Atomistry » Sodium » PDB 6e8u-6eqv » 6eku
Atomistry »
  Sodium »
    PDB 6e8u-6eqv »
      6eku »

Sodium in PDB 6eku: Vibrio Cholerae Neuraminidase Complexed with Zanamivir

Enzymatic activity of Vibrio Cholerae Neuraminidase Complexed with Zanamivir

All present enzymatic activity of Vibrio Cholerae Neuraminidase Complexed with Zanamivir:
3.2.1.18;

Protein crystallography data

The structure of Vibrio Cholerae Neuraminidase Complexed with Zanamivir, PDB code: 6eku was solved by A.Schuetz, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.553, 50.344, 86.087, 90.00, 107.24, 90.00
R / Rfree (%) 16.7 / 20.3

Other elements in 6eku:

The structure of Vibrio Cholerae Neuraminidase Complexed with Zanamivir also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir (pdb code 6eku). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir, PDB code: 6eku:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6eku

Go back to Sodium Binding Sites List in 6eku
Sodium binding site 1 out of 2 in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vibrio Cholerae Neuraminidase Complexed with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:30.4
occ:1.00
O A:SER223 2.2 41.9 1.0
OD1 A:ASN221 2.3 36.0 1.0
O A:HOH1143 2.3 29.1 1.0
O A:THR226 2.5 39.6 1.0
O A:GLY96 2.7 46.0 1.0
O A:GLY99 2.7 40.2 1.0
CG A:ASN221 3.3 35.6 1.0
C A:THR226 3.3 41.4 1.0
C A:SER223 3.4 43.1 1.0
C A:GLY99 3.5 49.8 1.0
C A:GLY96 3.6 46.1 1.0
ND2 A:ASN221 3.7 34.4 1.0
CA A:ASP227 3.8 40.3 1.0
N A:ASP227 3.9 40.6 1.0
O A:SER224 3.9 56.7 1.0
C A:SER224 4.1 52.5 1.0
CA A:GLY96 4.1 43.8 1.0
N A:GLY99 4.2 50.0 1.0
N A:ARG100 4.2 40.6 1.0
N A:GLY228 4.2 36.7 1.0
CA A:ARG100 4.2 39.5 1.0
CA A:SER224 4.3 49.0 1.0
N A:SER224 4.3 45.6 1.0
N A:THR226 4.3 44.2 1.0
CA A:SER223 4.3 41.1 1.0
CA A:GLY99 4.3 44.1 1.0
C A:ASP227 4.3 37.4 1.0
OD1 A:ASP227 4.4 44.1 1.0
CA A:THR226 4.4 44.3 1.0
CB A:SER223 4.4 39.9 1.0
N A:SER223 4.5 37.8 1.0
CB A:ASN221 4.7 35.7 1.0
N A:ILE97 4.7 47.3 1.0
N A:ASN225 4.7 51.0 1.0
OG A:SER223 4.9 41.2 1.0
C A:ASN225 4.9 48.7 1.0
O A:ASN221 4.9 38.0 1.0
CB A:ASP227 5.0 42.5 1.0

Sodium binding site 2 out of 2 in 6eku

Go back to Sodium Binding Sites List in 6eku
Sodium binding site 2 out of 2 in the Vibrio Cholerae Neuraminidase Complexed with Zanamivir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Vibrio Cholerae Neuraminidase Complexed with Zanamivir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:35.8
occ:1.00
OG1 A:THR339 2.2 40.5 1.0
O A:HOH1128 2.3 28.2 1.0
O A:ASN282 2.4 44.4 1.0
O A:ALA279 2.4 42.0 1.0
O A:THR339 2.4 36.5 1.0
OD2 A:ASP315 2.5 32.4 1.0
OD1 A:ASP315 2.9 30.1 1.0
CG A:ASP315 3.0 30.8 1.0
C A:ALA279 3.2 43.4 1.0
C A:THR339 3.2 34.0 1.0
CB A:THR339 3.3 38.9 1.0
CA A:THR339 3.3 33.3 1.0
C A:ASN282 3.4 43.7 1.0
N A:ALA279 3.5 40.1 1.0
CA A:ALA279 3.9 38.0 1.0
N A:ASN282 4.0 47.5 1.0
N A:LEU280 4.0 45.5 1.0
CA A:ASN282 4.1 46.7 1.0
CB A:ASN282 4.2 47.4 1.0
C A:GLY278 4.2 37.7 1.0
O A:HOH1082 4.2 39.6 1.0
N A:GLY278 4.3 36.2 1.0
CG2 A:THR339 4.3 36.8 1.0
CA A:LEU280 4.4 48.8 1.0
N A:THR283 4.4 40.2 1.0
CB A:ASP315 4.4 29.0 1.0
N A:ASP340 4.5 30.9 1.0
C A:LEU280 4.5 52.6 1.0
CA A:GLY278 4.6 36.3 1.0
CA A:THR283 4.6 37.3 1.0
CB A:ALA279 4.6 32.9 1.0
N A:THR339 4.7 31.7 1.0
N A:SER281 4.8 51.1 1.0
O A:HOH1387 4.8 38.6 1.0
O A:LEU280 4.9 54.9 1.0
O A:GLY278 5.0 37.0 1.0

Reference:

S.Quosdorf, A.Schuetz, H.Kolodziej. Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases As Assessed in A Cell-Free Fluorescence-Based Enzyme Inhibition Assay. Molecules V. 22 2017.
ISSN: ESSN 1420-3049
PubMed: 29149072
DOI: 10.3390/MOLECULES22111989
Page generated: Tue Oct 8 08:26:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy