Sodium in PDB 5by4: Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr

The structure of Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr, PDB code: 5by4 was solved by J.A.Wojdyla, R.Kaminska, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	51.727, 51.727, 155.029, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 21.5

The binding sites of Sodium atom in the Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr (pdb code 5by4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr, PDB code: 5by4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:25.6 occ:1.00 O A:HOH413 2.8 27.8 1.0 N A:GLU44 2.9 9.3 1.0 O A:HOH367 3.0 20.0 1.0 CB A:GLU44 3.7 12.0 1.0 CG2 A:VAL43 3.7 12.1 1.0 CA A:VAL43 3.8 9.2 1.0 C A:VAL43 3.8 12.7 1.0 CA A:GLU44 3.8 10.2 1.0 O A:HOH328 3.8 28.6 1.0 O A:GLU44 4.0 13.4 1.0 CB A:VAL43 4.4 11.4 1.0 C A:GLU44 4.4 12.6 1.0 O A:HOH360 4.4 31.6 1.0 OD1 A:ASN125 4.7 16.2 1.0 N A:VAL43 5.0 9.9 1.0

Sodium binding site 2 out of 3 in the Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:76.4 occ:1.00 OE2 A:GLU94 3.9 25.9 1.0 NE2 A:GLN90 4.0 36.7 1.0 CB A:ALA93 4.0 16.6 1.0 O A:ALA93 4.0 18.6 1.0 C A:ALA93 4.0 19.0 1.0 N A:GLU94 4.2 14.2 1.0 O A:HOH333 4.2 41.4 1.0 CA A:GLU94 4.3 17.4 1.0 O A:HOH343 4.6 35.1 1.0 O A:HOH396 4.6 44.3 1.0 CA A:ALA93 4.7 18.8 1.0 CB A:SER97 4.8 29.1 1.0 CD A:GLU94 4.9 35.6 1.0 CB A:GLU94 5.0 23.7 1.0

Sodium binding site 3 out of 3 in the Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:24.1 occ:1.00 OH A:TYR74 2.6 22.2 1.0 OE1 A:GLU119 2.7 29.6 0.6 O A:GLU119 2.8 11.3 1.0 CZ A:TYR74 3.3 16.2 1.0 CE1 A:TYR74 3.4 17.3 1.0 CB A:GLU119 3.4 15.6 0.5 CA A:GLU119 3.5 12.7 0.5 CA A:GLU119 3.5 12.7 0.6 C A:GLU119 3.5 12.0 1.0 CB A:GLU119 3.5 13.7 0.6 CB A:LYS122 3.7 11.6 1.0 CD A:GLU119 3.8 22.7 0.6 CG1 A:VAL68 3.8 24.7 1.0 O A:GLY72 3.9 37.4 0.5 N A:ALA123 4.0 9.4 1.0 CG A:GLU119 4.2 17.0 0.5 CG A:GLU119 4.2 17.7 0.6 CB A:ALA123 4.4 10.4 1.0 CD A:LYS122 4.4 20.8 1.0 CE2 A:TYR74 4.4 14.3 1.0 C A:LYS122 4.5 10.6 1.0 CA A:ALA123 4.5 10.8 1.0 CD1 A:TYR74 4.6 16.4 1.0 N A:GLY72 4.6 23.3 0.5 CA A:LYS122 4.6 10.2 1.0 CG A:LYS122 4.7 14.6 1.0 CA A:GLY72 4.7 26.8 0.5 O A:HOH313 4.7 49.9 1.0 N A:ILE120 4.7 10.0 1.0 CG2 A:VAL68 4.8 26.1 1.0 OE2 A:GLU119 4.8 29.4 0.6 N A:GLU119 4.9 13.2 1.0 CB A:VAL68 4.9 26.7 1.0 CD A:GLU119 4.9 20.1 0.5

J.A.Wojdyla, E.Cutts, R.Kaminska, G.Papadakos, J.T.Hopper, P.J.Stansfeld, D.Staunton, C.V.Robinson, C.Kleanthous. Structure and Function of the Escherichia Coli Tol-Pal Stator Protein Tolr. J.Biol.Chem. V. 290 26675 2015.
ISSN: ESSN 1083-351X
PubMed: 26354441
DOI: 10.1074/JBC.M115.671586