Sodium in PDB 7jz0: Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah).

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah)., PDB code: 7jz0 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)	30.00 / 2.15
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.238, 167.238, 98.867, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 19.8

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). (pdb code 7jz0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah)., PDB code: 7jz0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah).


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 (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7102 b:69.8 occ:1.00 O E:HOH102 2.3 70.2 1.0 O A:HOH7246 2.3 61.0 1.0 O E:HOH103 2.3 69.4 1.0 OD1 A:ASN6996 2.6 39.3 1.0 O2' E:U3 3.6 0.0 1.0 CG A:ASN6996 3.8 37.5 1.0 OP2 E:U2 4.1 97.3 1.0 OG A:SER6998 4.2 40.3 1.0 OP1 E:U2 4.3 94.2 1.0 O E:HOH104 4.3 69.1 1.0 ND2 A:ASN6996 4.3 37.1 1.0 OP1 E:A2M1 4.4 80.4 1.0 CB A:SER6999 4.6 33.9 1.0 CE A:MET6840 4.6 61.6 1.0 P E:U2 4.7 0.3 1.0 C2' E:U3 4.9 0.7 1.0 O A:ASP6830 4.9 78.1 1.0 CB A:ASN6996 5.0 36.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah).


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 (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7103 b:67.9 occ:1.00 O B:HOH4502 2.3 67.4 1.0 O A:LEU6887 2.4 42.2 1.0 O A:HOH7330 2.4 65.3 1.0 O A:GLN6885 2.6 42.4 1.0 O A:ARG6884 3.0 45.5 1.0 C A:GLN6885 3.4 42.2 1.0 O A:HOH7226 3.5 42.0 1.0 C A:LEU6887 3.6 43.0 1.0 CA A:GLN6885 3.9 43.6 1.0 OG1 B:THR4311 4.0 60.0 1.0 C A:ARG6884 4.1 44.1 1.0 N A:THR6889 4.1 54.4 0.5 CG2 A:THR6889 4.2 56.6 0.5 N A:THR6889 4.2 52.4 0.5 N A:LEU6887 4.2 40.2 1.0 O A:HOH7275 4.2 54.6 1.0 C A:TRP6886 4.3 41.1 1.0 C A:PRO6888 4.3 51.0 1.0 N A:TRP6886 4.3 41.9 1.0 CA A:PRO6888 4.4 47.6 1.0 CG2 A:THR6889 4.4 60.6 0.5 N A:PRO6888 4.4 45.0 1.0 O A:TRP6886 4.5 39.8 1.0 N A:GLN6885 4.5 44.5 1.0 CA A:LEU6887 4.5 42.1 1.0 CB B:THR4311 4.6 55.1 1.0 CA A:THR6889 4.6 57.6 0.5 O B:VAL4310 4.7 51.0 1.0 CA A:THR6889 4.8 54.4 0.5 O A:PRO6888 4.8 49.0 1.0 O A:HOH7322 4.8 57.4 1.0 CA A:TRP6886 4.8 40.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah).


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 (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). within 5.0Å range: probe atom residue distance (Å) B Occ C:Na7102 b:61.8 occ:1.00 O F:HOH102 2.3 63.0 1.0 O F:HOH105 2.3 55.8 0.5 O C:HOH7270 2.3 58.5 1.0 O F:HOH104 2.3 58.1 1.0 OD1 C:ASN6996 2.5 46.9 1.0 O F:HOH107 2.8 68.6 0.7 CG C:ASN6996 3.6 43.9 1.0 O2' F:U3 3.6 0.9 1.0 ND2 C:ASN6996 4.0 45.1 1.0 OP2 F:U2 4.0 63.1 1.0 O F:HOH106 4.2 61.2 1.0 OP1 F:U2 4.3 58.8 1.0 OG C:SER6998 4.3 44.4 1.0 CB C:SER6999 4.3 39.3 1.0 OP1 F:A2M1 4.5 56.6 1.0 P F:U2 4.6 64.4 1.0 O C:ASP6830 4.7 74.0 1.0 CE C:MET6840 4.8 58.1 1.0 C2' F:U3 4.8 0.2 1.0 CB C:ASN6996 4.8 41.1 1.0 C1' F:U3 5.0 0.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer in Complex with (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). within 5.0Å range: probe atom residue distance (Å) B Occ C:Na7103 b:58.5 occ:1.00 O C:HOH7338 2.2 58.5 1.0 O C:LEU6887 2.3 33.2 1.0 O D:HOH4520 2.4 55.9 1.0 O C:GLN6885 2.6 31.2 1.0 O C:ARG6884 2.8 36.6 1.0 C C:GLN6885 3.3 31.7 1.0 C C:LEU6887 3.5 32.9 1.0 O C:HOH7289 3.6 38.1 1.0 CA C:GLN6885 3.8 34.3 1.0 C C:ARG6884 3.8 36.4 1.0 OG1 D:THR4311 4.0 52.1 1.0 N C:LEU6887 4.1 31.6 1.0 C C:TRP6886 4.1 32.3 1.0 O C:HOH7266 4.1 40.7 1.0 N C:THR6889 4.2 40.0 1.0 N C:TRP6886 4.2 30.5 1.0 OG1 C:THR6889 4.2 49.5 1.0 C C:PRO6888 4.3 38.3 1.0 N C:GLN6885 4.3 34.0 1.0 O C:TRP6886 4.3 30.4 1.0 CA C:LEU6887 4.4 32.7 1.0 N C:PRO6888 4.4 33.7 1.0 CA C:PRO6888 4.4 35.9 1.0 CB D:THR4311 4.5 46.0 1.0 CA C:TRP6886 4.7 30.5 1.0 O C:HOH7308 4.7 49.8 1.0 O D:HOH4536 4.7 58.4 1.0 O D:VAL4310 4.8 39.7 1.0 O C:PRO6888 4.8 35.7 1.0 CA C:THR6889 4.8 44.2 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 (M7GPPPA2M)Pupupapapa (Cap-1) and S-Adenosyl-L-Homocysteine (Sah). To Be Published.