Atomistry » Calcium » PDB 4gzt-4h82 » 4gzw
Atomistry »
  Calcium »
    PDB 4gzt-4h82 »
      4gzw »

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

Go back to Calcium Binding Sites List in 4gzw
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: Sun Jul 14 07:32:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy