Sodium in PDB 2i9f: Structure of the Equine Arterivirus Nucleocapsid Protein

The structure of Structure of the Equine Arterivirus Nucleocapsid Protein, PDB code: 2i9f was solved by A.Deshpande, S.Wang, M.Walsh, T.Dokland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.94 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.230, 73.230, 138.960, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.8

The structure of Structure of the Equine Arterivirus Nucleocapsid Protein also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of the Equine Arterivirus Nucleocapsid Protein (pdb code 2i9f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Equine Arterivirus Nucleocapsid Protein, PDB code: 2i9f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Equine Arterivirus Nucleocapsid Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Equine Arterivirus Nucleocapsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:45.4 occ:1.00 OG1 C:THR89 2.8 20.8 1.0 CB C:ASP84 3.2 32.7 1.0 O C:HOH341 3.4 58.3 1.0 O C:GLY87 3.4 26.7 1.0 N C:ASP84 3.5 30.4 1.0 CB C:THR89 3.7 19.1 1.0 N C:THR89 3.9 19.5 1.0 CG C:ASP84 3.9 35.8 1.0 C C:LEU88 3.9 20.9 1.0 C C:ALA83 4.0 27.7 1.0 CA C:ASP84 4.0 32.3 1.0 C C:GLY87 4.1 25.6 1.0 O C:LEU88 4.1 20.7 1.0 CA C:ALA83 4.2 25.2 1.0 OD2 C:ASP84 4.3 37.2 1.0 O C:THR82 4.3 16.9 1.0 CA C:THR89 4.4 19.2 1.0 CA C:LEU88 4.4 21.8 1.0 N C:LEU88 4.5 23.4 1.0 N C:GLY87 4.5 29.5 1.0 OD1 C:ASP84 4.6 39.6 1.0 C C:THR82 4.7 18.7 1.0 N C:ALA83 4.7 21.4 1.0 O C:ALA83 4.7 27.4 1.0 OG D:SER93 4.8 31.2 1.0 OG1 C:THR82 4.9 17.9 1.0 CG2 C:THR89 5.0 19.0 1.0

Sodium binding site 2 out of 2 in the Structure of the Equine Arterivirus Nucleocapsid Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Equine Arterivirus Nucleocapsid Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:26.2 occ:1.00 O C:GLY79 2.7 12.7 1.0 O C:GLY77 2.7 13.3 1.0 N A:VAL95 3.1 10.1 1.0 N C:GLY79 3.4 11.2 1.0 O C:HOH309 3.5 31.9 1.0 CA A:TRP94 3.5 10.8 1.0 CA C:HIS78 3.5 12.8 1.0 C C:HIS78 3.5 12.1 1.0 CB A:TRP94 3.6 9.5 1.0 C C:GLY79 3.7 13.6 1.0 O C:HOH334 3.7 40.5 1.0 C C:GLY77 3.8 13.5 1.0 C A:TRP94 3.8 9.9 1.0 O A:VAL95 3.9 9.5 1.0 CA A:VAL95 4.0 9.5 1.0 CA C:GLY79 4.1 12.4 1.0 CB A:VAL95 4.1 9.2 1.0 CD2 D:HIS8 4.1 17.0 1.0 N C:HIS78 4.1 11.8 1.0 NH1 D:ARG55 4.2 15.0 1.0 CB D:PRO51 4.2 16.1 1.0 O C:HIS78 4.3 12.5 1.0 CG2 A:VAL95 4.3 8.0 1.0 NE2 D:HIS8 4.3 12.1 1.0 C A:VAL95 4.4 10.3 1.0 O B:HOH322 4.7 27.5 1.0 CG D:PRO51 4.7 14.4 1.0 CB C:HIS78 4.7 12.9 1.0 CG A:TRP94 4.8 12.9 1.0 N A:TRP94 4.8 12.2 1.0 O A:SER93 4.9 13.0 1.0 N C:SER80 4.9 14.5 1.0

A.Deshpande, S.Wang, M.A.Walsh, T.Dokland. Structure of the Equine Arteritis Virus Nucleocapsid Protein Reveals A Dimer-Dimer Arrangement. Acta Crystallogr.,Sect.D V. 63 581 2007.
ISSN: ISSN 0907-4449
PubMed: 17452783
DOI: 10.1107/S0907444907008372