Sodium in PDB 6a82: Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli

The structure of Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli, PDB code: 6a82 was solved by Y.Q.Zhao, Y.J.Gu, W.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	85.060, 85.060, 121.340, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.2

The binding sites of Sodium atom in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli (pdb code 6a82). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli, PDB code: 6a82:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli


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 C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:23.1 occ:1.00 O A:ALA518 2.3 22.9 1.0 O A:ALA299 2.3 20.7 1.0 O A:GLN294 2.4 21.9 1.0 O A:THR297 2.4 21.8 1.0 O A:HOH788 2.5 17.7 1.0 O A:HOH745 2.5 20.2 1.0 C A:THR297 3.4 23.0 1.0 C A:ALA299 3.4 23.5 1.0 C A:PHE298 3.4 21.7 1.0 C A:GLN294 3.4 22.9 1.0 C A:ALA518 3.5 21.3 1.0 N A:ALA299 3.6 22.1 1.0 CA A:PHE298 3.7 21.1 1.0 O A:PHE298 3.8 20.3 1.0 N A:PHE298 4.0 21.6 1.0 CA A:ALA299 4.1 22.9 1.0 CA A:GLN294 4.2 21.6 1.0 CA A:GLU519 4.3 21.3 1.0 N A:GLU519 4.4 20.1 1.0 CG2 A:ILE521 4.4 20.2 1.0 N A:ALA295 4.4 21.4 1.0 N A:ASN300 4.5 20.9 1.0 N A:THR297 4.5 20.6 1.0 CA A:ALA518 4.5 19.0 1.0 CA A:THR297 4.6 22.4 1.0 CB A:GLN294 4.6 21.4 1.0 CA A:ALA295 4.6 22.6 1.0 O A:ALA295 4.6 22.8 1.0 OE1 A:GLU519 4.6 24.1 1.0 C A:ALA295 4.7 20.9 1.0 OG1 A:THR297 4.7 22.5 1.0 CB A:ASN300 4.8 21.3 1.0 CA A:ASN300 4.8 23.6 1.0 C A:GLU519 4.9 21.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli


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 the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:23.8 occ:1.00 O B:GLN294 2.3 20.1 1.0 O B:ALA518 2.4 22.6 1.0 O B:ALA299 2.4 26.4 1.0 O B:THR297 2.4 19.1 1.0 O B:HOH757 2.4 19.4 1.0 O B:HOH747 2.6 19.6 1.0 C B:THR297 3.4 20.3 1.0 C B:GLN294 3.4 19.8 1.0 C B:PHE298 3.4 21.9 1.0 C B:ALA299 3.5 25.9 1.0 N B:ALA299 3.6 24.2 1.0 C B:ALA518 3.6 20.6 1.0 CA B:PHE298 3.7 22.2 1.0 O B:PHE298 3.8 24.3 1.0 N B:PHE298 3.9 22.8 1.0 CA B:GLN294 4.1 21.3 1.0 CA B:ALA299 4.1 26.8 1.0 CG2 B:ILE521 4.4 19.8 1.0 CA B:GLU519 4.4 20.0 1.0 N B:ALA295 4.4 19.9 1.0 N B:GLU519 4.4 19.6 1.0 N B:THR297 4.4 19.6 1.0 CA B:ALA518 4.5 21.7 1.0 CA B:THR297 4.5 22.2 1.0 N B:ASN300 4.5 24.0 1.0 CB B:GLN294 4.5 18.4 1.0 CA B:ALA295 4.6 21.5 1.0 OG1 B:THR297 4.6 21.3 1.0 O B:ALA295 4.6 19.8 1.0 C B:ALA295 4.6 20.0 1.0 OE1 B:GLU519 4.7 26.7 1.0 CB B:ASN300 4.8 25.0 1.0 CA B:ASN300 4.8 24.3 1.0 C B:GLU519 4.9 21.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the C-Terminal Periplasmic Domain of Eceptc From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:21.6 occ:1.00 O C:GLN294 2.3 19.5 1.0 O C:ALA518 2.4 24.5 1.0 O C:THR297 2.4 21.9 1.0 O C:ALA299 2.4 21.0 1.0 O C:HOH832 2.4 21.2 1.0 O C:HOH740 2.7 19.7 1.0 C C:THR297 3.4 22.7 1.0 C C:GLN294 3.4 20.1 1.0 C C:PHE298 3.4 20.6 1.0 C C:ALA299 3.5 22.0 1.0 C C:ALA518 3.6 24.6 1.0 N C:ALA299 3.6 21.9 1.0 CA C:PHE298 3.7 21.5 1.0 O C:PHE298 3.8 23.0 1.0 N C:PHE298 3.9 19.5 1.0 CA C:ALA299 4.1 22.0 1.0 CA C:GLN294 4.1 20.0 1.0 CG2 C:ILE521 4.4 19.8 1.0 N C:ALA295 4.4 20.7 1.0 CA C:GLU519 4.4 24.2 1.0 N C:GLU519 4.4 21.4 1.0 N C:THR297 4.5 19.6 1.0 CA C:ALA518 4.5 24.7 1.0 N C:ASN300 4.5 22.6 1.0 CA C:THR297 4.5 22.8 1.0 CA C:ALA295 4.6 22.2 1.0 CB C:GLN294 4.6 20.2 1.0 O C:ALA295 4.6 21.6 1.0 C C:ALA295 4.6 20.9 1.0 OG1 C:THR297 4.7 21.9 1.0 OE1 C:GLU519 4.8 25.1 1.0 CB C:ASN300 4.8 21.6 1.0 CA C:ASN300 4.8 22.5 1.0 C C:GLU519 4.9 22.1 1.0 CB C:ILE521 5.0 21.2 1.0

Y.Zhao, Q.Meng, Y.Lai, L.Wang, D.Zhou, C.Dou, Y.Gu, C.Nie, Y.Wei, W.Cheng. Structural and Mechanistic Insights Into Polymyxin Resistance Mediated By Eptc Originating From Escherichia Coli. Febs J. V. 286 750 2019.
ISSN: ISSN 1742-4658
PubMed: 30537137
DOI: 10.1111/FEBS.14719