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

Protein crystallography data

The structure of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Human Sialic Acid Receptor, PDB code: 4gzx 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 (°) 80.587, 110.176, 110.043, 90.00, 97.45, 90.00
R / Rfree (%) 21.2 / 27.1

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 4gzx

Go back to Calcium Binding Sites List in 4gzx
Calcium binding site 1 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Human 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 Human Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca811

b:62.4
occ:1.00
O A:HOH950 3.0 31.5 1.0
O B:HOH939 4.3 23.7 1.0
O A:HOH962 4.4 25.7 1.0
OD2 C:ASP113 4.5 31.9 1.0
OD2 D:ASP113 4.5 28.6 1.0
OD2 A:ASP113 4.7 32.6 1.0
OD2 B:ASP113 4.8 30.9 1.0

Calcium binding site 2 out of 5 in 4gzx

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Calcium binding site 2 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Human 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 Human Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca812

b:31.2
occ:1.00
O A:GLY345 2.1 37.6 1.0
O A:HIS347 2.2 32.5 1.0
O A:GLY297 2.4 24.1 1.0
O A:ASP293 2.5 23.7 1.0
OD2 A:ASP324 2.5 23.8 1.0
C A:GLY345 3.3 37.5 1.0
C A:HIS347 3.4 32.6 1.0
CG A:ASP324 3.5 26.9 1.0
C A:GLY297 3.6 23.8 1.0
C A:ASP293 3.7 23.0 1.0
O A:GLY346 3.8 35.0 1.0
C A:GLY346 4.0 35.1 1.0
CA A:GLY348 4.0 30.6 1.0
CA A:GLY345 4.0 38.2 1.0
N A:GLY348 4.2 31.6 1.0
OD1 A:ASP324 4.2 24.7 1.0
N A:GLY346 4.3 36.8 1.0
N A:HIS347 4.3 34.3 1.0
CA A:ASN294 4.3 24.1 1.0
CB A:ASP324 4.4 27.2 1.0
N A:SER298 4.5 23.2 1.0
CA A:SER298 4.5 22.8 1.0
CA A:GLY346 4.5 35.6 1.0
CA A:HIS347 4.5 33.4 1.0
N A:ASN294 4.5 23.5 1.0
C A:ASN294 4.5 24.1 1.0
O A:HOH918 4.5 19.0 1.0
N A:GLY297 4.6 23.8 1.0
CA A:GLY297 4.6 24.0 1.0
CA A:ASP293 4.8 22.4 1.0
N A:TRP295 4.8 24.3 1.0
CB A:ASP293 4.8 22.6 1.0
O A:PRO326 4.8 32.6 1.0
OD1 A:ASP293 4.9 19.6 1.0
O A:ASN294 4.9 24.7 1.0
N A:ASP293 4.9 21.9 1.0

Calcium binding site 3 out of 5 in 4gzx

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Calcium binding site 3 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Human 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 Human Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca811

b:32.6
occ:1.00
O B:GLY345 2.3 33.9 1.0
OD2 B:ASP324 2.4 29.5 1.0
O B:ASP293 2.4 24.3 1.0
O B:HIS347 2.4 30.5 1.0
O B:GLY297 2.4 26.5 1.0
C B:GLY345 3.3 34.4 1.0
O B:GLY346 3.5 31.6 1.0
CG B:ASP324 3.5 31.4 1.0
C B:HIS347 3.5 30.5 1.0
C B:GLY297 3.5 26.4 1.0
C B:ASP293 3.6 23.6 1.0
CA B:GLY345 3.9 35.1 1.0
C B:GLY346 4.0 32.0 1.0
CA B:GLY348 4.0 28.0 1.0
N B:GLY348 4.2 29.6 1.0
OD1 B:ASP324 4.2 32.5 1.0
CA B:ASN294 4.2 24.5 1.0
CA B:SER298 4.3 24.4 1.0
N B:SER298 4.3 25.5 1.0
N B:GLY346 4.3 33.5 1.0
N B:ASN294 4.4 23.9 1.0
C B:ASN294 4.4 25.1 1.0
CB B:ASP324 4.4 31.6 1.0
N B:GLY297 4.5 27.6 1.0
N B:HIS347 4.5 31.7 1.0
CA B:GLY297 4.6 27.0 1.0
CA B:GLY346 4.6 32.6 1.0
CA B:HIS347 4.6 31.3 1.0
OD1 B:ASP293 4.7 24.4 1.0
CA B:ASP293 4.7 23.1 1.0
O B:ASN294 4.7 25.0 1.0
CB B:ASP293 4.7 23.3 1.0
O B:GLU344 4.8 37.1 1.0
N B:TRP295 4.8 25.4 1.0
O B:PRO326 4.9 35.4 1.0
CB B:SER298 4.9 24.0 1.0
N B:ASP293 5.0 22.1 1.0

Calcium binding site 4 out of 5 in 4gzx

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

b:38.1
occ:1.00
O C:GLY345 2.2 40.0 1.0
O C:HIS347 2.4 36.5 1.0
O C:ASP293 2.4 25.6 1.0
OD2 C:ASP324 2.6 31.4 1.0
O C:GLY297 2.7 26.4 1.0
C C:GLY345 3.3 40.3 1.0
CG C:ASP324 3.3 30.9 1.0
C C:HIS347 3.5 36.2 1.0
C C:ASP293 3.6 25.2 1.0
C C:GLY297 3.8 25.8 1.0
CA C:GLY345 3.9 40.5 1.0
CA C:GLY348 3.9 33.6 1.0
OD1 C:ASP324 3.9 29.4 1.0
CA C:ASN294 4.2 25.9 1.0
CB C:ASP324 4.2 30.8 1.0
N C:GLY348 4.2 35.2 1.0
CA C:SER298 4.3 24.5 1.0
C C:GLY346 4.3 38.8 1.0
N C:ASN294 4.4 25.4 1.0
N C:GLY346 4.4 40.0 1.0
N C:SER298 4.4 25.3 1.0
O C:GLY346 4.4 38.9 1.0
C C:ASN294 4.4 25.8 1.0
N C:HIS347 4.5 38.0 1.0
CA C:HIS347 4.7 37.1 1.0
CA C:GLY346 4.7 39.3 1.0
CA C:ASP293 4.7 25.1 1.0
N C:TRP295 4.8 26.0 1.0
N C:GLY297 4.8 26.2 1.0
O C:ASN294 4.8 26.1 1.0
CA C:GLY297 4.8 25.9 1.0
OD1 C:ASP293 4.9 24.4 1.0
CB C:ASP293 4.9 25.1 1.0
O C:PRO326 4.9 32.6 1.0
O C:GLU344 4.9 41.5 1.0
N C:ASP293 5.0 24.5 1.0
CB C:SER298 5.0 24.3 1.0

Calcium binding site 5 out of 5 in 4gzx

Go back to Calcium Binding Sites List in 4gzx
Calcium binding site 5 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Human 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 Human Sialic Acid Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca811

b:40.8
occ:1.00
O D:GLY345 2.2 36.0 1.0
O D:HIS347 2.3 29.8 1.0
O D:GLY297 2.5 25.5 1.0
OD2 D:ASP324 2.6 29.9 1.0
O D:ASP293 2.6 23.7 1.0
C D:GLY345 3.3 36.2 1.0
C D:HIS347 3.5 30.2 1.0
CG D:ASP324 3.5 31.0 1.0
C D:GLY297 3.6 25.5 1.0
C D:ASP293 3.8 23.3 1.0
CA D:GLY345 3.9 37.2 1.0
CA D:GLY348 4.0 28.5 1.0
O D:HOH1030 4.0 23.9 1.0
CA D:SER298 4.1 25.2 1.0
N D:SER298 4.2 25.6 1.0
N D:GLY348 4.2 29.4 1.0
O D:GLY346 4.2 32.6 1.0
C D:GLY346 4.3 33.0 1.0
CB D:ASP324 4.3 31.3 1.0
OD1 D:ASP324 4.3 30.6 1.0
N D:GLY346 4.4 35.2 1.0
CA D:ASN294 4.4 23.1 1.0
N D:HIS347 4.5 32.1 1.0
N D:ASN294 4.6 23.0 1.0
CA D:GLY297 4.6 25.4 1.0
CA D:HIS347 4.7 30.8 1.0
C D:ASN294 4.7 23.1 1.0
N D:GLY297 4.7 25.6 1.0
CA D:GLY346 4.8 33.9 1.0
CB D:SER298 4.8 25.2 1.0
O D:PRO326 4.9 32.0 1.0
CA D:ASP293 4.9 23.0 1.0
N D:TRP295 4.9 23.5 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 04:49:26 2020

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