Atomistry » Calcium » PDB 3b1u-3biw » 3beq
Atomistry »
  Calcium »
    PDB 3b1u-3biw »
      3beq »

Calcium in PDB 3beq: Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain

Enzymatic activity of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain

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

Protein crystallography data

The structure of Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain, PDB code: 3beq 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) 44.86 / 1.64
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 117.728, 138.472, 117.860, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Neuraminidase of A/Brevig Mission/1/1918 H1N1 Strain (pdb code 3beq). 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, PDB code: 3beq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3beq

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:14.1
occ:1.00
 O A:ASN347 2.3 14.9 0.5
OD2 A:ASP324 2.3 12.6 1.0
O A:ASP293 2.4 13.6 1.0
O A:GLY345 2.4 16.5 1.0
O A:GLY297 2.4 13.4 1.0
O A:ASN347 2.4 14.6 0.5
O A:HOH3044 2.4 13.7 1.0
CG A:ASP324 3.5 12.0 1.0
C A:GLY345 3.5 16.3 1.0
C A:ASN347 3.5 14.7 0.5
C A:GLY297 3.5 13.7 1.0
C A:ASN347 3.5 14.6 0.5
C A:ASP293 3.6 12.4 1.0
O A:HOH3007 4.0 11.9 1.0
CA A:GLY348 4.0 13.4 1.0
O A:ALA346 4.1 16.2 1.0
CA A:GLY345 4.2 15.5 1.0
C A:ALA346 4.2 14.8 1.0
CB A:ASP324 4.2 13.3 1.0
N A:GLY348 4.2 15.4 1.0
CA A:ASN294 4.3 12.8 1.0
N A:GLY297 4.3 14.5 1.0
OD1 A:ASP324 4.3 13.8 1.0
N A:SER298 4.4 13.0 1.0
CA A:SER298 4.4 14.2 1.0
N A:ASN294 4.4 13.9 1.0
N A:ASN347 4.4 15.3 0.5
N A:ASN347 4.4 15.3 0.5
CA A:GLY297 4.5 13.1 1.0
N A:ALA346 4.5 15.9 1.0
CA A:ASP293 4.6 12.3 1.0
CA A:ASN347 4.6 15.4 0.5
CA A:ASN347 4.6 15.2 0.5
O A:ASN344 4.6 15.4 1.0
C A:ASN294 4.7 13.2 1.0
CA A:ALA346 4.7 15.9 1.0
N A:ASP293 4.7 13.9 1.0
CB A:ASP293 4.7 14.0 1.0
OD1 A:ASP293 4.7 14.1 1.0
O A:PRO326 4.9 16.0 1.0

Calcium binding site 2 out of 5 in 3beq

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:14.9
occ:1.00
 OD1 A:ASN381 2.2 11.9 1.0
OD1 A:ASP387 2.4 17.0 1.0
OD1 A:ASP379 2.4 15.4 1.0
O A:SER389 2.4 16.6 1.0
O A:HOH3043 2.4 17.9 1.0
O A:HOH3108 2.5 22.2 1.0
OD2 A:ASP379 2.6 15.3 1.0
CG A:ASP379 2.8 14.7 1.0
CG A:ASP387 3.3 17.4 1.0
CG A:ASN381 3.4 14.0 1.0
C A:SER389 3.5 18.0 1.0
OD2 A:ASP387 3.6 21.4 1.0
ND2 A:ASN381 3.9 12.5 1.0
O A:ASP387 4.0 15.4 1.0
N A:SER389 4.1 19.2 1.0
CA A:SER389 4.2 16.4 1.0
CB A:ASP379 4.3 12.8 1.0
N A:GLY382 4.4 12.7 1.0
CB A:SER389 4.4 19.5 1.0
C A:ASP387 4.4 17.1 1.0
N A:ASN381 4.4 12.0 1.0
C A:ASN381 4.5 13.9 1.0
CA A:GLY382 4.5 12.5 1.0
N A:PHE390 4.6 16.4 1.0
CB A:ASP387 4.6 16.3 1.0
CB A:ASN381 4.6 13.2 1.0
CA A:ASN381 4.7 12.8 1.0
O A:HOH3073 4.7 18.2 1.0
OG A:SER319 4.7 13.5 1.0
O A:HOH3371 4.8 42.9 1.0
CA A:PHE390 4.8 15.7 1.0
C A:SER388 4.9 20.1 1.0
O A:ASN381 4.9 13.1 1.0
CA A:ASP379 4.9 11.1 1.0
CA A:ASP387 4.9 16.4 1.0
C A:ASP379 5.0 11.6 1.0

Calcium binding site 3 out of 5 in 3beq

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:65.1
occ:0.50
 O B:HOH3262 2.5 36.5 1.0
O A:HOH3186 2.6 33.8 1.0
O B:HOH3278 2.9 36.6 0.5
OD2 B:ASP113 4.2 17.7 1.0
OD2 A:ASP113 4.3 17.2 1.0
OD1 B:ASP113 4.4 19.1 1.0
OD1 A:ASP113 4.5 20.3 1.0
CG B:ASP113 4.7 19.3 1.0
CG A:ASP113 4.8 17.6 1.0
O B:HOH3341 4.9 41.9 1.0

Calcium binding site 4 out of 5 in 3beq

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:15.8
occ:1.00
 OD1 B:ASN381 2.2 12.1 1.0
O B:HOH3092 2.3 20.9 1.0
OD1 B:ASP379 2.4 15.0 1.0
OD1 B:ASP387 2.4 15.7 1.0
O B:SER389 2.4 16.8 1.0
O B:HOH3023 2.4 17.3 1.0
OD2 B:ASP379 2.6 14.8 1.0
CG B:ASP379 2.8 17.8 1.0
CG B:ASP387 3.3 15.6 1.0
CG B:ASN381 3.3 14.0 1.0
C B:SER389 3.5 18.1 1.0
OD2 B:ASP387 3.5 22.9 1.0
O B:ASP387 3.9 18.1 1.0
ND2 B:ASN381 3.9 14.7 1.0
N B:SER389 4.0 16.5 1.0
CA B:SER389 4.1 16.7 1.0
CB B:SER389 4.3 19.0 1.0
CB B:ASP379 4.3 11.3 1.0
C B:ASP387 4.4 17.5 1.0
N B:GLY382 4.4 12.4 1.0
C B:ASN381 4.5 13.4 1.0
CA B:GLY382 4.5 10.8 1.0
N B:ASN381 4.5 12.0 1.0
N B:PHE390 4.6 15.1 1.0
CB B:ASP387 4.6 19.8 1.0
CB B:ASN381 4.6 13.4 1.0
O B:HOH3260 4.6 38.0 1.0
O B:HOH3087 4.7 20.5 1.0
CA B:ASN381 4.7 12.6 1.0
OG B:SER319 4.7 15.1 1.0
C B:SER388 4.8 18.6 1.0
CA B:PHE390 4.9 14.8 1.0
O B:ASN381 4.9 13.7 1.0
CA B:ASP387 4.9 17.1 1.0
CA B:ASP379 4.9 10.6 1.0

Calcium binding site 5 out of 5 in 3beq

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:14.5
occ:1.00
 OD2 B:ASP324 2.3 12.4 1.0
O B:ASN347 2.3 14.3 0.5
O B:GLY345 2.4 17.2 1.0
O B:GLY297 2.4 15.0 1.0
O B:ASP293 2.4 14.7 1.0
O B:HOH3057 2.4 18.2 1.0
O B:ASN347 2.4 14.0 0.5
CG B:ASP324 3.4 14.1 1.0
C B:GLY345 3.5 18.1 1.0
C B:GLY297 3.5 15.3 1.0
C B:ASN347 3.5 14.3 0.5
C B:ASN347 3.6 14.1 0.5
C B:ASP293 3.6 13.3 1.0
CA B:GLY348 4.0 14.2 1.0
O B:HOH3013 4.1 12.9 1.0
O B:ALA346 4.1 16.2 1.0
CA B:GLY345 4.1 16.5 1.0
C B:ALA346 4.2 14.0 1.0
CB B:ASP324 4.2 13.1 1.0
N B:GLY348 4.3 13.9 1.0
N B:GLY297 4.3 16.6 1.0
CA B:ASN294 4.3 13.5 1.0
OD1 B:ASP324 4.3 13.6 1.0
N B:SER298 4.3 13.2 1.0
CA B:SER298 4.4 15.2 1.0
N B:ASN347 4.4 14.5 0.5
N B:ASN294 4.4 13.4 1.0
N B:ASN347 4.4 14.3 0.5
CA B:GLY297 4.5 15.0 1.0
N B:ALA346 4.5 17.5 1.0
CA B:ASP293 4.6 13.5 1.0
CA B:ASN347 4.6 15.4 0.5
CA B:ASN347 4.6 14.7 0.5
O B:ASN344 4.7 17.8 1.0
CA B:ALA346 4.7 14.9 1.0
C B:ASN294 4.7 14.6 1.0
CB B:ASP293 4.7 14.2 1.0
N B:ASP293 4.8 14.1 1.0
OD1 B:ASP293 4.8 14.8 1.0
O B:PRO326 4.9 16.7 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 Jul 13 08:15:25 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