Calcium in PDB 6hp0: Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative

Enzymatic activity of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative

All present enzymatic activity of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative:
3.2.1.18;

Protein crystallography data

The structure of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative, PDB code: 6hp0 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) 48.34 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.842, 126.861, 96.906, 90.00, 93.93, 90.00
R / Rfree (%) 18.5 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative (pdb code 6hp0). 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 Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative, PDB code: 6hp0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6hp0

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Calcium binding site 1 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

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

b:17.3
occ:1.00
 OD2 A:ASP324 2.2 15.9 1.0
O A:ASP294 2.3 15.5 1.0
O A:ASN344 2.4 15.7 1.0
O A:GLY342 2.4 18.3 1.0
O A:GLY298 2.4 16.8 1.0
O A:HOH661 2.4 17.7 1.0
CG A:ASP324 3.4 16.2 1.0
C A:GLY342 3.5 18.8 1.0
C A:ASN344 3.5 17.4 1.0
C A:GLY298 3.5 18.2 1.0
C A:ASP294 3.6 15.3 1.0
CA A:GLY345 4.0 16.0 1.0
O A:ALA343 4.1 17.6 1.0
O A:HOH731 4.1 18.1 1.0
C A:ALA343 4.1 19.4 1.0
CB A:ASP324 4.2 16.5 1.0
CA A:GLY342 4.2 18.8 1.0
N A:GLY345 4.3 19.4 1.0
OD1 A:ASP324 4.3 16.1 1.0
N A:GLY298 4.3 17.1 1.0
N A:SER299 4.3 17.0 1.0
CA A:SER299 4.4 17.8 1.0
CA A:ASN295 4.4 17.2 1.0
N A:ASN344 4.4 18.5 1.0
N A:ASN295 4.4 15.5 1.0
N A:ALA343 4.5 17.3 1.0
CA A:GLY298 4.5 18.1 1.0
CA A:ASP294 4.6 16.4 1.0
CA A:ASN344 4.6 17.4 0.5
CA A:ASN344 4.6 18.0 0.5
O A:ASN341 4.7 20.1 1.0
CA A:ALA343 4.7 19.2 1.0
CB A:ASP294 4.7 16.5 1.0
C A:ASN295 4.8 19.6 1.0
N A:ASP294 4.8 16.5 1.0
OD1 A:ASP294 4.8 17.5 1.0
O A:PRO326 4.9 18.5 1.0

Calcium binding site 2 out of 8 in 6hp0

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Calcium binding site 2 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

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

b:34.6
occ:1.00
 O A:HOH707 2.2 22.0 1.0
O A:HOH744 2.2 29.3 1.0
OD1 A:ASP376 2.3 23.4 1.0
OD1 A:ASN378 2.3 33.2 1.0
O A:ASN386 2.4 29.5 1.0
OD1 A:ASP384 2.5 29.7 1.0
CG A:ASP376 2.9 19.5 1.0
OD2 A:ASP376 3.0 21.1 1.0
CG A:ASP384 3.2 29.8 1.0
OD2 A:ASP384 3.2 30.4 1.0
CG A:ASN378 3.5 31.5 1.0
C A:ASN386 3.6 29.8 1.0
N A:ASN386 3.9 28.7 1.0
O A:ASP384 4.0 30.2 1.0
ND2 A:ASN378 4.1 33.9 1.0
CA A:ASN386 4.1 29.8 1.0
CB A:ASN386 4.2 33.8 1.0
O A:HOH911 4.3 33.1 0.5
CB A:ASP376 4.4 19.4 1.0
C A:ASP384 4.4 32.4 1.0
N A:ASN378 4.4 23.2 1.0
C A:ASN378 4.5 25.3 1.0
N A:GLY379 4.5 23.5 1.0
CB A:ASP384 4.5 29.5 1.0
N A:PHE387 4.6 29.8 1.0
O A:HOH798 4.6 30.6 1.0
CB A:ASN378 4.7 27.2 1.0
CA A:GLY379 4.7 19.2 1.0
CA A:ASN378 4.8 24.6 1.0
O A:ASN378 4.8 23.7 1.0
CA A:ASP376 4.9 18.9 1.0
CA A:PHE387 4.9 27.0 1.0
C A:ASN385 4.9 33.7 1.0
CA A:ASP384 4.9 30.1 1.0
C A:ASP376 4.9 18.1 1.0

Calcium binding site 3 out of 8 in 6hp0

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Calcium binding site 3 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

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

b:22.0
occ:1.00
 O B:ASP294 2.2 20.4 1.0
O B:ASN344 2.3 21.0 1.0
O B:GLY298 2.3 26.2 1.0
OD2 B:ASP324 2.3 18.8 1.0
O B:GLY342 2.4 23.6 1.0
O B:HOH650 2.5 20.0 1.0
C B:GLY298 3.5 27.2 1.0
C B:ASN344 3.5 23.1 1.0
C B:GLY342 3.5 22.5 1.0
CG B:ASP324 3.5 22.2 1.0
C B:ASP294 3.5 21.0 1.0
CA B:GLY345 4.0 17.8 1.0
O B:ALA343 4.0 24.5 1.0
O B:HOH671 4.0 21.0 1.0
C B:ALA343 4.1 24.2 1.0
CA B:GLY342 4.2 24.0 1.0
N B:GLY345 4.2 20.7 1.0
CB B:ASP324 4.2 22.4 1.0
N B:GLY298 4.2 25.3 1.0
N B:SER299 4.3 26.4 1.0
CA B:ASN295 4.3 21.0 1.0
N B:ASN295 4.3 21.8 1.0
CA B:GLY298 4.4 25.2 1.0
N B:ASN344 4.4 22.0 1.0
CA B:SER299 4.4 24.6 1.0
OD1 B:ASP324 4.4 24.6 1.0
N B:ALA343 4.5 21.6 1.0
CA B:ASP294 4.5 21.1 1.0
CA B:ASN344 4.6 26.4 1.0
CB B:ASP294 4.7 24.0 1.0
O B:ASN341 4.7 24.3 1.0
CA B:ALA343 4.7 25.3 1.0
C B:ASN295 4.7 22.5 1.0
OD1 B:ASP294 4.7 22.3 1.0
N B:ASP294 4.7 22.1 1.0
O B:PRO326 4.9 26.3 1.0

Calcium binding site 4 out of 8 in 6hp0

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Calcium binding site 4 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

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

b:42.7
occ:1.00
 O B:HOH616 2.3 34.5 1.0
OD1 B:ASN378 2.3 38.2 1.0
O B:HOH674 2.3 34.4 1.0
O B:ASN386 2.5 36.2 1.0
OD1 B:ASP376 2.5 26.6 1.0
OD1 B:ASP384 2.5 45.8 1.0
OD2 B:ASP376 2.8 23.3 1.0
CG B:ASP376 2.9 25.3 1.0
CG B:ASP384 3.2 40.4 1.0
OD2 B:ASP384 3.3 44.9 1.0
CG B:ASN378 3.3 39.8 1.0
C B:ASN386 3.5 37.7 1.0
ND2 B:ASN378 3.7 43.5 1.0
O B:ASP384 3.7 35.3 1.0
N B:ASN386 3.8 39.6 1.0
CA B:ASN386 4.1 39.4 1.0
C B:ASP384 4.3 38.2 1.0
CB B:ASN386 4.3 46.7 1.0
CB B:ASP376 4.3 23.9 1.0
N B:GLY379 4.6 25.7 1.0
N B:ASN378 4.6 25.6 1.0
CB B:ASP384 4.6 36.9 1.0
C B:ASN378 4.6 29.7 1.0
N B:PHE387 4.6 34.1 1.0
CB B:ASN378 4.6 35.6 1.0
CA B:GLY379 4.7 23.5 1.0
CA B:ASN378 4.8 30.7 1.0
OG B:SER319 4.8 27.6 1.0
O B:HOH867 4.9 44.4 1.0
CA B:ASP384 4.9 33.8 1.0
C B:ASN385 4.9 40.1 1.0
O B:ASN378 4.9 28.4 1.0
CA B:ASP376 5.0 23.3 1.0
CA B:PHE387 5.0 34.6 1.0
N B:ASP384 5.0 29.3 1.0
N B:ASN385 5.0 38.5 1.0

Calcium binding site 5 out of 8 in 6hp0

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Calcium binding site 5 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:19.5
occ:1.00
 O C:GLY298 2.3 17.4 1.0
O C:ASN344 2.3 17.2 1.0
OD2 C:ASP324 2.3 14.2 1.0
O C:ASP294 2.4 16.3 1.0
O C:HOH681 2.4 17.1 1.0
O C:GLY342 2.4 21.2 1.0
C C:GLY298 3.4 18.7 1.0
C C:GLY342 3.5 22.8 1.0
CG C:ASP324 3.5 14.6 1.0
C C:ASN344 3.5 18.7 1.0
C C:ASP294 3.6 16.7 1.0
O C:HOH753 4.0 17.5 1.0
CA C:GLY345 4.0 16.8 1.0
CA C:GLY342 4.1 22.9 1.0
O C:ALA343 4.2 22.1 1.0
CB C:ASP324 4.2 16.2 1.0
C C:ALA343 4.2 20.5 1.0
N C:SER299 4.3 17.9 1.0
N C:GLY345 4.3 19.5 1.0
N C:GLY298 4.3 17.7 1.0
CA C:SER299 4.3 19.8 1.0
OD1 C:ASP324 4.4 15.8 1.0
CA C:ASN295 4.4 17.4 1.0
CA C:GLY298 4.4 18.4 1.0
N C:ASN295 4.4 17.0 1.0
N C:ASN344 4.4 20.7 1.0
N C:ALA343 4.5 21.2 1.0
CA C:ASP294 4.5 18.8 1.0
CB C:ASP294 4.6 18.3 1.0
CA C:ASN344 4.7 19.4 1.0
CA C:ALA343 4.7 22.5 1.0
O C:ASN341 4.7 23.1 1.0
N C:ASP294 4.8 18.0 1.0
C C:ASN295 4.8 20.4 1.0
OD1 C:ASP294 4.8 18.2 1.0
O C:PRO326 4.9 18.1 1.0

Calcium binding site 6 out of 8 in 6hp0

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Calcium binding site 6 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:35.5
occ:1.00
 O C:HOH755 2.3 33.8 1.0
O C:HOH831 2.3 27.1 1.0
OD1 C:ASN378 2.3 33.3 1.0
OD1 C:ASP376 2.4 25.2 1.0
OD1 C:ASP384 2.4 30.5 1.0
O C:ASN386 2.5 30.8 1.0
OD2 C:ASP376 2.9 21.1 1.0
CG C:ASP376 2.9 21.9 1.0
CG C:ASP384 3.2 30.4 1.0
OD2 C:ASP384 3.3 34.1 1.0
CG C:ASN378 3.5 31.5 1.0
C C:ASN386 3.6 31.6 1.0
O C:ASP384 3.9 29.5 1.0
N C:ASN386 3.9 30.5 1.0
ND2 C:ASN378 4.1 36.2 1.0
CA C:ASN386 4.1 30.4 1.0
CB C:ASN386 4.2 38.1 1.0
CB C:ASP376 4.4 19.7 1.0
N C:GLY379 4.4 23.9 1.0
C C:ASP384 4.4 29.5 1.0
C C:ASN378 4.4 23.1 1.0
N C:ASN378 4.5 22.7 1.0
CB C:ASP384 4.6 30.6 1.0
N C:PHE387 4.6 27.7 1.0
CB C:ASN378 4.7 26.2 1.0
CA C:GLY379 4.7 20.6 1.0
O C:HOH787 4.7 32.8 1.0
CA C:ASN378 4.7 23.8 1.0
O C:ASN378 4.9 21.1 1.0
CA C:ASP376 4.9 20.8 1.0
CA C:ASP384 4.9 30.4 1.0
C C:ASN385 4.9 33.8 1.0
CA C:PHE387 4.9 28.5 1.0
C C:ASP376 4.9 18.6 1.0
OG C:SER319 5.0 19.8 1.0

Calcium binding site 7 out of 8 in 6hp0

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Calcium binding site 7 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:20.4
occ:1.00
 O D:GLY298 2.2 22.9 1.0
O D:GLY342 2.3 24.0 1.0
O D:ASP294 2.3 19.4 1.0
O D:ASN344 2.3 21.2 1.0
OD2 D:ASP324 2.3 18.9 1.0
O D:HOH638 2.5 18.5 1.0
C D:GLY342 3.4 24.5 1.0
C D:GLY298 3.4 24.4 1.0
CG D:ASP324 3.5 20.1 1.0
C D:ASP294 3.5 19.2 1.0
C D:ASN344 3.6 22.0 1.0
O D:HOH721 4.0 22.6 1.0
CA D:GLY345 4.1 16.5 1.0
CA D:GLY342 4.1 24.9 1.0
CB D:ASP324 4.2 22.1 1.0
O D:ALA343 4.2 23.2 1.0
N D:GLY298 4.2 24.9 1.0
C D:ALA343 4.2 24.7 1.0
N D:GLY345 4.3 19.0 1.0
N D:SER299 4.3 20.9 1.0
N D:ASN295 4.3 21.8 1.0
CA D:ASN295 4.3 22.7 1.0
CA D:SER299 4.4 20.9 1.0
CA D:GLY298 4.4 24.9 1.0
OD1 D:ASP324 4.4 20.0 1.0
N D:ALA343 4.4 23.3 1.0
N D:ASN344 4.4 20.8 1.0
CA D:ASP294 4.5 22.0 1.0
OD1 D:ASP294 4.7 23.2 1.0
O D:ASN341 4.7 26.4 1.0
C D:ASN295 4.7 24.1 1.0
CA D:ASN344 4.7 20.9 0.5
CA D:ALA343 4.7 23.6 1.0
CA D:ASN344 4.7 21.5 0.5
N D:ASP294 4.8 21.2 1.0
CB D:ASP294 4.8 23.2 1.0
O D:PRO326 4.9 23.7 1.0
CG D:ASP294 5.0 23.8 1.0

Calcium binding site 8 out of 8 in 6hp0

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Calcium binding site 8 out of 8 in the Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of Neuraminidase From H1N1 Influenza Virus in Complex with Oseltamivir Triazol Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:41.5
occ:1.00
 OD1 D:ASN378 2.3 29.7 1.0
O D:HOH670 2.4 34.3 1.0
O D:HOH669 2.4 35.2 1.0
OD1 D:ASP384 2.4 42.4 1.0
OD1 D:ASP376 2.4 27.9 1.0
O D:ASN386 2.6 33.7 1.0
OD2 D:ASP376 2.9 22.1 1.0
CG D:ASP376 2.9 25.6 1.0
CG D:ASP384 3.1 40.5 1.0
OD2 D:ASP384 3.3 43.9 1.0
CG D:ASN378 3.3 35.8 1.0
C D:ASN386 3.6 37.5 1.0
ND2 D:ASN378 3.7 44.8 1.0
O D:ASP384 3.9 32.8 1.0
N D:ASN386 3.9 41.9 1.0
CA D:ASN386 4.2 40.7 1.0
CB D:ASN386 4.3 47.9 1.0
C D:ASP384 4.4 37.2 1.0
CB D:ASP376 4.4 24.0 1.0
N D:GLY379 4.5 28.0 1.0
C D:ASN378 4.5 29.6 1.0
N D:ASN378 4.5 26.0 1.0
CB D:ASP384 4.5 36.9 1.0
O D:HOH782 4.5 46.4 1.0
CB D:ASN378 4.6 34.3 1.0
CA D:GLY379 4.7 25.2 1.0
N D:PHE387 4.7 35.6 1.0
CA D:ASN378 4.8 32.1 1.0
O D:ASN378 4.8 30.8 1.0
CA D:ASP384 4.9 33.0 1.0
OG D:SER319 4.9 27.1 1.0
O D:HOH802 4.9 42.0 1.0
C D:ASN385 5.0 40.6 1.0
N D:ASP384 5.0 28.1 1.0
CD D:PRO377 5.0 30.8 1.0

Reference:

V.Zima, C.B.Albinana, K.Rojikova, J.Pokorna, P.Pachl, P.Rezacova, J.Hudlicky, V.Navratil, P.Majer, J.Konvalinka, M.Kozisek, A.Machara. Investigation of Flexibility of Neuraminidase 150-Loop Using Tamiflu Derivatives in Influenza A Viruses H1N1 and H5N1. Bioorg.Med.Chem. V. 27 2935 2019.
ISSN: ESSN 1464-3391
PubMed: 31128993
DOI: 10.1016/J.BMC.2019.05.024
Page generated: Sat Dec 12 06:10:06 2020

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