Sodium in PDB 5i5a: Quasi Racemic Structure of Allo-ILE7-Shk and D-Shk

The structure of Quasi Racemic Structure of Allo-ILE7-Shk and D-Shk, PDB code: 5i5a was solved by B.Dang, T.Kubota, K.Mandal, R.Shen, F.Bezanilla, B.Roux, S.B.H.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.46 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.849, 17.656, 49.469, 90.00, 101.61, 90.00
R / Rfree (%)	15.4 / 19.5

The binding sites of Sodium atom in the Quasi Racemic Structure of Allo-ILE7-Shk and D-Shk (pdb code 5i5a). 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 Quasi Racemic Structure of Allo-ILE7-Shk and D-Shk, PDB code: 5i5a:

Sodium binding site 1 out of 1 in the Quasi Racemic Structure of Allo-ILE7-Shk and D-Shk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Quasi Racemic Structure of Allo-ILE7-Shk and D-Shk within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:29.7 occ:1.00 O A:HOH214 2.5 12.7 0.5 O A:ASP5 2.6 14.7 1.0 O A:HOH214 3.1 23.8 0.5 C A:ASP5 3.7 10.8 1.0 N A:ASP5 3.9 11.7 1.0 NZ A:LYS9 3.9 5.2 0.2 CB A:ILE4 4.0 14.2 1.0 CA A:ASP5 4.2 11.1 1.0 CD1 A:ILE4 4.3 16.8 1.0 CB A:ASP5 4.4 10.4 1.0 CG1 A:ILE4 4.6 14.0 1.0 CE A:LYS9 4.7 16.8 0.5 O A:HOH239 4.7 58.3 1.0 C A:ILE4 4.7 10.8 1.0 CG2 A:ILE4 4.7 17.3 1.0 CA A:ILE4 4.8 12.4 1.0 N A:THR6 4.8 10.0 1.0

B.Dang, R.Shen, T.Kubota, K.Mandal, F.Bezanilla, B.Roux, S.B.Kent. Inversion of the Side-Chain Stereochemistry of Indvidual Thr or Ile Residues in A Protein Molecule: Impact on the Folding, Stability, and Structure of the Shk Toxin. Angew. Chem. Int. Ed. Engl. V. 56 3324 2017.
ISSN: ESSN 1521-3773
PubMed: 28194851
DOI: 10.1002/ANIE.201612398