Sodium in PDB 4ka8: Structure of Organellar Oligopeptidase

The structure of Structure of Organellar Oligopeptidase, PDB code: 4ka8 was solved by R.P.-A.Berntsson, B.Kmiec, P.F.Teixeira, L.M.Svensson, A.Bakali, E.Glaser, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.39 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.817, 101.339, 132.908, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.8

The structure of Structure of Organellar Oligopeptidase also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Structure of Organellar Oligopeptidase (pdb code 4ka8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Organellar Oligopeptidase, PDB code: 4ka8:

Sodium binding site 1 out of 1 in the Structure of Organellar Oligopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Organellar Oligopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na806 b:31.9 occ:1.00 O A:HOH1038 2.2 41.1 1.0 O A:MET379 2.3 30.2 1.0 O A:LYS382 2.3 27.8 1.0 O A:ALA384 2.4 29.7 1.0 O A:HOH1082 2.5 43.2 1.0 C A:LYS382 3.3 28.1 1.0 C A:MET379 3.4 29.9 1.0 O A:HOH1050 3.5 41.9 1.0 C A:ALA384 3.6 29.2 1.0 N A:LYS382 3.9 27.9 1.0 C A:MET383 3.9 29.7 1.0 O A:MET383 4.0 27.1 1.0 CA A:LYS382 4.0 27.9 1.0 N A:ALA384 4.0 28.3 1.0 CB A:MET379 4.2 32.4 1.0 CA A:MET379 4.2 31.1 1.0 N A:MET383 4.3 27.8 1.0 CB A:LYS382 4.4 30.1 1.0 N A:ALA380 4.4 29.4 1.0 CA A:ALA384 4.4 28.6 1.0 N A:THR385 4.5 29.9 1.0 CA A:MET383 4.5 29.6 1.0 C A:ALA380 4.5 30.1 1.0 CG2 A:THR385 4.6 32.0 1.0 CA A:ALA380 4.6 30.5 1.0 O A:ALA380 4.6 30.1 1.0 CA A:THR385 4.7 30.4 1.0 N A:MET381 5.0 31.3 1.0

B.Kmiec, P.F.Teixeira, R.P.-A.Berntsson, M.W.Murcha, R.M.M.Branca, J.Radomiljac, J.Regberg, L.M.Svensson, A.Bakali, U.Langel, J.Lehtio, J.Whelan, P.Stenmark, E.Glaser. Organellar Oligopeptidase (Oop) Provides A Complementary Pathway For Targeting Peptide Degradation in Mitochondria and Chloroplasts Proc.Natl.Acad.Sci.Usa 2013.
ISSN: ESSN 1091-6490