Sodium in PDB 4cdu: Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3

The structure of Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3, PDB code: 4cdu was solved by L.De Colibus, X.Wang, J.A.B.Spyrou, J.Kelly, J.Ren, J.Grimes, G.Puerstinger, N.Stonehouse, T.S.Walter, Z.Hu, J.Wang, X.Li, W.Peng, D.Rowlands, E.E.Fry, Z.Rao, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.97 / 2.80
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	599.681, 599.681, 599.681, 90.00, 90.00, 90.00
R / Rfree (%)	27.8 / 28.2

The structure of Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3 (pdb code 4cdu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3, PDB code: 4cdu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3


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 Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1243 b:28.2 occ:1.00 N C:GLY1 3.9 12.1 1.0 O C:HOH2001 4.3 18.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3


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 Human Enterovirus 71 in Complex with the Uncoating Inhibitor GPP3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1070 b:27.9 occ:1.00 OD2 D:ASP35 3.0 14.4 1.0 CE D:LYS34 3.3 15.3 1.0 CG C:PRO23 3.5 4.9 1.0 CB C:PRO26 3.7 6.2 1.0 CG D:LYS34 3.9 14.8 1.0 CD D:LYS34 4.1 15.4 1.0 NZ D:LYS34 4.2 15.6 1.0 CG D:ASP35 4.2 12.8 1.0 CA C:PRO26 4.2 14.5 1.0 CD C:PRO23 4.5 4.9 1.0 O C:PRO23 4.6 13.2 1.0 CB C:PRO23 4.7 4.9 1.0 CG C:PRO26 4.8 6.4 1.0 N C:PRO26 4.9 14.3 1.0 N D:LYS34 4.9 7.6 1.0 CB D:TYR33 5.0 8.4 1.0 CB D:ASP35 5.0 10.9 1.0

L.De Colibus, X.Wang, J.A.B.Spyrou, J.Kelly, J.Ren, J.Grimes, G.Puerstinger, N.Stonehouse, T.S.Walter, Z.Hu, J.Wang, X.Li, W.Peng, D.J.Rowlands, E.E.Fry, Z.Rao, D.I.Stuart. More-Powerful Virus Inhibitors From Structure-Based Analysis of HEV71 Capsid-Binding Molecules Nat.Struct.Mol.Biol. V. 21 282 2014.
ISSN: ISSN 1545-9993
PubMed: 24509833
DOI: 10.1038/NSMB.2769