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Calcium in PDB 4gzs: N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Hepes

Protein crystallography data

The structure of N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Hepes, PDB code: 4gzs 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 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.812, 110.205, 110.587, 90.00, 97.46, 90.00
R / Rfree (%) 22.5 / 28.7

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 4gzs

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Calcium binding site 1 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Hepes


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 Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:34.4
occ:1.00
 O A:HIS347 2.4 29.0 1.0
O A:GLY345 2.4 34.9 1.0
O A:ASP293 2.6 25.9 1.0
OD2 A:ASP324 2.6 33.4 1.0
O A:GLY297 2.7 29.0 1.0
C A:GLY345 3.2 35.1 1.0
CG A:ASP324 3.5 32.2 1.0
O A:GLY346 3.5 30.9 1.0
C A:GLY297 3.5 28.1 1.0
C A:HIS347 3.6 28.8 1.0
C A:ASP293 3.8 26.0 1.0
CA A:GLY345 3.8 36.1 1.0
C A:GLY346 3.9 31.1 1.0
OD1 A:ASP324 4.0 31.7 1.0
N A:SER298 4.1 27.4 1.0
CA A:GLY348 4.2 26.4 1.0
CA A:SER298 4.2 26.6 1.0
N A:GLY346 4.2 33.8 1.0
CA A:ASN294 4.2 26.7 1.0
N A:GLY348 4.3 28.0 1.0
CB A:ASP324 4.4 30.6 1.0
OD1 A:ASP293 4.4 29.4 1.0
N A:HIS347 4.5 29.9 1.0
O A:GLU344 4.5 39.1 1.0
N A:ASN294 4.5 26.3 1.0
N A:GLY297 4.5 28.9 1.0
CA A:GLY297 4.5 28.2 1.0
CA A:GLY346 4.6 32.2 1.0
C A:ASN294 4.6 27.0 1.0
CA A:HIS347 4.7 29.4 1.0
O A:PRO326 4.8 32.9 1.0
CB A:SER298 4.9 26.2 1.0
CD A:PRO326 4.9 31.8 1.0
N A:TRP295 4.9 27.0 1.0
CA A:ASP293 4.9 25.6 1.0
N A:GLY345 5.0 37.9 1.0

Calcium binding site 2 out of 5 in 4gzs

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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 Hepes


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 Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:30.8
occ:1.00
 O B:GLY345 2.4 37.1 1.0
O B:HIS347 2.4 32.8 1.0
O B:GLY297 2.4 28.1 1.0
OD2 B:ASP324 2.4 24.7 1.0
O B:ASP293 2.6 26.0 1.0
CG B:ASP324 3.3 26.0 1.0
C B:GLY345 3.4 37.4 1.0
C B:GLY297 3.5 27.5 1.0
O B:GLY346 3.5 34.5 1.0
C B:HIS347 3.6 32.9 1.0
C B:ASP293 3.8 25.5 1.0
C B:GLY346 3.9 34.8 1.0
OD1 B:ASP324 4.0 24.8 1.0
CA B:GLY345 4.0 38.1 1.0
CA B:SER298 4.1 26.4 1.0
CB B:ASP324 4.1 26.5 1.0
N B:SER298 4.2 26.8 1.0
CA B:GLY348 4.2 30.5 1.0
N B:GLY346 4.3 36.5 1.0
N B:GLY348 4.3 31.8 1.0
CA B:ASN294 4.3 25.0 1.0
N B:HIS347 4.4 34.3 1.0
C B:ASN294 4.5 25.4 1.0
N B:ASN294 4.6 25.5 1.0
CA B:GLY346 4.6 35.4 1.0
CA B:GLY297 4.6 27.9 1.0
CA B:HIS347 4.6 33.5 1.0
N B:GLY297 4.7 28.3 1.0
CB B:SER298 4.7 25.6 1.0
O B:GLU344 4.7 41.2 1.0
N B:TRP295 4.8 25.9 1.0
CA B:ASP293 4.9 25.3 1.0
OD1 B:ASP293 4.9 28.9 1.0
O B:ASN294 4.9 25.8 1.0
O B:PRO326 4.9 30.4 1.0
CB B:ASP293 5.0 25.1 1.0

Calcium binding site 3 out of 5 in 4gzs

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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 Hepes


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 Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:65.0
occ:1.00
 OD2 D:ASP113 4.7 28.1 1.0
OD2 C:ASP113 4.9 32.8 1.0

Calcium binding site 4 out of 5 in 4gzs

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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 Hepes


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 Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:34.1
occ:1.00
 O C:GLY297 2.3 28.0 1.0
OD2 C:ASP324 2.3 36.7 1.0
O C:HIS347 2.4 35.5 1.0
O C:GLY345 2.4 41.1 1.0
O C:ASP293 2.4 27.1 1.0
O C:HOH601 2.5 23.4 1.0
CG C:ASP324 3.5 36.8 1.0
C C:GLY297 3.5 28.1 1.0
C C:GLY345 3.5 41.3 1.0
C C:HIS347 3.6 35.6 1.0
C C:ASP293 3.6 26.8 1.0
O C:HOH618 3.8 23.6 1.0
CA C:GLY348 4.0 32.9 1.0
CA C:ASN294 4.2 27.4 1.0
O C:GLY346 4.2 38.3 1.0
OD1 C:ASP324 4.2 38.2 1.0
CA C:GLY345 4.2 42.0 1.0
N C:GLY348 4.3 34.4 1.0
C C:GLY346 4.3 38.2 1.0
N C:ASN294 4.3 26.9 1.0
N C:SER298 4.3 27.7 1.0
CB C:ASP324 4.4 35.5 1.0
CA C:SER298 4.4 27.4 1.0
CA C:GLY297 4.4 28.3 1.0
C C:ASN294 4.4 27.7 1.0
N C:GLY297 4.4 28.7 1.0
OD1 C:ASP293 4.6 25.8 1.0
N C:GLY346 4.6 40.5 1.0
N C:HIS347 4.6 37.4 1.0
CA C:ASP293 4.7 26.7 1.0
CA C:HIS347 4.7 36.3 1.0
N C:ASP293 4.8 26.8 1.0
N C:TRP295 4.8 28.3 1.0
O C:ASN294 4.8 27.1 1.0
CA C:GLY346 4.8 39.1 1.0
CB C:ASP293 4.9 27.1 1.0

Calcium binding site 5 out of 5 in 4gzs

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Calcium binding site 5 out of 5 in the N2 Neuraminidase D151G Mutant of A/Tanzania/205/2010 H3N2 in Complex with Hepes


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 Hepes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:32.1
occ:1.00
 OD2 D:ASP324 2.2 29.8 1.0
O D:GLY297 2.3 29.0 1.0
O D:HOH608 2.3 27.8 1.0
O D:ASP293 2.3 27.2 1.0
O D:HIS347 2.4 33.0 1.0
O D:GLY345 2.4 36.8 1.0
CG D:ASP324 3.4 31.5 1.0
O D:HOH684 3.4 12.9 1.0
C D:GLY297 3.5 29.0 1.0
C D:GLY345 3.5 37.0 1.0
C D:ASP293 3.6 27.3 1.0
C D:HIS347 3.6 33.0 1.0
CA D:GLY345 4.1 37.3 1.0
CA D:GLY348 4.1 30.5 1.0
OD1 D:ASP324 4.3 29.8 1.0
N D:SER298 4.3 28.8 1.0
N D:GLY348 4.3 32.2 1.0
CA D:SER298 4.3 28.3 1.0
OD1 D:ASP293 4.3 31.0 1.0
CB D:ASP324 4.3 31.8 1.0
CA D:ASN294 4.4 28.2 1.0
C D:GLY346 4.4 35.0 1.0
N D:ASN294 4.4 27.6 1.0
O D:GLY346 4.5 35.0 1.0
CA D:ASP293 4.5 26.6 1.0
CA D:GLY297 4.5 28.9 1.0
O D:GLU344 4.5 38.9 1.0
N D:GLY297 4.6 28.5 1.0
N D:HIS347 4.6 34.6 1.0
C D:ASN294 4.6 28.0 1.0
N D:ASP293 4.6 26.2 1.0
CB D:ASP293 4.6 27.1 1.0
N D:GLY346 4.6 36.3 1.0
CA D:HIS347 4.7 33.4 1.0
N D:TRP295 4.8 28.1 1.0
CG D:ASP293 4.9 29.1 1.0
CA D:GLY346 5.0 35.5 1.0
O D:PRO326 5.0 36.4 1.0
O D:ASN294 5.0 27.4 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: Sun Jul 14 07:29:33 2024

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