Sodium in PDB 8kg4: Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form

The structure of Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form, PDB code: 8kg4 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)	39.71 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.825, 50.853, 125.488, 90, 90, 90
R / Rfree (%)	16.9 / 18.8

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

Iodine

(I)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of M- and C-Domains of the Shaft Pilin Lrpa From Ligilactobacillus Ruminis - Orthorhombic Form (pdb code 8kg4). 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 - Orthorhombic Form, PDB code: 8kg4:
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 - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:11.2 occ:1.00 OH A:TYR230 2.7 6.6 1.0 O A:GLU339 2.8 5.8 1.0 O A:ILE320 2.8 5.0 1.0 OG A:SER338 3.2 6.0 1.0 N A:ASN322 3.4 4.9 1.0 CA A:PRO321 3.5 5.4 1.0 CZ A:TYR230 3.6 5.8 1.0 CE1 A:TYR230 3.6 5.5 1.0 CG1 A:VAL341 3.6 6.5 1.0 N A:VAL341 3.7 5.2 1.0 C A:PRO321 3.7 5.1 1.0 C A:ILE320 3.9 5.2 1.0 CG2 A:VAL341 3.9 6.7 1.0 C A:GLU339 4.0 5.3 1.0 CA A:GLU340 4.2 5.4 1.0 C A:GLU340 4.2 5.5 1.0 N A:PRO321 4.2 5.5 1.0 CB A:VAL341 4.2 6.1 1.0 CD2 A:LEU256 4.5 6.8 1.0 CB A:ASN322 4.5 4.8 1.0 CB A:SER338 4.5 5.8 1.0 N A:GLU340 4.5 5.3 1.0 CA A:ASN322 4.5 4.9 1.0 CA A:VAL341 4.5 5.5 1.0 O A:PRO321 4.6 5.9 1.0 CB A:PRO321 4.8 5.7 1.0 CE2 A:TYR230 4.9 6.3 1.0 CD1 A:TYR230 4.9 5.7 1.0 CD1 A:LEU213 5.0 6.0 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 - Orthorhombic Form


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 - Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na513 b:15.4 occ:1.00 OG1 A:THR302 2.8 10.3 1.0 O A:LEU300 2.9 8.5 1.0 OG1 A:THR234 3.0 9.3 1.0 O A:ILE232 3.2 8.6 1.0 CB A:THR302 3.5 9.0 1.0 CD1 A:ILE248 3.6 9.5 1.0 N A:THR302 3.6 7.6 1.0 C A:LEU300 3.6 8.2 1.0 N A:THR234 3.8 6.6 1.0 C A:ILE232 3.8 6.8 1.0 CG2 A:THR234 3.9 9.0 1.0 CB A:THR234 3.9 8.1 1.0 CG2 A:ILE232 4.0 9.1 1.0 CB A:LEU300 4.0 10.4 1.0 CD2 A:LEU300 4.1 11.8 1.0 CG A:LEU300 4.1 11.1 1.0 C A:LYS301 4.2 7.6 1.0 N A:LYS301 4.2 8.1 1.0 CA A:THR302 4.2 7.2 1.0 CA A:GLU233 4.2 7.1 1.0 CA A:LYS301 4.2 8.2 1.0 N A:GLU233 4.3 6.0 1.0 C A:GLU233 4.3 6.3 1.0 CB A:ILE232 4.3 7.1 1.0 CA A:LEU300 4.4 9.2 1.0 CA A:THR234 4.4 7.3 1.0 CA A:ILE232 4.7 6.5 1.0 CG1 A:ILE248 4.7 8.3 1.0 CG2 A:THR302 4.8 10.1 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