 23.5 1.0
CA B:PHE387 4.9 31.9 1.0
CD1 B:ILE321 4.9 27.5 1.0
C B:ASN385 5.0 33.9 1.0
C B:ASP376 5.0 23.1 1.0
CD B:PRO377 5.0 23.2 1.0

Calcium binding site 6 out of 9 in 5nzf

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Calcium binding site 6 out of 9 in the Complex of H275Y/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 6 of Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:16.5
occ:1.00
 OD2 C:ASP324 2.3 12.6 1.0
O C:GLY298 2.3 17.4 1.0
O C:ASN344 2.4 16.6 1.0
O C:HOH694 2.4 20.2 1.0
O C:ASP294 2.4 13.3 1.0
O C:GLY342 2.4 18.0 1.0
CG C:ASP324 3.5 14.4 1.0
C C:GLY298 3.5 17.9 1.0
C C:GLY342 3.5 20.2 1.0
C C:ASP294 3.6 13.8 1.0
C C:ASN344 3.6 18.4 1.0
CA C:GLY345 4.1 15.6 1.0
O C:HOH732 4.1 15.7 1.0
CA C:GLY342 4.1 21.1 1.0
O C:ALA343 4.1 19.1 1.0
CB C:ASP324 4.2 14.4 1.0
C C:ALA343 4.2 19.4 1.0
N C:GLY298 4.2 17.5 1.0
N C:SER299 4.3 16.9 1.0
N C:GLY345 4.3 16.7 1.0
CA C:ASN295 4.3 15.3 1.0
OD1 C:ASP324 4.3 14.3 1.0
CA C:SER299 4.4 17.6 1.0
N C:ASN295 4.4 14.0 1.0
CA C:GLY298 4.4 17.7 1.0
N C:ALA343 4.5 19.2 1.0
N C:ASN344 4.5 20.3 1.0
CA C:ASP294 4.6 14.3 1.0
CA C:ALA343 4.7 20.1 1.0
CB C:ASP294 4.7 14.5 1.0
C C:ASN295 4.7 16.6 1.0
CA C:ASN344 4.7 20.7 1.0
O C:ASN341 4.7 21.9 1.0
O C:PRO326 4.8 17.5 1.0
N C:ASP294 4.8 14.7 1.0
O C:ASN295 5.0 12.6 1.0

Calcium binding site 7 out of 9 in 5nzf

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Calcium binding site 7 out of 9 in the Complex of H275Y/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 7 of Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:25.8
occ:1.00
 O C:HOH734 2.1 26.1 1.0
OD1 C:ASN378 2.2 25.2 1.0
OD1 C:ASP376 2.3 18.8 1.0
O C:HOH650 2.4 30.4 1.0
OD1 C:ASP384 2.4 24.9 1.0
O C:ASN386 2.4 24.2 1.0
OD2 C:ASP376 2.9 19.7 1.0
CG C:ASP376 2.9 19.6 1.0
CG C:ASP384 3.3 25.9 1.0
CG C:ASN378 3.4 26.1 1.0
OD2 C:ASP384 3.5 27.0 1.0
C C:ASN386 3.6 26.0 1.0
ND2 C:ASN378 3.9 29.0 1.0
O C:ASP384 4.0 22.7 1.0
N C:ASN386 4.1 25.8 1.0
CA C:ASN386 4.2 27.5 1.0
CB C:ASN386 4.3 30.4 1.0
CB C:ASP376 4.3 19.8 1.0
N C:GLY379 4.3 17.5 1.0
N C:ASN378 4.4 19.8 1.0
C C:ASN378 4.4 20.5 1.0
C C:ASP384 4.5 25.5 1.0
CB C:ASN378 4.6 23.3 1.0
N C:PHE387 4.6 24.9 1.0
CB C:ASP384 4.6 25.7 1.0
CA C:ASN378 4.7 21.0 1.0
CA C:GLY379 4.7 16.1 1.0
O C:HOH884 4.7 28.5 1.0
CA C:PHE387 4.8 25.6 1.0
CA C:ASP376 4.9 19.6 1.0
CD C:PRO377 4.9 20.7 1.0
O C:ASN378 4.9 21.5 1.0
C C:ASP376 4.9 18.5 1.0

Calcium binding site 8 out of 9 in 5nzf

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Calcium binding site 8 out of 9 in the Complex of H275Y/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 8 of Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:22.6
occ:1.00
 O D:ASN344 2.2 20.0 1.0
O D:ASP294 2.2 17.8 1.0
OD2 D:ASP324 2.3 16.9 1.0
O D:GLY342 2.4 21.7 1.0
O D:GLY298 2.4 21.7 1.0
O D:HOH657 2.5 19.5 1.0
C D:ASN344 3.4 17.7 1.0
C D:GLY342 3.4 22.0 1.0
C D:ASP294 3.5 18.4 1.0
CG D:ASP324 3.5 19.8 1.0
C D:GLY298 3.5 22.1 1.0
CA D:GLY345 4.0 14.9 1.0
O D:HOH757 4.0 21.7 1.0
C D:ALA343 4.1 21.9 1.0
N D:GLY345 4.1 16.0 1.0
CA D:GLY342 4.2 22.0 1.0
CA D:ASN295 4.2 18.2 1.0
O D:ALA343 4.2 23.2 1.0
N D:ASN344 4.2 17.8 1.0
N D:GLY298 4.2 25.5 1.0
CB D:ASP324 4.2 19.1 1.0
N D:ASN295 4.2 18.2 1.0
OD1 D:ASP324 4.4 19.4 1.0
N D:SER299 4.4 21.0 1.0
CA D:GLY298 4.4 23.2 1.0
N D:ALA343 4.4 22.2 1.0
CA D:ASN344 4.5 20.6 1.0
CA D:SER299 4.5 20.6 1.0
CA D:ASP294 4.6 19.1 1.0
CA D:ALA343 4.6 22.8 1.0
C D:ASN295 4.6 19.9 1.0
O D:ASN341 4.6 25.6 1.0
CB D:ASP294 4.9 21.7 1.0
N D:ASP294 4.9 19.5 1.0
O D:PRO326 4.9 21.2 1.0
OD1 D:ASP294 4.9 22.9 1.0
O D:ASN295 4.9 17.5 1.0

Calcium binding site 9 out of 9 in 5nzf

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Calcium binding site 9 out of 9 in the Complex of H275Y/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 9 of Complex of H275Y/I223V Mutant Variant of Neuraminidase From H1N1 Influenza Virus with Oseltamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:29.7
occ:1.00
 OD1 D:ASN378 2.3 27.3 1.0
OD1 D:ASP376 2.4 23.7 1.0
O D:ASN386 2.4 31.4 1.0
OD1 D:ASP384 2.4 31.8 1.0
O D:HOH646 2.5 29.2 1.0
O D:HOH608 2.5 32.0 1.0
OD2 D:ASP376 2.7 20.7 1.0
CG D:ASP376 2.9 24.9 1.0
CG D:ASP384 3.3 33.6 1.0
CG D:ASN378 3.4 32.0 1.0
C D:ASN386 3.5 33.3 1.0
OD2 D:ASP384 3.5 33.7 1.0
O D:ASP384 3.8 32.3 1.0
ND2 D:ASN378 3.8 35.2 1.0
N D:ASN386 4.0 35.0 1.0
CA D:ASN386 4.2 37.3 1.0
CB D:ASP376 4.3 24.2 1.0
C D:ASP384 4.4 33.8 1.0
N D:GLY379 4.4 24.1 1.0
C D:ASN378 4.5 26.5 1.0
N D:ASN378 4.5 26.3 1.0
N D:PHE387 4.5 31.9 1.0
CB D:ASN386 4.6 41.4 1.0
CA D:GLY379 4.6 23.1 1.0
CB D:ASN378 4.6 29.1 1.0
CB D:ASP384 4.6 31.5 1.0
OG D:SER319 4.8 24.3 1.0
CA D:ASN378 4.8 27.3 1.0
O D:HOH817 4.8 35.7 1.0
CA D:PHE387 4.9 31.8 1.0
C D:ASN385 4.9 34.1 1.0
O D:ASN378 4.9 22.0 1.0
CD1 D:ILE321 4.9 27.9 1.0
CA D:ASP376 4.9 23.4 1.0
CA D:ASP384 5.0 30.0 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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