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Sodium in PDB 5abj: Structure of Coxsackievirus A16 in Complex with GPP3

Protein crystallography data

The structure of Structure of Coxsackievirus A16 in Complex with GPP3, PDB code: 5abj was solved by L.De Colibus, X.Wang, A.Tijsma, J.Neyts, J.A.B.Spyrou, J.Ren, J.M.Grimes, G.Puerstinger, P.Leyssen, 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) 49.95 / 2.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 491.600, 491.600, 709.560, 90.00, 90.00, 90.00
R / Rfree (%) 30.5 / 30.7

Other elements in 5abj:

The structure of Structure of Coxsackievirus A16 in Complex with GPP3 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Coxsackievirus A16 in Complex with GPP3 (pdb code 5abj). 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 Structure of Coxsackievirus A16 in Complex with GPP3, PDB code: 5abj:

Sodium binding site 1 out of 1 in 5abj

Go back to Sodium Binding Sites List in 5abj
Sodium binding site 1 out of 1 in the Structure of Coxsackievirus A16 in Complex with GPP3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Coxsackievirus A16 in Complex with GPP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1243

b:13.6
occ:1.00
O C:PRO8 2.7 13.3 1.0
C C:PRO8 3.9 12.4 1.0
CB C:LYS7 4.5 11.4 1.0
N C:PRO8 4.6 12.1 1.0
CA C:PRO8 4.7 12.2 1.0
N C:GLY9 4.8 12.8 1.0
CB C:PRO8 4.8 11.7 1.0
CA C:GLY9 4.8 11.9 1.0
C C:LYS7 4.9 12.4 1.0
CD C:PRO8 5.0 11.1 1.0

Reference:

L.De Colibus, X.Wang, A.Tijsma, J.Neyts, J.A.B.Spyrou, J.Ren, J.M.Grimes, G.Puerstinger, P.Leyssen, E.E.Fry, Z.Rao, D.I.Stuart. Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs A Systematic Review of Highly Potent Capsid Binders to Enteroviruses. Plos Pathog. V. 11 5165 2015.
ISSN: ISSN 1553-7366
PubMed: 26485389
DOI: 10.1371/JOURNAL.PPAT.1005165
Page generated: Tue Dec 15 10:19:02 2020

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