Sodium in PDB 7c67: Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose

The structure of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose, PDB code: 7c67 was solved by S.P.Kanaujia, M.Chandravanshi, R.Samanta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.670, 109.880, 110.890, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 23.1

The structure of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose (pdb code 7c67). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose, PDB code: 7c67:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose


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 Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:33.9 occ:1.00 O A:HOH611 2.6 34.9 1.0 O A:HOH692 2.7 26.6 1.0 O A:HOH714 3.2 41.4 1.0 CG2 B:THR50 3.5 26.6 1.0 CB B:THR50 3.6 25.4 1.0 NH1 A:ARG273 3.7 36.5 1.0 CD A:ARG273 3.8 29.9 1.0 OG1 B:THR50 3.8 22.0 1.0 CD B:LYS47 3.9 33.0 1.0 CB A:ALA245 3.9 23.7 1.0 OE2 A:GLU265 4.1 43.7 1.0 CA A:ALA245 4.1 21.9 1.0 CA B:LYS47 4.1 22.6 1.0 N A:ALA245 4.4 20.7 1.0 CZ A:ARG273 4.4 35.9 1.0 NE A:ARG273 4.4 35.5 1.0 O B:THR46 4.5 20.3 1.0 NZ B:LYS47 4.6 40.0 1.0 CG A:ARG273 4.6 27.7 1.0 CD A:GLU265 4.6 45.0 1.0 OE1 A:GLU265 4.6 42.2 1.0 CB B:LYS47 4.7 25.5 1.0 O A:ALA241 4.7 21.2 1.0 C A:GLN244 4.7 21.2 1.0 O B:LYS47 4.8 21.0 1.0 CG B:LYS47 4.8 29.2 1.0 N B:LYS47 4.8 20.4 1.0 C B:THR46 4.9 20.0 1.0 O A:GLN244 4.9 20.3 1.0 CE B:LYS47 4.9 36.8 1.0 CG2 B:THR46 4.9 22.1 1.0 CB A:GLN244 4.9 21.0 1.0 C B:LYS47 5.0 20.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Beta-Glycosides-Binding Protein of Abc Transporter in A Closed State Bound to Cellotriose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:33.2 occ:1.00 O B:HOH739 2.8 30.9 1.0 O A:HOH846 3.1 36.2 1.0 O A:HOH815 3.1 35.9 1.0 C B:GLN14 3.5 27.2 1.0 N B:GLU17 3.6 28.3 1.0 N B:ALA16 3.7 24.7 1.0 CA B:GLN14 3.8 30.3 1.0 N B:PRO15 3.8 25.7 1.0 CB B:GLN14 3.9 32.1 1.0 O B:GLN14 3.9 25.9 1.0 CB B:GLU17 4.0 35.6 1.0 CB B:ALA16 4.0 24.9 1.0 CD B:PRO15 4.1 26.2 1.0 CA B:ALA16 4.2 25.5 1.0 CG B:GLU17 4.2 40.7 1.0 C B:ALA16 4.4 26.4 1.0 CA B:GLU17 4.4 30.9 1.0 O A:HOH770 4.5 24.0 1.0 C B:PRO15 4.5 24.5 1.0 O A:HOH719 4.6 42.6 1.0 OE1 B:GLU17 4.7 48.2 1.0 O B:HOH773 4.7 41.8 1.0 CA B:PRO15 4.7 24.8 1.0 CG B:GLN14 4.8 35.1 1.0 CL A:CL502 4.9 39.5 1.0 CD B:GLU17 5.0 44.7 1.0

M.Chandravanshi, R.Samanta, S.P.Kanaujia. Conformational Trapping of A Beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of Abc Importers. J.Mol.Biol. V. 432 5711 2020.
ISSN: ESSN 1089-8638
PubMed: 32866452
DOI: 10.1016/J.JMB.2020.08.021