Sodium in PDB 5vf5: Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement

The structure of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement, PDB code: 5vf5 was solved by P.J.Porebski, A.Wlodawer, Z.Dauter, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.71 / 1.49
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	119.330, 119.330, 158.190, 90.00, 90.00, 120.00
R / Rfree (%)	13.1 / 16.3

The structure of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement (pdb code 5vf5). 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 the Vicilin From Solanum Melongena, Re-Refinement, PDB code: 5vf5:

Sodium binding site 1 out of 1 in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement


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 the Vicilin From Solanum Melongena, Re-Refinement within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:12.6 occ:1.00 O A:HOH910 2.3 16.9 1.0 O A:ALA25 2.3 11.4 1.0 O A:GLY28 2.4 12.0 1.0 O A:HOH847 2.4 13.4 1.0 O A:HOH827 2.5 13.2 1.0 C A:GLY28 3.5 11.8 1.0 C A:ALA25 3.5 11.3 1.0 N A:ALA25 4.0 11.4 1.0 CA A:ALA25 4.2 11.8 1.0 N A:GLY28 4.2 11.1 1.0 CB A:ASP29 4.3 14.3 1.0 O A:HOH691 4.3 33.3 1.0 CA A:GLY28 4.4 12.6 1.0 O A:HOH612 4.4 29.5 1.0 N A:ASP29 4.4 13.0 1.0 O A:HOH887 4.5 38.8 1.0 CB A:ALA25 4.5 12.1 1.0 CA A:ASP29 4.5 13.7 1.0 N A:SER26 4.6 10.7 1.0 O A:SER26 4.6 13.1 1.0 C A:SER26 4.6 11.4 1.0 CG A:ASP29 4.6 18.2 1.0 OD1 A:ASP29 4.7 20.2 1.0 CA A:SER26 4.8 11.6 1.0

A.Wlodawer, Z.Dauter, P.J.Porebski, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp. Detect, Correct, Retract: How to Manage Incorrect Structural Models. Febs J. V. 285 444 2018.
ISSN: ISSN 1742-4658
PubMed: 29113027
DOI: 10.1111/FEBS.14320