Sodium in PDB 2xyv: Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex

The structure of Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex, PDB code: 2xyv was solved by E.Decroly, C.Debarnot, F.Ferron, M.Bouvet, B.Coutard, I.Imbert, L.Gluais, N.Papageorgiou, M.Ortiz-Lombardia, J.Lescar, B.Canard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.41 / 2.06
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.151, 184.800, 129.015, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.4

The structure of Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	2 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex (pdb code 2xyv). 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 the NSP16 NSP10 Sars Coronavirus Complex, PDB code: 2xyv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex


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 the NSP16 NSP10 Sars Coronavirus Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1293 b:69.0 occ:1.00 O A:HOH2203 2.2 45.2 1.0 O A:HOH2201 2.3 38.7 1.0 O A:HOH2202 2.7 44.9 1.0 OD2 A:ASP220 2.9 35.2 1.0 CG A:ASP220 3.7 30.9 1.0 OD1 A:ASP220 3.8 31.6 1.0 OG1 A:THR223 4.8 28.9 1.0 O A:HOH2205 4.9 30.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex


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 the NSP16 NSP10 Sars Coronavirus Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1294 b:31.5 occ:1.00 O A:HOH2086 2.6 19.9 1.0 O A:GLY164 2.7 21.9 1.0 OG A:SER166 2.7 21.5 1.0 N A:ALA60 3.0 25.0 1.0 ND2 A:ASN210 3.4 22.7 1.0 N A:SER166 3.5 21.8 1.0 C A:GLY165 3.5 21.9 1.0 CB A:SER166 3.5 21.6 1.0 CA A:LEU59 3.6 24.8 1.0 CA A:GLY165 3.8 21.8 1.0 CB A:ALA60 3.8 25.1 1.0 C A:LEU59 3.8 24.8 1.0 C A:GLY164 3.8 22.1 1.0 CA A:ALA60 3.9 25.2 1.0 O A:GLY165 4.0 21.7 1.0 O A:ALA60 4.1 25.1 1.0 CG A:LEU59 4.1 25.1 1.0 CA A:SER166 4.1 21.6 1.0 CB A:LEU59 4.2 24.8 1.0 N A:GLY165 4.3 22.0 1.0 O A:ASP125 4.3 24.8 1.0 N A:ASN210 4.4 22.9 1.0 C A:ALA60 4.5 25.2 1.0 O A:THR58 4.5 24.5 1.0 CG A:ASN210 4.5 23.8 1.0 CA A:ASN210 4.6 23.6 1.0 CD1 A:LEU59 4.8 25.5 1.0 N A:LEU59 4.8 24.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the NSP16 NSP10 Sars Coronavirus Complex


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 the NSP16 NSP10 Sars Coronavirus Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1295 b:28.3 occ:1.00 O A:HOH2149 2.1 43.7 1.0 OG1 A:THR172 3.0 26.2 1.0 O A:HOH2170 3.0 53.7 1.0 OD1 A:ASN29 3.3 53.1 1.0 N A:HIS174 3.4 28.1 1.0 CB A:THR172 3.5 25.8 1.0 CD2 A:HIS174 3.8 30.7 1.0 CB A:HIS174 3.8 28.9 1.0 N A:GLU173 3.8 26.9 1.0 CB A:GLU173 4.1 27.6 1.0 OG A:SER202 4.1 24.6 1.0 CG A:HIS174 4.1 30.0 1.0 CA A:HIS174 4.1 28.7 1.0 CA A:GLU173 4.3 27.6 1.0 CG A:ASN29 4.3 52.9 1.0 OH A:TYR132 4.3 37.9 1.0 C A:GLU173 4.3 27.6 1.0 O A:HOH2042 4.4 33.4 1.0 C A:THR172 4.5 26.2 1.0 CG2 A:THR172 4.5 25.8 1.0 N A:SER175 4.5 28.6 1.0 CA A:THR172 4.7 25.8 1.0 ND2 A:ASN29 4.7 52.2 1.0 CE1 A:TYR132 4.8 36.7 1.0 C A:HIS174 4.8 28.8 1.0 OE1 A:GLU173 4.9 28.9 1.0

E.Decroly, C.Debarnot, F.Ferron, M.Bouvet, B.Coutard, I.Imbert, L.Gluais, N.Papageorgiou, A.Sharff, G.Bricogne, M.Ortiz-Lombardia, J.Lescar, B.Canard. Crystal Structure and Functional Analysis of the Sars-Coronavirus Rna Cap 2'-O-Methyltransferase NSP10/NSP16 Complex. Plos Pathog. V. 7 2059 2011.
ISSN: ISSN 1553-7366
PubMed: 21637813
DOI: 10.1371/JOURNAL.PPAT.1002059