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Calcium in PDB 4gzt: N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate

Protein crystallography data

The structure of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate, PDB code: 4gzt was solved by X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.244, 110.194, 109.847, 90.00, 98.27, 90.00
R / Rfree (%) 19 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate (pdb code 4gzt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate, PDB code: 4gzt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4gzt

Go back to Calcium Binding Sites List in 4gzt
Calcium binding site 1 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca511

b:34.0
occ:1.00
 O A:HOH609 1.9 40.2 1.0
O A:ASP293 2.1 28.7 1.0
O A:GLY297 2.1 40.0 1.0
O A:HIS347 2.3 33.2 1.0
OD2 A:ASP324 2.4 31.5 1.0
O A:GLY345 2.5 34.4 1.0
C A:ASP293 3.3 27.0 1.0
C A:GLY297 3.4 40.8 1.0
CG A:ASP324 3.5 33.3 1.0
C A:HIS347 3.6 38.6 1.0
C A:GLY345 3.6 38.6 1.0
CA A:ASN294 4.1 28.3 1.0
CA A:GLY348 4.1 32.8 1.0
CA A:GLY345 4.2 40.3 1.0
N A:ASN294 4.2 26.9 1.0
CA A:ASP293 4.2 29.4 1.0
CB A:ASP324 4.3 32.0 1.0
N A:SER298 4.3 36.2 1.0
N A:GLY348 4.3 38.8 1.0
CB A:ASP293 4.3 29.3 1.0
CA A:GLY297 4.3 39.8 1.0
CA A:SER298 4.3 35.5 1.0
O A:GLY346 4.4 35.0 1.0
C A:ASN294 4.4 33.0 1.0
OD1 A:ASP324 4.4 30.1 1.0
N A:GLY297 4.4 35.6 1.0
N A:ASP293 4.4 30.1 1.0
C A:GLY346 4.5 34.8 1.0
OD1 A:ASP293 4.5 24.3 1.0
N A:TRP295 4.6 30.1 1.0
N A:GLY346 4.7 40.4 1.0
N A:HIS347 4.7 35.3 1.0
CA A:HIS347 4.8 34.4 1.0
O A:ASN294 4.8 31.9 1.0
CG A:ASP293 4.9 33.0 1.0
O A:GLU344 5.0 42.9 1.0

Calcium binding site 2 out of 5 in 4gzt

Go back to Calcium Binding Sites List in 4gzt
Calcium binding site 2 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca512

b:61.7
occ:1.00
 O B:HOH658 2.3 36.6 1.0
O A:HOH652 2.8 33.6 1.0
O B:HOH654 4.1 34.5 1.0
OD2 D:ASP113 4.5 35.0 1.0
OD2 C:ASP113 4.5 32.7 1.0
OD2 B:ASP113 4.5 33.8 1.0
OD2 A:ASP113 4.8 35.6 1.0
OD1 A:ASP113 4.9 37.8 1.0

Calcium binding site 3 out of 5 in 4gzt

Go back to Calcium Binding Sites List in 4gzt
Calcium binding site 3 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca510

b:35.6
occ:1.00
 O B:HOH727 2.0 33.3 1.0
O B:HIS347 2.1 39.3 1.0
O B:GLY345 2.3 31.1 1.0
O B:GLY297 2.4 35.0 1.0
O B:ASP293 2.5 25.6 1.0
OD2 B:ASP324 2.5 37.0 1.0
C B:GLY345 3.2 38.8 1.0
C B:HIS347 3.3 36.0 1.0
CG B:ASP324 3.5 42.1 1.0
C B:GLY297 3.5 34.3 1.0
C B:ASP293 3.6 25.6 1.0
O B:GLY346 3.8 38.4 1.0
CA B:GLY348 3.8 34.1 1.0
CA B:GLY345 3.9 43.1 1.0
C B:GLY346 4.0 37.4 1.0
N B:GLY348 4.0 37.3 1.0
CA B:ASN294 4.1 31.2 1.0
N B:SER298 4.2 34.5 1.0
OD1 B:ASP324 4.2 41.0 1.0
N B:GLY346 4.2 35.8 1.0
CA B:SER298 4.3 32.2 1.0
N B:HIS347 4.3 38.0 1.0
N B:ASN294 4.3 25.7 1.0
CB B:ASP324 4.3 38.1 1.0
C B:ASN294 4.3 30.1 1.0
CA B:HIS347 4.4 36.6 1.0
N B:GLY297 4.5 35.7 1.0
CA B:GLY297 4.5 35.8 1.0
CA B:GLY346 4.6 40.6 1.0
N B:TRP295 4.7 31.2 1.0
O B:GLU344 4.7 48.5 1.0
O B:ASN294 4.7 36.6 1.0
CA B:ASP293 4.8 24.7 1.0
OD1 B:ASP293 4.9 31.5 1.0
O B:PRO326 4.9 40.2 1.0
N B:ASP293 4.9 24.9 1.0
CB B:SER298 4.9 31.1 1.0

Calcium binding site 4 out of 5 in 4gzt

Go back to Calcium Binding Sites List in 4gzt
Calcium binding site 4 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca510

b:38.1
occ:1.00
 O C:HOH747 2.0 42.4 1.0
O C:ASP293 2.2 27.1 1.0
O C:GLY297 2.3 37.7 1.0
O C:HIS347 2.3 31.1 1.0
O C:GLY345 2.4 41.0 1.0
OD2 C:ASP324 2.7 38.1 1.0
C C:ASP293 3.5 27.7 1.0
C C:GLY297 3.5 35.0 1.0
C C:GLY345 3.5 41.2 1.0
C C:HIS347 3.6 32.5 1.0
CG C:ASP324 3.6 38.3 1.0
CA C:GLY348 4.0 33.1 1.0
CA C:ASN294 4.1 31.8 1.0
CA C:GLY345 4.1 45.1 1.0
O C:GLY346 4.1 39.6 1.0
N C:ASN294 4.2 27.2 1.0
N C:GLY348 4.3 31.6 1.0
C C:GLY346 4.3 36.1 1.0
N C:SER298 4.3 33.4 1.0
OD1 C:ASP324 4.3 40.3 1.0
CA C:SER298 4.4 31.2 1.0
C C:ASN294 4.4 32.2 1.0
CB C:ASP324 4.4 34.0 1.0
CA C:GLY297 4.5 35.8 1.0
OD1 C:ASP293 4.5 28.5 1.0
N C:GLY297 4.5 41.4 1.0
N C:GLY346 4.5 41.6 1.0
CA C:ASP293 4.5 26.6 1.0
N C:HIS347 4.6 32.6 1.0
N C:TRP295 4.7 34.6 1.0
CB C:ASP293 4.7 26.6 1.0
CA C:HIS347 4.7 31.2 1.0
N C:ASP293 4.8 29.6 1.0
CA C:GLY346 4.8 36.2 1.0
O C:GLU344 4.9 46.2 1.0
O C:ASN294 4.9 33.1 1.0
O C:PRO326 5.0 39.5 1.0
CG C:ASP293 5.0 30.0 1.0

Calcium binding site 5 out of 5 in 4gzt

Go back to Calcium Binding Sites List in 4gzt
Calcium binding site 5 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Oseltamivir Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca513

b:33.2
occ:1.00
 O D:HOH608 2.1 32.2 1.0
O D:HIS347 2.3 32.6 1.0
O D:ASP293 2.3 32.3 1.0
O D:GLY297 2.3 33.1 1.0
OD2 D:ASP324 2.4 34.3 1.0
O D:GLY345 2.5 32.0 1.0
C D:GLY345 3.5 37.0 1.0
C D:GLY297 3.5 33.7 1.0
C D:HIS347 3.5 32.9 1.0
CG D:ASP324 3.5 37.5 1.0
C D:ASP293 3.5 27.8 1.0
CA D:GLY345 3.9 39.3 1.0
CA D:GLY348 4.1 31.9 1.0
CA D:ASN294 4.2 28.3 1.0
N D:GLY348 4.2 33.0 1.0
N D:SER298 4.3 32.0 1.0
CA D:SER298 4.3 32.1 1.0
OD1 D:ASP324 4.3 37.6 1.0
N D:ASN294 4.3 26.8 1.0
CB D:ASP324 4.4 31.6 1.0
C D:ASN294 4.5 28.8 1.0
N D:GLY297 4.5 34.5 1.0
O D:GLY346 4.5 32.8 1.0
C D:GLY346 4.5 32.6 1.0
CA D:GLY297 4.5 33.0 1.0
N D:HIS347 4.5 33.8 1.0
CA D:ASP293 4.5 28.6 1.0
OD1 D:ASP293 4.5 26.7 1.0
CB D:ASP293 4.6 27.0 1.0
N D:GLY346 4.6 35.9 1.0
CA D:HIS347 4.6 33.2 1.0
N D:TRP295 4.7 29.8 1.0
N D:ASP293 4.8 29.1 1.0
O D:GLU344 4.8 47.2 1.0
O D:ASN294 4.9 31.3 1.0
O D:PRO326 4.9 35.3 1.0
CB D:SER298 4.9 31.3 1.0

Reference:

X.Zhu, R.Mcbride, C.M.Nycholat, W.Yu, J.C.Paulson, I.A.Wilson. Influenza Virus Neuraminidases with Reduced Enzymatic Activity That Avidly Bind Sialic Acid Receptors. J.Virol. V. 86 13371 2012.
ISSN: ISSN 0022-538X
PubMed: 23015718
DOI: 10.1128/JVI.01426-12
Page generated: Sat Dec 12 04:49:23 2020

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