Sodium in PDB 7jx6: Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein

The structure of Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein, PDB code: 7jx6 was solved by P.D.Hall, C.A.Nelson, D.H.Fremont, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.02 / 1.61
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.647, 50.647, 168.065, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.3

The binding sites of Sodium atom in the Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein (pdb code 7jx6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein, PDB code: 7jx6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:42.4 occ:1.00 O A:ASP35 2.7 27.2 1.0 O A:CYS37 2.7 26.4 1.0 O A:HOH386 3.5 18.9 0.5 C A:CYS37 3.6 23.0 1.0 CG2 A:ILE39 3.7 39.3 1.0 C A:ASP35 3.9 24.4 1.0 C A:PRO36 3.9 23.4 1.0 N A:CYS37 4.0 22.0 1.0 O A:PRO36 4.2 23.0 1.0 CA A:PRO36 4.3 20.8 1.0 N A:PRO38 4.3 21.0 1.0 CA A:CYS37 4.4 18.7 1.0 CA A:PRO38 4.4 20.9 1.0 N A:ILE39 4.5 26.2 1.0 N A:PRO36 4.5 19.7 1.0 CG A:ASP35 4.7 36.4 1.0 OD2 A:ASP35 4.7 39.6 1.0 C A:PRO38 4.8 24.7 1.0 CB A:ASP35 4.8 35.2 1.0 CB A:ILE39 4.9 32.7 1.0 CA A:ASP35 4.9 32.9 1.0

Sodium binding site 2 out of 4 in the Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:43.2 occ:1.00 OE1 A:GLU92 2.4 57.3 1.0 O A:HOH339 2.9 25.1 1.0 CD A:GLU92 3.1 48.0 1.0 NH2 A:ARG115 3.1 26.4 1.0 OE2 A:GLU92 3.6 28.4 1.0 O A:HOH393 3.7 42.7 1.0 CG A:GLU92 4.1 36.5 1.0 CZ A:ARG115 4.1 21.2 1.0 NE A:ARG115 4.2 20.1 1.0 CB A:GLU92 4.4 33.0 1.0 CA A:SER97 4.5 22.7 1.0 O A:HOH347 4.6 28.0 1.0 O A:GLY96 4.6 26.3 1.0 O B:HOH403 4.6 43.2 1.0 CB A:SER97 4.8 20.0 1.0 CG1 A:VAL117 4.8 33.3 1.0

Sodium binding site 3 out of 4 in the Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:37.1 occ:1.00 O A:HOH405 2.7 44.3 1.0 O A:ASP107 2.8 21.1 1.0 O A:HOH328 2.8 32.3 1.0 O A:HOH422 3.0 42.7 1.0 O A:PHE108 3.7 22.0 1.0 O A:HOH344 3.7 23.4 1.0 C A:PHE108 3.8 22.1 1.0 CB A:PHE108 3.8 19.9 1.0 C A:ASP107 3.9 22.7 1.0 O A:HOH413 4.1 46.7 1.0 CD2 A:LEU109 4.1 25.6 1.0 CA A:PHE108 4.2 20.2 1.0 N A:LEU109 4.2 18.0 1.0 O A:HOH348 4.4 36.9 1.0 CA A:LEU109 4.5 20.5 1.0 N A:PHE108 4.5 22.3 1.0 O A:HOH428 4.6 55.4 1.0 CG A:LEU109 4.8 22.6 1.0 O A:HOH351 4.9 41.8 1.0

Sodium binding site 4 out of 4 in the Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Sars-Cov-2 ORF8 Encoded Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:45.6 occ:1.00 O B:HOH341 2.5 34.9 1.0 O B:ASP113 3.0 25.1 1.0 CB B:HIS112 3.7 25.5 1.0 N B:GLN18 3.7 35.7 1.0 O B:HOH338 3.8 27.5 1.0 N B:ASP113 3.9 21.8 1.0 N B:GLU19 3.9 21.1 1.0 CD2 B:HIS112 4.0 24.8 1.0 CB B:GLU19 4.0 19.1 1.0 C B:ASP113 4.0 19.4 1.0 O B:HOH313 4.0 55.7 1.0 O B:HOH378 4.1 28.2 1.0 CA B:GLN18 4.1 28.3 1.0 CG B:HIS112 4.1 27.1 1.0 C B:GLN18 4.2 28.1 1.0 O B:HOH408 4.4 43.3 1.0 C B:HIS112 4.4 21.1 1.0 CA B:HIS112 4.4 21.2 1.0 CA B:ASP113 4.6 20.2 1.0 CA B:GLU19 4.6 20.6 1.0 OE1 B:GLU19 4.7 23.9 1.0 O B:GLN18 4.9 31.0 1.0

C.A.Nelson, P.D.Hall, D.H.Fremont. Crystal Structure of the Sars-Cov-2 ORF8 Protein To Be Published.