Sodium in PDB 7xxk: Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp

The structure of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk was solved by R.J.Zhou, X.C.Ni, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.783, 116.992, 127.039, 90, 90, 90
R / Rfree (%)	17.8 / 23.2

The structure of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp also contains other interesting chemical elements:

Potassium	(K)	9 atoms
Chlorine	(Cl)	13 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp (pdb code 7xxk). 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 Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na409 b:33.7 occ:1.00 CG C:GLN303 3.8 28.8 1.0 C C:PRO302 3.8 20.8 1.0 N C:GLN303 3.9 20.2 1.0 O C:PRO302 3.9 21.0 1.0 CA C:GLN303 4.0 20.3 1.0 CB C:PRO302 4.1 21.1 1.0 CB C:GLN303 4.5 22.7 1.0 O C:HOH554 4.5 24.8 1.0 NE2 C:GLN306 4.6 21.1 1.0 CA C:PRO302 4.6 20.1 1.0 O C:HOH576 4.7 17.4 1.0 CD C:GLN306 4.7 23.1 1.0 O C:HOH532 4.8 27.4 1.0 OE1 C:GLN306 4.9 24.3 1.0 O C:HOH608 5.0 41.0 1.0 CB C:GLN306 5.0 19.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na405 b:43.9 occ:1.00 O F:HOH599 2.7 50.5 1.0 CG F:GLN303 3.2 35.8 1.0 O F:HOH559 3.2 37.3 1.0 O F:HOH535 3.6 63.3 1.0 CB F:GLN303 3.7 29.1 1.0 CB F:ASP348 3.7 28.6 1.0 N F:GLN349 4.0 24.3 1.0 C F:ASP348 4.0 25.3 1.0 CG F:GLN349 4.1 27.3 1.0 O F:ASP348 4.2 25.6 1.0 CA F:GLN349 4.3 24.3 1.0 CD F:GLN303 4.4 43.3 1.0 CA F:ASP348 4.5 26.1 1.0 O F:ASN345 4.6 35.3 1.0 CD2 F:LEU352 4.6 31.6 1.0 O F:HOH590 4.6 46.7 1.0 O F:HOH542 4.7 35.5 1.0 CB F:ASN345 4.8 38.3 1.0 CB F:GLN349 4.8 24.4 1.0 NE2 F:GLN306 4.9 27.1 1.0 CG F:ASP348 4.9 34.8 1.0 OE1 F:GLN303 5.0 45.1 1.0 CB F:LEU352 5.0 29.1 1.0 CA F:GLN303 5.0 26.0 1.0

R.J.Zhou, X.C.Ni, J.Lei. Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp To Be Published.