Sodium in PDB 7jyy: Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam).

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam)., PDB code: 7jyy was solved by G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, J.S.Brunzelle, 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)	29.97 / 2.05
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.948, 166.948, 98.810, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 18.5

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam). also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam). (pdb code 7jyy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam)., PDB code: 7jyy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam).


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 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7103 b:64.4 occ:1.00 O A:HOH7371 2.2 64.4 1.0 O B:HOH4514 2.4 56.2 1.0 O A:LEU6887 2.5 39.0 1.0 O A:GLN6885 2.5 36.5 1.0 O A:ARG6884 3.1 39.5 1.0 C A:GLN6885 3.3 36.0 1.0 C A:LEU6887 3.7 38.5 1.0 CA A:GLN6885 3.9 37.4 1.0 OG1 B:THR4311 3.9 50.8 1.0 O A:HOH7293 3.9 37.9 1.0 C A:ARG6884 4.1 39.1 1.0 O A:HOH7249 4.1 45.2 1.0 O A:HOH7275 4.2 61.4 1.0 C A:TRP6886 4.2 35.2 1.0 OG1 A:THR6889 4.2 53.3 1.0 N A:TRP6886 4.3 35.3 1.0 N A:LEU6887 4.3 35.7 1.0 N A:THR6889 4.3 46.1 1.0 O A:TRP6886 4.3 33.1 1.0 CB B:THR4311 4.3 48.6 1.0 C A:PRO6888 4.4 44.1 1.0 N A:GLN6885 4.5 37.1 1.0 CA A:PRO6888 4.5 41.9 1.0 N A:PRO6888 4.5 39.8 1.0 CA A:LEU6887 4.6 37.0 1.0 O A:HOH7327 4.6 52.3 1.0 O B:VAL4310 4.7 43.8 1.0 CA A:TRP6886 4.7 34.6 1.0 CA A:THR6889 4.9 48.8 1.0 O A:PRO6888 4.9 41.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam).


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 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam). within 5.0Å range: probe atom residue distance (Å) B Occ C:Na7103 b:64.2 occ:1.00 O C:HOH7293 2.3 56.3 1.0 O C:HOH7302 2.4 38.7 0.5 O C:HOH7368 2.6 41.5 1.0 O C:PRO7049 2.6 29.7 1.0 O C:LYS7047 3.0 41.7 1.0 ND2 C:ASN6853 3.6 29.7 1.0 C C:PRO7049 3.7 29.9 1.0 CG C:ASN6853 3.7 29.5 1.0 OD1 C:ASN6853 3.9 29.6 1.0 O C:PHE7048 4.0 29.4 1.0 C C:LYS7047 4.0 41.3 1.0 C C:PHE7048 4.2 31.5 1.0 N C:LYS7051 4.3 32.3 1.0 CB C:ASN6853 4.3 28.9 1.0 CA C:LEU7050 4.3 28.9 1.0 N C:LEU7050 4.4 28.9 1.0 N C:PRO7049 4.5 32.3 1.0 CA C:PRO7049 4.7 31.9 1.0 C C:LEU7050 4.7 31.1 1.0 N C:PHE7048 4.8 36.1 1.0 CA C:LYS7047 4.8 45.0 1.0 CA C:PHE7048 4.8 31.8 1.0 O C:HOH7359 4.9 46.7 1.0 CB C:LYS7047 4.9 50.2 1.0 O C:HOH7344 4.9 40.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam). within 5.0Å range: probe atom residue distance (Å) B Occ C:Na7104 b:50.0 occ:1.00 O C:HOH7370 2.1 50.1 1.0 O C:LEU6887 2.3 27.5 1.0 O C:HOH7295 2.4 51.9 1.0 O C:GLN6885 2.5 27.4 1.0 O C:ARG6884 2.8 31.4 1.0 C C:GLN6885 3.2 27.4 1.0 C C:LEU6887 3.5 28.1 1.0 O C:HOH7314 3.7 33.7 1.0 CA C:GLN6885 3.8 29.2 1.0 C C:ARG6884 3.9 31.3 1.0 OG1 D:THR4311 4.0 45.3 1.0 N C:LEU6887 4.1 27.0 1.0 C C:TRP6886 4.1 27.4 1.0 N C:TRP6886 4.1 26.3 1.0 O C:HOH7219 4.1 40.8 0.5 N C:THR6889 4.2 34.4 1.0 O C:HOH7225 4.2 37.5 1.0 OG1 C:THR6889 4.3 41.7 1.0 O C:TRP6886 4.3 26.2 1.0 N C:GLN6885 4.3 29.2 1.0 C C:PRO6888 4.3 33.0 1.0 CA C:LEU6887 4.4 27.7 1.0 N C:PRO6888 4.4 29.6 1.0 CB D:THR4311 4.4 40.0 1.0 O D:HOH4539 4.4 50.7 1.0 CA C:PRO6888 4.5 31.6 1.0 CA C:TRP6886 4.6 26.4 1.0 O C:HOH7325 4.8 41.2 1.0 O D:VAL4310 4.8 33.4 1.0 O C:PRO6888 4.8 31.8 1.0 CA C:THR6889 4.9 37.9 1.0

G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, J.S.Brunzelle, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA)Pupupapapa (Cap-0) and S-Adenosylmethionine (Sam). To Be Published.