Sodium in PDB 5c4w: Crystal Structure of Coxsackievirus A16

The structure of Crystal Structure of Coxsackievirus A16, PDB code: 5c4w was solved by J.Ren, X.Wang, L.Zhu, Z.Hu, Q.Gao, P.Yang, X.Li, J.Wang, X.Shen, 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)	49.87 / 2.65
Space group	P 41 21 2 24
Cell size a, b, c (Å), α, β, γ (°)	491.200, 491.200, 708.700, 90.00, 90.00, 90.00
R / Rfree (%)	27.8 / 28.3

The structure of Crystal Structure of Coxsackievirus A16 also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the Crystal Structure of Coxsackievirus A16 (pdb code 5c4w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Coxsackievirus A16, PDB code: 5c4w:

Sodium binding site 1 out of 1 in the Crystal Structure of Coxsackievirus A16


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 Coxsackievirus A16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:34.6 occ:1.00 O A:LEU47 2.8 33.4 1.0 O D:ALA65 3.0 0.8 1.0 O A:VAL44 3.3 41.9 1.0 NE2 A:GLN48 3.3 40.6 1.0 CD D:PRO67 3.6 0.3 1.0 O A:PRO45 3.6 33.4 1.0 CA A:PRO45 3.6 31.6 1.0 C D:GLU63 3.8 1.0 1.0 O D:GLU63 3.8 0.5 1.0 C A:PRO45 3.8 31.8 1.0 O D:HIS62 3.9 0.5 1.0 CG D:PRO67 3.9 91.1 1.0 CA D:GLU63 4.0 0.9 1.0 C A:LEU47 4.0 26.2 1.0 C A:VAL44 4.1 30.6 1.0 OD1 A:ASN57 4.1 89.3 1.0 C D:ALA65 4.1 0.8 1.0 CD A:GLN48 4.2 43.6 1.0 N A:PRO45 4.2 31.6 1.0 N D:MET64 4.2 0.6 1.0 O D:MET64 4.4 0.3 1.0 C D:MET64 4.4 0.7 1.0 N D:PRO67 4.6 0.8 1.0 N A:LEU47 4.6 24.1 1.0 OE1 A:GLN48 4.7 57.2 1.0 CA D:PRO66 4.7 1.0 1.0 N D:ALA65 4.7 0.3 1.0 CA D:MET64 4.8 0.1 1.0 C D:HIS62 4.8 0.9 1.0 N A:ALA46 4.8 31.4 1.0 CA A:LEU47 4.8 25.6 1.0 CB A:PRO45 4.8 20.8 1.0 N D:PRO66 4.9 0.4 1.0 N D:GLU63 4.9 0.7 1.0 N A:GLN48 5.0 25.9 1.0 CG A:ASN57 5.0 64.2 1.0 ND2 A:ASN57 5.0 80.9 1.0

J.Ren, X.Wang, L.Zhu, Z.Hu, Q.Gao, P.Yang, X.Li, J.Wang, X.Shen, E.E.Fry, Z.Rao, D.I.Stuart. Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications For Particle Expansion, Receptor Binding, and Immunogenicity. J.Virol. V. 89 10500 2015.
ISSN: ESSN 1098-5514
PubMed: 26269176
DOI: 10.1128/JVI.01102-15