Sodium in PDB 4q4b: Crystal Structure of Limp-2 (Space Group C2221)

The structure of Crystal Structure of Limp-2 (Space Group C2221), PDB code: 4q4b was solved by Y.Zhao, J.Ren, S.Padilla-Parra, L.E.Fry, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.82
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	63.729, 95.943, 217.816, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.6

The binding sites of Sodium atom in the Crystal Structure of Limp-2 (Space Group C2221) (pdb code 4q4b). 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 Limp-2 (Space Group C2221), PDB code: 4q4b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Limp-2 (Space Group C2221)


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 Limp-2 (Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na530 b:58.4 occ:1.00 OG1 A:THR398 2.3 55.3 1.0 O A:LEU392 2.3 59.1 1.0 O A:PHE395 2.3 60.1 1.0 O A:GLY399 2.3 55.9 1.0 C A:GLY399 3.3 54.8 1.0 N A:GLY399 3.3 54.0 1.0 C A:LEU392 3.4 59.1 1.0 C A:PHE395 3.5 60.3 1.0 CB A:THR398 3.6 53.5 1.0 CA A:GLY399 3.6 54.8 1.0 C A:THR398 3.7 53.3 1.0 N A:LEU392 3.8 55.3 1.0 CA A:VAL396 4.0 61.0 1.0 CA A:THR398 4.1 53.3 1.0 CG A:LYS391 4.1 56.7 1.0 CA A:LEU392 4.2 57.1 1.0 N A:VAL396 4.2 60.7 1.0 N A:THR398 4.3 54.6 1.0 O A:THR398 4.4 52.8 1.0 N A:ASP393 4.5 61.5 1.0 N A:ASP400 4.5 54.9 1.0 NZ A:LYS391 4.5 60.7 1.0 C A:VAL396 4.5 59.5 1.0 CA A:PHE395 4.7 59.9 1.0 CG2 A:THR398 4.7 52.9 1.0 CE A:LYS391 4.7 59.7 1.0 CA A:ASP393 4.7 63.6 1.0 CB A:LEU392 4.8 56.5 1.0 C A:LYS391 4.8 54.7 1.0 N A:PHE395 4.9 61.3 1.0 O A:VAL396 4.9 59.0 1.0 CA A:LYS391 4.9 53.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Limp-2 (Space Group C2221)


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 Limp-2 (Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na531 b:77.8 occ:1.00 O2 A:BMA516 2.2 73.8 1.0 O4 A:MAN519 2.2 84.0 1.0 C4 A:MAN519 3.4 87.8 1.0 C2 A:BMA516 3.6 71.6 1.0 C5 A:MAN519 3.9 89.7 1.0 C3 A:MAN519 3.9 88.1 1.0 O5 A:BMA516 3.9 69.5 1.0 C1 A:BMA516 4.1 68.7 1.0 O3 A:BMA516 4.1 76.9 1.0 O6 A:MAN519 4.2 89.9 1.0 C3 A:BMA516 4.2 73.2 1.0 C4 A:BMA516 4.2 72.9 1.0 O4 A:NAG515 4.2 66.0 1.0 O6 A:BMA516 4.2 72.9 1.0 C1 A:MAN518 4.3 83.5 1.0 O3 A:MAN519 4.5 88.0 1.0 C6 A:MAN519 4.5 91.0 1.0 C5 A:BMA516 4.6 70.6 1.0 C3 A:MAN517 4.6 78.7 1.0 O3 A:NAG515 4.6 60.7 1.0 O5 A:MAN518 4.7 83.6 1.0 O2 A:MAN518 4.8 88.1 1.0 C2 A:MAN517 5.0 76.3 1.0

Y.Zhao, J.Ren, S.Padilla-Parra, E.E.Fry, D.I.Stuart. Lysosome Sorting of Beta-Glucocerebrosidase By Limp-2 Is Targeted By the Mannose 6-Phosphate Receptor. Nat Commun V. 5 4321 2014.
ISSN: ESSN 2041-1723
PubMed: 25027712
DOI: 10.1038/NCOMMS5321