Sodium in PDB 8r6e: Sars-Cov-2 Nucleocapsid Dimerization Domain

The structure of Sars-Cov-2 Nucleocapsid Dimerization Domain, PDB code: 8r6e was solved by J.Fahoum, R.Wiener, A.Rouvinski, M.N.Isupov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.73 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.62, 47.372, 134.625, 90, 90, 90
R / Rfree (%)	22.5 / 26.7

The binding sites of Sodium atom in the Sars-Cov-2 Nucleocapsid Dimerization Domain (pdb code 8r6e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Sars-Cov-2 Nucleocapsid Dimerization Domain, PDB code: 8r6e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Sars-Cov-2 Nucleocapsid Dimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Nucleocapsid Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:51.2 occ:1.00 OE1 A:GLN48 2.2 50.8 1.0 N A:LYS53 2.9 30.7 1.0 OE2 A:GLU44 3.0 67.5 1.0 CD A:GLN48 3.2 42.0 1.0 CB A:LYS53 3.5 35.5 0.5 CB A:LYS53 3.5 34.8 0.5 NE2 A:GLN48 3.6 52.9 1.0 CG A:LYS53 3.7 40.4 0.5 CA A:TYR52 3.7 29.5 1.0 C A:TYR52 3.8 29.2 1.0 CA A:LYS53 3.8 33.8 0.5 CA A:LYS53 3.8 33.4 0.5 CD2 A:TYR52 3.8 38.1 1.0 CD A:GLU44 3.9 57.7 1.0 CD A:LYS53 4.0 42.8 0.5 CG A:GLU44 4.1 46.9 1.0 O A:ASP51 4.3 29.8 1.0 CG A:TYR52 4.4 35.8 1.0 CB A:TYR52 4.5 30.4 1.0 CE A:LYS53 4.5 42.4 0.5 CE2 A:TYR52 4.5 38.0 1.0 CG A:GLN48 4.6 37.4 1.0 N A:TYR52 4.7 31.2 1.0 CB A:GLN48 4.9 31.1 1.0 C A:ASP51 4.9 31.8 1.0 O A:TYR52 4.9 27.6 1.0 CG A:LYS53 5.0 38.8 0.5

Sodium binding site 2 out of 3 in the Sars-Cov-2 Nucleocapsid Dimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Nucleocapsid Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:50.0 occ:1.00 OD2 A:ASP102 2.2 39.9 1.0 OD1 A:ASN99 2.6 28.7 1.0 CG A:ASP102 3.1 43.7 1.0 CG A:ASN99 3.7 26.7 1.0 O A:HOH321 3.8 47.8 1.0 CB A:ASP102 3.9 32.3 1.0 OD1 A:ASP102 3.9 40.7 1.0 CA A:ASN99 4.0 23.6 1.0 CB A:ASN99 4.1 25.8 1.0 O A:PRO98 4.4 27.4 1.0 ND2 A:ASN99 4.8 28.6 1.0 C A:ASN99 4.9 25.6 1.0 N A:ASN99 5.0 25.1 1.0 O A:ASN99 5.0 23.0 1.0 O A:HOH316 5.0 56.2 1.0

Sodium binding site 3 out of 3 in the Sars-Cov-2 Nucleocapsid Dimerization Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sars-Cov-2 Nucleocapsid Dimerization Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:52.0 occ:1.00 OG1 B:THR36 2.2 37.2 1.0 O B:THR36 2.8 39.2 1.0 CB B:THR36 2.9 45.2 1.0 C B:THR36 3.4 41.9 1.0 CA B:THR36 3.7 37.9 1.0 CG2 B:THR36 4.2 38.1 1.0 N B:GLN37 4.4 40.4 1.0 O A:HOH320 4.5 31.5 1.0 N B:THR36 4.6 37.9 1.0 CZ3 B:TRP84 4.6 31.8 1.0 CH2 B:TRP84 4.7 30.5 1.0 O A:HOH364 4.9 42.9 1.0

J.Fahoum, R.Wiener, A.Rouvinski, M.N.Isupov. Sars-Cov-2 Nucleocapsid Dimerization Domain To Be Published.