Sodium in PDB 8zbf: Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd

The structure of Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd, PDB code: 8zbf was solved by X.Chen, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.48 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.97, 92.48, 77.92, 90, 90.54, 90
R / Rfree (%)	21.7 / 26.1

The binding sites of Sodium atom in the Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd (pdb code 8zbf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd, PDB code: 8zbf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:67.1 occ:1.00 OD1 A:ASP144 3.4 71.5 1.0 OD2 A:ASP144 3.7 73.1 1.0 CG A:ASP144 3.9 80.7 1.0 O A:GLY114 4.6 59.1 1.0 CB A:PRO142 4.6 69.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the A58-T10 Dna Aptamer in Complex with Sars-Cov- 2 N-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:118.5 occ:1.00 O2 G:DT14 2.9 50.2 1.0 NH2 C:ARG149 2.9 52.5 1.0 O C:SER51 3.2 55.7 1.0 O C:PHE53 3.4 50.4 1.0 C1' G:DT14 3.4 53.4 1.0 CE1 C:TYR109 3.6 46.6 1.0 C2 G:DT14 3.6 51.9 1.0 C2' G:DT14 3.7 49.2 1.0 CD1 C:TYR109 3.8 49.9 1.0 N C:SER51 3.8 54.9 1.0 CB C:SER51 3.8 52.7 1.0 C C:SER51 3.9 55.6 1.0 N1 G:DT14 3.9 50.3 1.0 O3' G:DT14 4.0 53.8 1.0 CA C:SER51 4.0 56.7 1.0 CZ C:ARG149 4.2 51.4 1.0 CB C:ALA50 4.2 63.2 1.0 C C:PHE53 4.3 47.5 1.0 C3' G:DT14 4.5 48.7 1.0 O4' G:DT14 4.6 49.0 1.0 CB C:ALA156 4.6 47.2 1.0 NE C:ARG149 4.6 54.1 1.0 OG C:SER51 4.6 52.1 1.0 N C:PHE53 4.7 48.7 1.0 C C:ALA50 4.7 61.1 1.0 CZ C:TYR109 4.8 53.5 1.0 N3 G:DT14 4.8 49.0 1.0 N C:THR54 4.8 46.0 1.0 CA C:THR54 5.0 47.2 1.0

X.Chen, L.Huang. Molecular Characterization and Broad-Spectrum Mechanism of Coronavirus N Protein Aptamer To Be Published.