Sodium in PDB 6wjt: 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine

The structure of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine, PDB code: 6wjt was solved by G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.79 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.917, 166.917, 98.099, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 19.1

The structure of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine (pdb code 6wjt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine, PDB code: 6wjt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7101 b:49.2 occ:1.00 O A:HOH7385 2.2 54.5 1.0 O A:HOH7247 2.3 42.7 1.0 O A:LEU6887 2.3 31.9 1.0 O A:GLN6885 2.5 31.6 1.0 O A:ARG6884 2.7 32.6 1.0 C A:GLN6885 3.2 31.1 1.0 C A:LEU6887 3.5 31.6 1.0 O A:HOH7291 3.6 30.9 1.0 CA A:GLN6885 3.7 31.5 1.0 C A:ARG6884 3.8 31.9 1.0 OG1 A:THR6889 3.9 36.1 0.5 N A:LEU6887 4.0 30.1 1.0 N A:TRP6886 4.0 30.1 1.0 C A:TRP6886 4.1 30.2 1.0 N A:THR6889 4.1 35.0 0.5 N A:GLN6885 4.2 31.4 1.0 OG1 B:THR4311 4.2 43.4 1.0 O B:HOH4521 4.3 54.4 1.0 C A:PRO6888 4.3 34.1 1.0 O A:HOH7234 4.3 40.3 1.0 O A:TRP6886 4.3 30.6 1.0 CA A:LEU6887 4.4 30.6 1.0 N A:PRO6888 4.5 32.3 1.0 N A:THR6889 4.5 35.4 0.5 CA A:PRO6888 4.5 33.6 1.0 CA A:TRP6886 4.6 29.8 1.0 CB B:THR4311 4.6 40.2 1.0 CA A:THR6889 4.6 35.7 0.5 O A:PRO6888 4.7 33.6 1.0 O B:VAL4310 4.7 35.8 1.0 O B:HOH4554 4.7 55.9 1.0 O A:HOH7358 4.7 44.4 1.0 OG1 A:THR6889 4.9 37.3 0.5 CB A:THR6889 4.9 36.7 0.5 CA A:THR6889 5.0 36.2 0.5

Sodium binding site 2 out of 2 in the 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na7101 b:39.8 occ:1.00 O C:LEU6887 2.2 27.4 1.0 O C:HOH7396 2.3 45.9 1.0 O C:HOH7276 2.4 41.5 1.0 O C:GLN6885 2.5 27.1 1.0 O C:ARG6884 2.6 28.1 1.0 C C:GLN6885 3.1 27.1 1.0 C C:LEU6887 3.4 27.2 1.0 O C:HOH7311 3.6 28.6 1.0 C C:ARG6884 3.7 28.0 1.0 CA C:GLN6885 3.7 27.6 1.0 N C:LEU6887 3.9 26.1 1.0 C C:TRP6886 4.0 26.2 1.0 N C:TRP6886 4.0 26.3 1.0 OG1 D:THR4311 4.1 39.7 1.0 N C:GLN6885 4.2 27.5 1.0 N C:THR6889 4.2 31.6 1.0 O C:TRP6886 4.2 26.4 1.0 CA C:LEU6887 4.3 26.4 1.0 C C:PRO6888 4.3 30.2 1.0 O C:HOH7260 4.3 39.5 0.5 O C:HOH7219 4.3 33.4 1.0 OG1 C:THR6889 4.4 34.1 1.0 N C:PRO6888 4.4 28.1 1.0 CA C:PRO6888 4.4 29.2 1.0 CA C:TRP6886 4.5 26.1 1.0 O D:HOH4550 4.5 57.7 1.0 CB D:THR4311 4.6 36.5 1.0 O C:PRO6888 4.7 30.1 1.0 O D:VAL4310 4.8 30.9 1.0 O C:HOH7333 4.8 38.0 1.0 CA C:THR6889 4.8 32.9 1.0 CA C:ARG6884 5.0 28.2 1.0

G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.0 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with S-Adenosyl-L-Homocysteine To Be Published.