Calcium in PDB 4bcu: Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer

The structure of Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer, PDB code: 4bcu was solved by R.J.Ford, A.M.Barker, S.E.Bakker, R.H.Coutts, N.A.Ranson, S.E.V.Phillips, A.R.Pearson, P.G.Stockley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	217.15 / 2.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	315.020, 300.550, 183.510, 90.00, 94.37, 90.00
R / Rfree (%)	15.512 / 19.821

The binding sites of Calcium atom in the Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer (pdb code 4bcu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer, PDB code: 4bcu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:12.5 occ:1.00 OD1 A:ASP194 2.2 16.2 1.0 O A:GLN64 2.3 10.6 1.0 O A:SER61 2.3 13.6 1.0 O A:HOH2103 2.4 15.3 1.0 CG A:ASP194 3.4 14.1 1.0 C A:GLN64 3.5 10.7 1.0 C A:SER61 3.5 13.4 1.0 N A:GLN64 4.0 10.6 1.0 O A:ASP194 4.0 16.5 1.0 OD2 A:ASP194 4.1 13.0 1.0 CA A:GLN64 4.2 10.6 1.0 C A:ASP194 4.2 14.2 1.0 CB A:SER61 4.3 13.3 1.0 CA A:ASP194 4.3 13.4 1.0 N A:SER61 4.3 12.5 1.0 CA A:SER61 4.3 13.5 1.0 CB A:ASP194 4.4 12.4 1.0 N A:GLY62 4.4 13.1 1.0 CA A:GLY62 4.5 12.9 1.0 N A:VAL65 4.5 9.5 1.0 C A:GLY62 4.5 13.0 1.0 O A:ALA195 4.5 18.5 1.0 N A:ASP63 4.7 12.1 1.0 O A:HOH2110 4.7 16.6 1.0 CB A:GLN64 4.7 9.9 1.0 CG1 A:VAL65 4.7 4.7 1.0 CA A:VAL65 4.8 9.1 1.0 N A:ALA195 4.9 15.2 1.0 O A:GLY62 5.0 12.6 1.0

Calcium binding site 2 out of 2 in the Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Satellite Tobacco Necrosis Virus (Stnv) Virus Like Particle in Complex with the B3 Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:10.9 occ:0.20 O A:HOH2186 2.3 9.8 0.2 O A:THR138 2.3 13.7 1.0 O A:HOH2187 2.9 4.1 0.2 C A:THR138 3.4 12.8 1.0 N A:GLY139 4.1 11.9 1.0 CA A:GLY139 4.1 11.0 1.0 CA A:THR138 4.5 12.6 1.0 CB A:THR138 4.9 12.2 1.0

R.J.Ford, A.M.Barker, S.E.Bakker, R.H.Coutts, N.A.Ranson, S.E.V.Phillips, A.R.Pearson, P.G.Stockley. Sequence-Specific, Rna-Protein Interactions Overcome Electrostatic Barriers Preventing Assembly of Satellite Tobacco Necrosis Virus Coat Protein. J.Mol.Biol. V. 425 1050 2013.
ISSN: ISSN 0022-2836
PubMed: 23318955
DOI: 10.1016/J.JMB.2013.01.004