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Calcium in PDB 4gzw: N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor

Protein crystallography data

The structure of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor, PDB code: 4gzw 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) 50.00 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.439, 110.555, 109.928, 90.00, 97.79, 90.00
R / Rfree (%) 19.7 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor (pdb code 4gzw). 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 Avian Sialic Acid Receptor, PDB code: 4gzw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4gzw

Go back to Calcium Binding Sites List in 4gzw
Calcium binding site 1 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor


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 Avian Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca513

b:27.6
occ:1.00
 O A:HIS347 2.3 32.0 1.0
O A:GLY345 2.3 38.5 1.0
O A:ASP293 2.4 25.1 1.0
O A:GLY297 2.5 28.8 1.0
OD2 A:ASP324 2.5 31.2 1.0
C A:GLY345 3.4 38.4 1.0
C A:HIS347 3.5 32.1 1.0
C A:GLY297 3.6 28.3 1.0
C A:ASP293 3.6 25.0 1.0
CG A:ASP324 3.6 31.5 1.0
O A:GLY346 4.0 35.2 1.0
CA A:GLY345 4.0 38.9 1.0
CA A:GLY348 4.1 29.2 1.0
CA A:ASN294 4.1 26.3 1.0
C A:GLY346 4.2 35.3 1.0
O A:HOH907 4.2 33.1 1.0
N A:GLY348 4.3 30.8 1.0
N A:SER298 4.3 27.9 1.0
N A:ASN294 4.3 25.4 1.0
CA A:SER298 4.4 26.9 1.0
C A:ASN294 4.4 26.6 1.0
CB A:ASP324 4.4 31.8 1.0
N A:HIS347 4.5 34.1 1.0
N A:GLY346 4.5 37.5 1.0
OD1 A:ASP324 4.5 30.9 1.0
N A:GLY297 4.6 29.1 1.0
CA A:GLY297 4.6 28.7 1.0
CA A:HIS347 4.6 33.0 1.0
OD1 A:ASP293 4.6 22.4 1.0
O A:GLU344 4.7 40.5 1.0
CA A:ASP293 4.8 24.7 1.0
N A:TRP295 4.8 27.4 1.0
O A:ASN294 4.8 26.6 1.0
CA A:GLY346 4.8 36.0 1.0
N A:ASP293 5.0 24.8 1.0

Calcium binding site 2 out of 5 in 4gzw

Go back to Calcium Binding Sites List in 4gzw
Calcium binding site 2 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor


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 Avian Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca512

b:30.9
occ:1.00
 O B:HOH906 2.1 32.7 1.0
O B:ASP293 2.3 23.5 1.0
O B:GLY297 2.3 29.0 1.0
O B:GLY345 2.4 36.7 1.0
OD2 B:ASP324 2.4 35.0 1.0
O B:HIS347 2.5 32.0 1.0
C B:GLY297 3.5 28.9 1.0
C B:GLY345 3.5 36.9 1.0
C B:ASP293 3.5 23.8 1.0
CG B:ASP324 3.5 34.4 1.0
C B:HIS347 3.7 32.1 1.0
CA B:GLY348 4.0 29.6 1.0
CA B:GLY345 4.1 37.7 1.0
CA B:ASN294 4.2 24.7 1.0
N B:SER298 4.2 28.6 1.0
CA B:SER298 4.2 27.8 1.0
N B:ASN294 4.3 24.1 1.0
CB B:ASP324 4.3 34.2 1.0
N B:GLY348 4.3 31.1 1.0
O B:GLY346 4.3 34.1 1.0
OD1 B:ASP324 4.4 34.7 1.0
C B:GLY346 4.5 34.4 1.0
N B:GLY297 4.5 29.4 1.0
C B:ASN294 4.5 25.5 1.0
CA B:GLY297 4.5 28.9 1.0
CA B:ASP293 4.6 23.6 1.0
N B:GLY346 4.6 36.1 1.0
OD1 B:ASP293 4.6 27.3 1.0
N B:ASP293 4.7 23.1 1.0
N B:HIS347 4.7 33.6 1.0
O B:GLU344 4.8 39.6 1.0
CB B:ASP293 4.8 23.5 1.0
CA B:HIS347 4.9 33.1 1.0
O B:ASN294 4.9 25.5 1.0
N B:TRP295 4.9 26.4 1.0
CA B:GLY346 4.9 35.0 1.0

Calcium binding site 3 out of 5 in 4gzw

Go back to Calcium Binding Sites List in 4gzw
Calcium binding site 3 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor


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 Avian Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca812

b:29.3
occ:1.00
 O C:HOH982 2.3 44.2 1.0
O C:GLY345 2.4 38.1 1.0
OD2 C:ASP324 2.4 28.3 1.0
O C:ASP293 2.4 23.8 1.0
O C:HIS347 2.4 32.9 1.0
O C:GLY297 2.5 27.6 1.0
C C:GLY345 3.3 38.5 1.0
CG C:ASP324 3.4 29.6 1.0
C C:GLY297 3.5 27.6 1.0
C C:HIS347 3.6 33.5 1.0
C C:ASP293 3.6 24.3 1.0
CA C:GLY345 3.9 39.0 1.0
O C:HOH983 4.0 20.6 1.0
O C:GLY346 4.0 35.7 1.0
CA C:SER298 4.1 27.0 1.0
N C:SER298 4.1 27.5 1.0
CA C:GLY348 4.1 30.9 1.0
CB C:ASP324 4.2 29.6 1.0
C C:GLY346 4.3 35.9 1.0
OD1 C:ASP324 4.3 30.2 1.0
CA C:ASN294 4.3 24.6 1.0
N C:GLY348 4.3 32.4 1.0
N C:ASN294 4.4 24.2 1.0
N C:GLY346 4.5 37.9 1.0
N C:GLY297 4.5 28.3 1.0
CA C:GLY297 4.5 27.9 1.0
N C:HIS347 4.6 35.1 1.0
C C:ASN294 4.6 25.1 1.0
O C:GLU344 4.6 40.7 1.0
CA C:ASP293 4.7 24.2 1.0
OD1 C:ASP293 4.7 26.6 1.0
CA C:HIS347 4.7 34.3 1.0
CB C:SER298 4.7 27.2 1.0
CB C:ASP293 4.8 24.4 1.0
CA C:GLY346 4.8 36.8 1.0
O C:PRO326 4.9 31.5 1.0
N C:ASP293 4.9 24.4 1.0
N C:TRP295 4.9 25.4 1.0

Calcium binding site 4 out of 5 in 4gzw

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Calcium binding site 4 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor


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 Avian Sialic Acid Receptor within 5.0Å range:

Calcium binding site 5 out of 5 in 4gzw

Go back to Calcium Binding Sites List in 4gzw
Calcium binding site 5 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Avian Sialic Acid Receptor


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 Avian Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca513

b:26.4
occ:1.00
 O D:HOH613 2.2 25.6 1.0
O D:ASP293 2.3 24.9 1.0
O D:GLY297 2.3 25.3 1.0
O D:HIS347 2.5 28.7 1.0
O D:GLY345 2.5 34.2 1.0
OD2 D:ASP324 2.5 29.6 1.0
CG D:ASP324 3.4 31.1 1.0
C D:ASP293 3.5 24.6 1.0
C D:GLY297 3.5 25.7 1.0
C D:GLY345 3.5 34.2 1.0
C D:HIS347 3.6 28.7 1.0
CA D:GLY348 4.1 26.3 1.0
CA D:GLY345 4.1 35.0 1.0
OD1 D:ASP324 4.1 30.6 1.0
CA D:ASN294 4.2 25.1 1.0
O D:HOH674 4.2 26.7 1.0
CB D:ASP324 4.2 30.9 1.0
N D:ASN294 4.3 24.6 1.0
O D:GLY346 4.3 30.9 1.0
N D:GLY348 4.3 27.6 1.0
N D:SER298 4.4 25.4 1.0
CA D:SER298 4.4 25.7 1.0
C D:ASN294 4.4 25.3 1.0
C D:GLY346 4.5 31.1 1.0
CA D:GLY297 4.5 26.0 1.0
CA D:ASP293 4.5 24.4 1.0
N D:GLY297 4.5 26.5 1.0
OD1 D:ASP293 4.7 25.4 1.0
N D:GLY346 4.7 33.1 1.0
N D:HIS347 4.7 30.4 1.0
N D:ASP293 4.7 24.2 1.0
CB D:ASP293 4.7 24.2 1.0
O D:GLU344 4.8 37.2 1.0
CA D:HIS347 4.8 29.4 1.0
O D:ASN294 4.8 25.1 1.0
N D:TRP295 4.8 25.3 1.0
O D:PRO326 5.0 33.1 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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