Sodium in PDB 9lks: Crystal Structure of N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis.

The structure of Crystal Structure of N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis., PDB code: 9lks was solved by V.Sharma, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.63 / 1.79
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.182, 68.182, 127.412, 90, 90, 120
R / Rfree (%)	16.5 / 21.9

The binding sites of Sodium atom in the Crystal Structure of N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis. (pdb code 9lks). 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 N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis., PDB code: 9lks:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis.


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 N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:35.5 occ:1.00 O A:HOH360 2.6 42.4 1.0 O A:ALA157 2.6 22.3 1.0 O A:HOH372 2.7 31.8 1.0 O A:HOH357 2.8 29.2 1.0 O A:PRO159 3.5 21.9 1.0 C A:ALA157 3.8 20.2 1.0 O A:HOH306 4.0 39.1 1.0 CA A:VAL160 4.1 21.8 1.0 CB A:ALA157 4.1 22.9 1.0 CG2 A:VAL160 4.1 22.7 1.0 CA A:ALA157 4.3 20.1 1.0 C A:PRO159 4.4 22.8 1.0 N A:ALA157 4.4 21.4 1.0 CB A:VAL160 4.5 22.4 1.0 CG1 A:VAL160 4.5 24.0 1.0 N A:VAL160 4.6 22.1 1.0 NZ A:LYS100 4.6 37.7 1.0 N A:PHE158 4.9 20.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis.


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 N-Terminal Flexible Domain of the Shaft Pilin Ebpc From Enterococcus Faecalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:35.3 occ:1.00 O A:PRO185 2.8 26.8 1.0 O A:LYS46 2.8 30.9 1.0 NZ A:LYS45 2.9 28.0 1.0 O2 A:EDO203 2.9 44.5 1.0 O1 A:EDO203 3.3 43.8 1.0 C2 A:EDO203 3.4 44.6 1.0 CE A:LYS45 3.5 27.4 1.0 O A:HOH320 3.6 25.0 1.0 CA A:LYS186 3.7 29.2 1.0 CD A:LYS45 3.8 25.6 1.0 C A:PRO185 3.8 25.3 1.0 O A:HOH309 3.8 34.0 1.0 C1 A:EDO203 3.9 46.7 1.0 C A:LYS46 4.0 30.3 1.0 N A:LYS186 4.2 25.9 1.0 CG A:MET48 4.3 45.1 1.0 N A:LYS46 4.3 26.9 1.0 CB A:LYS186 4.4 33.3 1.0 CE A:MET48 4.4 46.5 1.0 C A:LYS186 4.6 29.4 1.0 N A:ASN187 4.6 32.9 1.0 O A:VAL149 4.7 30.0 1.0 SD A:MET48 4.7 48.9 1.0 CA A:LYS46 4.7 27.2 1.0 CB A:ALA151 4.7 24.5 1.0 N A:MET48 4.8 40.0 1.0 CB A:MET48 4.9 42.9 1.0

V.Sharma, V.Krishnan. Structural Basis of Ebp Pilus Shaft Formation and Anchoring in Vancomycin-Resistant Enterococci. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40608565
DOI: 10.1111/FEBS.70173