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Calcium in PDB 3b7e: Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir

Enzymatic activity of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir

All present enzymatic activity of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir:
3.2.1.18;

Protein crystallography data

The structure of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir, PDB code: 3b7e was solved by X.Xu, X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.71 / 1.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.044, 129.247, 118.845, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 16

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir (pdb code 3b7e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir, PDB code: 3b7e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3b7e

Go back to Calcium Binding Sites List in 3b7e
Calcium binding site 1 out of 5 in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:10.1
occ:1.00
 OD1 A:ASN381 2.3 11.1 1.0
OD1 A:ASP379 2.3 9.8 1.0
OD1 A:ASP387 2.4 10.7 1.0
O A:SER389 2.4 11.4 1.0
O A:HOH1064 2.4 13.3 1.0
O A:HOH1071 2.4 11.0 1.0
OD2 A:ASP379 2.6 10.2 1.0
CG A:ASP379 2.8 8.7 1.0
CG A:ASP387 3.3 12.6 1.0
CG A:ASN381 3.4 9.8 1.0
C A:SER389 3.5 11.7 1.0
OD2 A:ASP387 3.5 13.6 1.0
ND2 A:ASN381 3.9 11.3 1.0
O A:ASP387 4.0 10.9 1.0
N A:SER389 4.1 10.7 1.0
CA A:SER389 4.2 11.4 1.0
CB A:ASP379 4.3 6.9 1.0
CB A:SER389 4.4 12.5 1.0
N A:GLY382 4.4 8.2 1.0
C A:ASP387 4.4 10.9 1.0
N A:ASN381 4.5 8.7 1.0
C A:ASN381 4.5 8.7 1.0
CA A:GLY382 4.5 7.8 1.0
N A:PHE390 4.5 12.0 1.0
CB A:ASP387 4.6 11.0 1.0
CB A:ASN381 4.7 8.6 1.0
O A:HOH1093 4.7 14.9 1.0
CA A:ASN381 4.8 8.0 1.0
OG A:SER319 4.8 10.7 1.0
CA A:PHE390 4.8 10.8 1.0
C A:SER388 4.8 12.4 1.0
CA A:ASP379 4.9 8.2 1.0
O A:ASN381 4.9 9.1 1.0
CA A:ASP387 4.9 11.0 1.0
O A:HOH1337 5.0 42.4 1.0

Calcium binding site 2 out of 5 in 3b7e

Go back to Calcium Binding Sites List in 3b7e
Calcium binding site 2 out of 5 in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:7.8
occ:1.00
 OD2 A:ASP324 2.3 7.5 1.0
O A:ASP293 2.3 8.1 1.0
O A:GLY345 2.4 9.2 1.0
O A:ASN347 2.4 8.1 1.0
O A:GLY297 2.4 8.4 1.0
O A:HOH1041 2.4 9.3 1.0
C A:GLY345 3.4 10.4 1.0
CG A:ASP324 3.5 8.3 1.0
C A:GLY297 3.5 8.0 1.0
C A:ASN347 3.5 8.8 1.0
C A:ASP293 3.6 7.4 1.0
CA A:GLY348 4.0 7.2 1.0
O A:HOH1021 4.1 8.6 1.0
CA A:GLY345 4.1 9.9 1.0
O A:ALA346 4.2 9.8 1.0
C A:ALA346 4.2 9.2 1.0
CB A:ASP324 4.2 8.7 1.0
N A:GLY348 4.2 8.4 1.0
CA A:ASN294 4.3 8.2 1.0
N A:GLY297 4.3 8.8 1.0
N A:SER298 4.3 7.8 1.0
OD1 A:ASP324 4.3 8.7 1.0
CA A:SER298 4.4 8.7 1.0
N A:ASN294 4.4 7.0 1.0
N A:ASN347 4.4 8.8 1.0
N A:ALA346 4.5 8.9 1.0
CA A:GLY297 4.5 8.3 1.0
CA A:ASP293 4.6 7.8 1.0
CA A:ASN347 4.6 9.7 0.5
CA A:ASN347 4.6 9.6 0.5
O A:ASN344 4.7 11.4 1.0
C A:ASN294 4.7 8.3 1.0
CA A:ALA346 4.7 9.5 1.0
CB A:ASP293 4.7 7.7 1.0
OD1 A:ASP293 4.8 8.2 1.0
N A:ASP293 4.8 7.3 1.0
O A:PRO326 4.9 9.4 1.0

Calcium binding site 3 out of 5 in 3b7e

Go back to Calcium Binding Sites List in 3b7e
Calcium binding site 3 out of 5 in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:31.8
occ:0.50
 O A:HOH1480 2.5 26.5 1.0
O A:HOH1481 2.5 26.5 1.0
O A:HOH1479 3.1 33.0 0.5
OD2 B:ASP113 4.3 14.9 1.0
OD2 A:ASP113 4.4 13.3 1.0
OD1 B:ASP113 4.4 15.3 1.0
O A:HOH1471 4.5 40.9 1.0
OD1 A:ASP113 4.5 13.2 1.0
CG B:ASP113 4.8 13.2 1.0
CG A:ASP113 4.9 12.7 1.0

Calcium binding site 4 out of 5 in 3b7e

Go back to Calcium Binding Sites List in 3b7e
Calcium binding site 4 out of 5 in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:10.4
occ:1.00
 OD1 B:ASN381 2.3 10.3 1.0
OD1 B:ASP379 2.4 9.8 1.0
O B:HOH1076 2.4 14.0 1.0
OD1 B:ASP387 2.4 11.3 1.0
O B:SER389 2.4 11.4 1.0
O B:HOH1054 2.4 11.7 1.0
OD2 B:ASP379 2.6 10.2 1.0
CG B:ASP379 2.8 11.6 1.0
CG B:ASP387 3.3 11.6 1.0
CG B:ASN381 3.4 9.9 1.0
C B:SER389 3.5 11.5 1.0
OD2 B:ASP387 3.5 12.1 1.0
O B:ASP387 4.0 10.9 1.0
ND2 B:ASN381 4.0 10.9 1.0
N B:SER389 4.1 10.4 1.0
CA B:SER389 4.2 11.4 1.0
CB B:ASP379 4.3 8.5 1.0
CB B:SER389 4.3 12.4 1.0
N B:GLY382 4.4 8.3 1.0
C B:ASP387 4.4 11.2 1.0
C B:ASN381 4.5 8.6 1.0
CA B:GLY382 4.5 8.2 1.0
N B:ASN381 4.5 8.7 1.0
N B:PHE390 4.6 11.6 1.0
CB B:ASP387 4.6 10.8 1.0
O B:HOH1293 4.6 31.6 1.0
CB B:ASN381 4.7 8.5 1.0
OG B:SER319 4.7 10.7 1.0
O B:HOH1094 4.8 15.4 1.0
CA B:ASN381 4.8 8.1 1.0
CA B:PHE390 4.8 10.9 1.0
C B:SER388 4.9 11.9 1.0
O B:ASN381 4.9 8.6 1.0
CA B:ASP387 4.9 10.7 1.0
CA B:ASP379 4.9 7.5 1.0

Calcium binding site 5 out of 5 in 3b7e

Go back to Calcium Binding Sites List in 3b7e
Calcium binding site 5 out of 5 in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain in Complex with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:7.4
occ:1.00
 OD2 B:ASP324 2.3 7.4 1.0
O B:ASP293 2.3 7.6 1.0
O B:ASN347 2.4 8.5 1.0
O B:GLY345 2.4 8.7 1.0
O B:GLY297 2.4 8.5 1.0
O B:HOH1041 2.4 8.6 1.0
C B:GLY345 3.4 10.3 1.0
CG B:ASP324 3.5 8.8 1.0
C B:GLY297 3.5 8.0 1.0
C B:ASN347 3.5 8.7 1.0
C B:ASP293 3.6 6.9 1.0
CA B:GLY348 4.0 7.7 1.0
CA B:GLY345 4.1 9.6 1.0
O B:HOH1014 4.1 7.7 1.0
C B:ALA346 4.2 9.0 1.0
O B:ALA346 4.2 9.9 1.0
N B:GLY348 4.2 7.9 1.0
CB B:ASP324 4.3 7.0 1.0
CA B:ASN294 4.3 7.5 1.0
N B:SER298 4.3 7.9 1.0
N B:GLY297 4.3 8.6 1.0
CA B:SER298 4.3 8.7 1.0
OD1 B:ASP324 4.3 8.5 1.0
N B:ASN294 4.4 7.8 1.0
N B:ALA346 4.4 8.6 1.0
N B:ASN347 4.4 9.4 1.0
CA B:GLY297 4.5 8.0 1.0
CA B:ASP293 4.6 7.8 1.0
O B:ASN344 4.6 10.9 1.0
CA B:ALA346 4.6 9.2 1.0
CA B:ASN347 4.6 9.6 0.5
CA B:ASN347 4.7 9.4 0.5
C B:ASN294 4.7 7.7 1.0
CB B:ASP293 4.7 8.0 1.0
OD1 B:ASP293 4.8 8.8 1.0
N B:ASP293 4.8 7.6 1.0
O B:PRO326 4.9 9.1 1.0

Reference:

X.Xu, X.Zhu, R.A.Dwek, J.Stevens, I.A.Wilson. Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase J.Virol. V. 82 10493 2008.
ISSN: ISSN 0022-538X
PubMed: 18715929
DOI: 10.1128/JVI.00959-08
Page generated: Sat Dec 12 04:05:41 2020

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