Sodium in PDB 8kb2: Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative

The structure of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative, PDB code: 8kb2 was solved by A.Prajapati, A.Palva, I.Von Ossowski, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.58 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.903, 50.898, 125.623, 90, 90, 90
R / Rfree (%)	17.9 / 21.1

The structure of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative also contains other interesting chemical elements:

Iodine	(I)	13 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative (pdb code 8kb2). 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 M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative, PDB code: 8kb2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


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 M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Na514 b:21.8 occ:1.00 OH A:TYR230 2.5 14.2 1.0 O A:ILE320 2.8 13.9 1.0 O A:GLU339 2.9 15.2 1.0 OG A:SER338 3.3 13.8 1.0 CZ A:TYR230 3.4 12.8 1.0 N A:ASN322 3.4 15.1 1.0 CE1 A:TYR230 3.5 13.0 1.0 CA A:PRO321 3.6 15.3 1.0 CG1 A:VAL341 3.6 13.2 1.0 N A:VAL341 3.7 13.7 1.0 C A:PRO321 3.8 15.0 1.0 C A:ILE320 3.9 14.9 1.0 C A:GLU339 4.0 16.7 1.0 CG2 A:VAL341 4.0 13.3 1.0 CA A:GLU340 4.2 15.9 1.0 C A:GLU340 4.2 14.7 1.0 N A:PRO321 4.2 15.5 1.0 CD2 A:LEU256 4.3 16.8 1.0 CB A:VAL341 4.3 12.9 1.0 CB A:ASN322 4.5 13.7 1.0 CA A:ASN322 4.5 14.2 1.0 CB A:SER338 4.5 14.5 1.0 N A:GLU340 4.5 16.1 1.0 CA A:VAL341 4.6 13.5 1.0 O A:PRO321 4.7 15.1 1.0 CE2 A:TYR230 4.7 13.8 1.0 CD1 A:TYR230 4.8 13.2 1.0 CB A:PRO321 4.9 15.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative


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 M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Iodide Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Na515 b:24.8 occ:0.75 OG1 A:THR302 2.7 28.6 1.0 O A:LEU300 3.0 20.4 1.0 OG1 A:THR234 3.1 22.5 1.0 O A:ILE232 3.2 20.6 1.0 CB A:THR302 3.5 25.0 1.0 N A:THR302 3.6 21.2 1.0 C A:LEU300 3.6 21.4 1.0 CD1 A:ILE248 3.6 19.8 1.0 C A:ILE232 3.8 21.1 1.0 CG2 A:THR234 3.8 23.1 1.0 N A:THR234 3.9 19.6 1.0 CB A:THR234 4.0 21.8 1.0 CG2 A:ILE232 4.0 21.6 1.0 N A:LYS301 4.1 20.6 1.0 C A:LYS301 4.1 22.1 1.0 CB A:LEU300 4.1 22.8 1.0 CA A:THR302 4.2 22.2 1.0 CG A:LEU300 4.2 25.3 1.0 CA A:LYS301 4.2 23.1 1.0 CA A:GLU233 4.3 21.8 1.0 CD2 A:LEU300 4.3 25.5 1.0 CB A:ILE232 4.3 20.4 1.0 N A:GLU233 4.3 20.3 1.0 C A:GLU233 4.3 20.8 1.0 CA A:LEU300 4.5 21.9 1.0 CA A:THR234 4.5 20.6 1.0 CA A:ILE232 4.7 19.7 1.0 CG2 A:THR302 4.7 25.5 1.0 CG1 A:ILE248 4.9 18.3 1.0

A.Prajapati, A.Palva, I.Von Ossowski, V.Krishnan. The Crystal Structure of the N-Terminal Domain of the Backbone Pilin Lrpa Reveals A New Closure-and-Twist Motion For Assembling Dynamic Pili in Ligilactobacillus Ruminis. Acta Crystallogr D Struct 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38935340
DOI: 10.1107/S2059798324005114