Sodium in PDB 9lj6: Crystal Structure of C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb From Enterococcus Faecalis.

The structure of Crystal Structure of C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb From Enterococcus Faecalis., PDB code: 9lj6 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)	102.87 / 2.16
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.538, 118.538, 69.781, 90, 90, 120
R / Rfree (%)	16.1 / 19

The binding sites of Sodium atom in the Crystal Structure of C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb From Enterococcus Faecalis. (pdb code 9lj6). 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 C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb From Enterococcus Faecalis., PDB code: 9lj6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb 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 C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:35.5 occ:1.00 OD1 A:ASP267 2.4 37.8 1.0 O A:PHE268 2.5 32.3 1.0 O A:PHE225 2.5 27.8 1.0 O A:HOH667 2.8 36.9 1.0 N A:PHE225 3.0 25.9 1.0 C A:PHE225 3.2 25.3 1.0 N A:PHE268 3.2 24.4 1.0 C A:PHE268 3.4 28.6 1.0 CA A:PHE225 3.5 24.7 1.0 CG A:ASP267 3.7 32.7 1.0 CA A:PHE268 3.8 24.0 1.0 C A:ASP267 3.9 24.9 1.0 CG A:ARG226 3.9 32.3 1.0 C A:GLU224 4.0 28.3 1.0 CB A:PHE225 4.0 23.5 1.0 CA A:GLU224 4.1 30.9 1.0 CA A:ASP267 4.2 24.7 1.0 N A:ARG226 4.2 25.7 1.0 CG A:GLU224 4.3 51.1 1.0 CB A:PHE268 4.3 21.6 1.0 CB A:ASP267 4.5 27.8 1.0 OD2 A:ASP267 4.5 39.1 1.0 CA A:ARG226 4.7 25.0 1.0 O A:HOH665 4.7 29.6 1.0 O A:ASP267 4.7 25.0 1.0 N A:SER269 4.7 30.0 1.0 CD1 A:ILE270 4.8 33.0 1.0 CD A:ARG226 4.8 36.2 1.0 CB A:GLU224 4.9 35.6 1.0 CB A:ARG226 4.9 26.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb 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 C-Terminal Rigid Fragment Containing Middle and C-Terminal Domains of the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:46.0 occ:1.00 O A:THR423 2.5 45.0 1.0 OG A:SER324 2.5 35.4 1.0 O A:TYR416 2.5 36.7 1.0 NE A:ARG422 3.2 44.6 1.0 N A:THR423 3.3 41.2 1.0 C A:THR423 3.4 41.5 1.0 C A:TYR416 3.4 33.0 1.0 CB A:SER324 3.4 32.7 1.0 CA A:THR423 3.6 40.0 1.0 O A:HOH627 3.7 30.9 1.0 CA A:TYR416 3.8 33.4 1.0 CD1 A:TYR416 3.8 33.0 1.0 CB A:THR423 3.9 37.2 1.0 CD A:ARG422 3.9 46.8 1.0 C A:ARG422 3.9 43.0 1.0 NH2 A:ARG422 4.0 44.2 1.0 CB A:ARG422 4.0 44.8 1.0 CZ A:ARG422 4.0 41.4 1.0 CG A:TYR416 4.1 31.4 1.0 CE1 A:TYR416 4.1 33.2 1.0 CA A:ARG422 4.2 46.1 1.0 N A:SER324 4.3 35.1 1.0 O A:SER415 4.5 34.4 1.0 CA A:SER324 4.5 32.6 1.0 CB A:TYR416 4.5 31.2 1.0 N A:ALA424 4.6 41.3 1.0 CG A:ARG422 4.6 45.9 1.0 OG1 A:THR423 4.6 38.0 1.0 CD2 A:TYR416 4.6 32.7 1.0 N A:ALA417 4.7 33.6 1.0 CZ A:TYR416 4.7 31.9 1.0 O A:ARG422 4.7 42.3 1.0 N A:TYR416 4.9 32.2 1.0 CE2 A:TYR416 4.9 33.8 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