Sodium in PDB 4wfx: Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form

All present enzymatic activity of Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form:
2.7.7.48;

The structure of Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form, PDB code: 4wfx was solved by O.B.Peersen, S.M.Mcdonald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.58 / 1.81
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.360, 74.360, 288.050, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.3

The binding sites of Sodium atom in the Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form (pdb code 4wfx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form, PDB code: 4wfx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:24.6 occ:1.00 OD1 A:ASP330 2.3 14.4 1.0 O A:HOH750 2.4 19.6 1.0 O A:HOH833 2.4 18.7 1.0 O A:HOH788 2.4 20.6 1.0 O A:HOH803 2.4 17.5 1.0 O A:HOH740 2.5 19.1 1.0 CG A:ASP330 3.5 16.2 1.0 OD1 A:ASP233 3.7 28.5 1.0 O A:HOH812 3.8 27.3 1.0 O A:THR373 3.8 14.9 1.0 O A:VAL331 4.0 11.2 1.0 O A:HOH747 4.1 18.8 1.0 OD2 A:ASP330 4.1 15.7 1.0 N A:VAL331 4.2 10.7 1.0 O A:HOH801 4.2 22.7 1.0 O A:ALA231 4.5 19.7 1.0 CA A:ASP330 4.5 11.2 1.0 O A:LEU232 4.6 18.1 1.0 CB A:ASP330 4.6 10.6 1.0 O A:HOH1055 4.7 34.3 1.0 C A:THR373 4.7 15.8 1.0 O A:HOH741 4.7 20.5 1.0 C A:VAL331 4.8 12.2 1.0 OG1 A:THR373 4.8 12.2 1.0 CG A:ASP233 4.8 24.8 1.0 C A:ASP330 4.8 12.4 1.0 CA A:PHE374 4.9 11.6 1.0 CD1 A:PHE374 4.9 10.9 1.0

Sodium binding site 2 out of 4 in the Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:30.0 occ:1.00 O A:HOH731 2.3 14.6 1.0 O A:GLY286 2.4 12.8 1.0 O A:GLY285 2.4 12.1 1.0 O A:LEU269 2.5 14.0 1.0 O A:CYS270 2.6 14.3 1.0 OG A:SER272 2.6 13.5 1.0 C A:CYS270 3.3 13.4 1.0 C A:GLY285 3.3 13.8 1.0 C A:GLY286 3.4 15.6 1.0 C A:LEU269 3.6 14.3 1.0 CB A:SER272 3.7 14.7 1.0 CA A:CYS270 3.7 13.6 1.0 CA A:GLY286 3.9 11.9 1.0 N A:GLY286 4.0 11.2 1.0 N A:CYS270 4.1 14.0 1.0 CD A:PRO288 4.1 10.9 1.0 CG A:PRO288 4.2 16.7 1.0 N A:SER272 4.2 15.6 1.0 N A:ASN271 4.2 16.7 1.0 CA A:GLY285 4.3 15.2 1.0 N A:GLY285 4.3 14.1 1.0 O A:VAL283 4.3 16.0 1.0 CG1 A:VAL283 4.3 11.4 1.0 CB A:VAL283 4.4 14.6 1.0 N A:MET287 4.5 12.5 1.0 CA A:SER272 4.6 13.7 1.0 N A:PRO288 4.7 12.0 1.0 CA A:ASN271 4.8 16.0 1.0 NE2 A:HIS274 4.8 14.5 1.0 C A:VAL283 4.8 14.9 1.0 CA A:LEU269 4.9 13.9 1.0 CA A:MET287 4.9 10.9 1.0 C A:ASN271 4.9 16.5 1.0 C A:MET287 5.0 12.5 1.0

Sodium binding site 3 out of 4 in the Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:23.7 occ:1.00 O A:ILE339 2.2 17.1 1.0 O A:HOH1323 2.3 24.8 1.0 O A:HOH738 2.4 21.1 1.0 O A:HOH848 2.5 23.5 1.0 O A:HOH722 2.5 18.1 1.0 C A:ILE339 3.4 17.3 1.0 O A:HOH780 3.5 25.8 1.0 O A:HOH799 3.9 22.4 1.0 N A:ILE339 3.9 17.0 1.0 N A:ALA341 4.0 17.9 1.0 CA A:ILE339 4.2 15.5 1.0 O A:HOH904 4.2 28.6 1.0 N A:ASP340 4.4 13.1 1.0 O A:LEU229 4.4 18.2 1.0 CA A:ASP340 4.4 15.2 1.0 O A:HOH1025 4.5 31.2 1.0 CB A:ALA341 4.5 17.6 1.0 O A:HOH989 4.7 39.1 1.0 CB A:ILE339 4.7 13.7 1.0 O A:HOH1110 4.7 42.1 1.0 C A:ASP340 4.7 18.7 1.0 CA A:ALA341 4.9 17.4 1.0 O A:HOH745 4.9 15.9 1.0

Sodium binding site 4 out of 4 in the Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Coxsackievirus B3 Polymerase - F232L Mutant - Nacl Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:30.0 occ:1.00 O A:HOH1107 2.3 43.8 1.0 O A:GLU362 2.4 48.3 1.0 O A:PHE364 2.5 42.6 1.0 O A:ASP359 2.6 38.1 1.0 O A:HOH1259 2.8 45.4 1.0 O A:HOH1274 2.8 43.4 1.0 C A:GLU362 3.4 47.7 1.0 C A:PHE364 3.6 44.1 1.0 C A:ASP359 3.7 40.6 1.0 N A:GLU362 3.7 46.6 1.0 CA A:GLU362 4.0 45.5 1.0 O A:HOH1157 4.0 41.2 1.0 N A:PHE364 4.1 44.5 1.0 OD2 A:ASP359 4.2 44.8 1.0 CB A:ASP359 4.3 37.7 1.0 CB A:GLU362 4.3 43.8 1.0 N A:CYS363 4.4 51.9 1.0 N A:GLY361 4.4 41.1 1.0 CA A:ASN365 4.4 46.0 1.0 N A:ASN365 4.4 45.9 1.0 CA A:ASP359 4.5 33.6 1.0 C A:CYS363 4.5 49.5 1.0 CA A:PHE364 4.5 46.2 1.0 N A:LYS360 4.5 38.4 1.0 CA A:LYS360 4.6 38.6 1.0 C A:LYS360 4.7 39.8 1.0 CG A:ASP359 4.7 39.1 1.0 CA A:CYS363 4.8 53.4 1.0 C A:GLY361 4.8 48.5 1.0 CB A:ASN365 5.0 49.5 1.0

G.Campagnola, S.Mcdonald, S.Beaucourt, M.Vignuzzi, O.B.Peersen. Structure-Function Relationships Underlying the Replication Fidelity of Viral Rna-Dependent Rna Polymerases. J.Virol. 2014.
ISSN: ESSN 1098-5514
PubMed: 25320316
DOI: 10.1128/JVI.01574-14