Sodium in PDB 8pzo: Lpdd

The structure of Lpdd, PDB code: 8pzo was solved by D.Gahloth, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.42 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.143, 92.849, 125.009, 90, 90, 90
R / Rfree (%)	18.5 / 23.1

The binding sites of Sodium atom in the Lpdd (pdb code 8pzo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Lpdd, PDB code: 8pzo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Lpdd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lpdd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:61.6 occ:1.00 O A:HOH312 2.2 51.2 1.0 O A:HOH424 2.3 56.3 1.0 O A:HOH315 2.3 38.8 1.0 O A:HOH322 2.4 43.7 1.0 O A:HOH420 2.4 37.3 1.0 O A:HOH414 2.4 63.6 1.0 O A:HOH404 3.9 46.4 1.0 OD2 A:ASP38 3.9 60.5 1.0 O A:HOH399 4.2 65.1 1.0 O A:HOH338 4.2 39.3 1.0 O A:PHE53 4.2 33.9 1.0 O A:HOH429 4.2 39.4 1.0 O A:GLY37 4.3 20.9 1.0 OD1 A:ASP38 4.4 55.2 1.0 O A:HOH336 4.4 41.5 1.0 CG A:ASP38 4.5 46.7 1.0 CG A:ASP63 4.7 54.4 1.0 O A:HOH382 4.7 38.8 1.0 OD2 A:ASP63 4.7 58.7 1.0 O A:HOH426 4.8 44.5 1.0 OD1 A:ASP63 4.8 51.0 1.0 O A:HOH302 4.9 49.0 1.0 CB A:LYS52 4.9 22.4 1.0 C A:GLY37 4.9 20.6 1.0

Sodium binding site 2 out of 4 in the Lpdd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lpdd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:63.4 occ:1.00 O A:HOH321 2.3 18.1 1.0 O A:HOH437 2.3 47.8 1.0 O A:HOH356 2.4 58.9 1.0 O A:HOH384 2.4 42.8 1.0 OE1 A:GLN111 4.2 23.2 1.0 OG1 A:THR5 4.2 25.1 1.0 O A:THR3 4.3 18.5 1.0 O A:HOH339 4.5 29.9 1.0 N A:THR5 4.6 15.6 1.0 CA A:PHE4 4.8 25.4 1.0 O A:HOH413 4.9 49.1 1.0

Sodium binding site 3 out of 4 in the Lpdd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lpdd within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:53.7 occ:1.00 O B:HOH310 2.3 21.3 1.0 O B:HOH367 2.4 52.1 1.0 O B:HOH426 2.4 50.0 1.0 O B:HOH336 2.4 46.9 1.0 OG1 B:THR5 4.0 24.2 1.0 O B:THR3 4.2 24.2 1.0 OE1 B:GLN111 4.2 20.0 1.0 N B:THR5 4.5 17.4 1.0 O B:HOH418 4.5 40.5 1.0 O B:HOH305 4.7 33.3 1.0 CA B:PHE4 4.7 19.5 1.0

Sodium binding site 4 out of 4 in the Lpdd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Lpdd within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:55.0 occ:1.00 O B:HOH324 2.2 47.7 1.0 O B:HOH393 2.3 54.6 1.0 O B:HOH410 2.3 43.6 1.0 O B:HOH327 2.3 46.1 1.0 O B:HOH396 2.4 47.8 1.0 O B:HOH322 2.5 59.3 1.0 OD2 B:ASP38 3.9 52.2 1.0 O B:HOH372 4.3 42.9 1.0 O B:PHE53 4.3 36.9 1.0 OD1 B:ASP38 4.3 47.2 1.0 O B:HOH348 4.3 47.5 1.0 O B:HOH317 4.3 40.6 1.0 O B:HOH365 4.4 46.4 1.0 O B:HOH413 4.5 40.0 1.0 CG B:ASP38 4.5 41.7 1.0 O B:HOH423 4.5 40.8 1.0 O B:GLY37 4.5 19.4 1.0 CG B:ASP63 4.6 58.7 1.0 OD1 B:ASP63 4.7 50.7 1.0 OD2 B:ASP63 4.7 65.6 1.0 CB B:LYS52 4.9 29.9 1.0

D.Gahloth, D.Leys. Structure of Lpdd From Lactobacillus Plantarum. To Be Published.