Sodium in PDB 4dka: Structure of Editosome Protein

The structure of Structure of Editosome Protein, PDB code: 4dka was solved by Y.-J.Park, W.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.97
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.653, 105.912, 40.580, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.9

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

Sodium binding site 1 out of 2 in the Structure of Editosome Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Editosome Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:17.5 occ:1.00 O D:HOH801 2.2 30.8 1.0 O A:GLU113 2.3 24.1 1.0 O D:HOH806 2.4 29.6 1.0 OD1 A:ASP99 2.4 20.9 1.0 OD2 A:ASP115 2.4 25.4 1.0 O A:HOH327 2.5 34.5 1.0 OD1 A:ASP115 2.7 28.9 1.0 CG A:ASP115 2.9 26.4 1.0 C A:GLU113 3.5 23.8 1.0 CG A:ASP99 3.6 20.9 1.0 O A:HOH303 4.0 31.5 1.0 N A:ARG100 4.1 22.1 1.0 CA A:GLU113 4.2 24.7 1.0 OD2 A:ASP99 4.2 22.1 1.0 OD1 D:ASP637 4.4 27.0 1.0 CB A:ASP115 4.4 27.2 1.0 CB A:GLU113 4.4 24.9 1.0 N A:PHE101 4.4 21.8 1.0 O A:HOH318 4.5 34.8 1.0 N A:TYR114 4.5 23.5 1.0 O A:HOH320 4.5 38.7 1.0 OD2 D:ASP637 4.5 27.4 1.0 CB A:ASP99 4.6 20.4 1.0 N A:ASP115 4.6 23.4 1.0 CA A:ASP99 4.6 21.0 1.0 C A:TYR114 4.6 24.3 1.0 CA A:TYR114 4.6 23.1 1.0 C A:ASP99 4.9 21.9 1.0 CB A:PHE101 4.9 20.1 1.0 CG D:ASP637 4.9 26.0 1.0 CA A:ARG100 4.9 23.9 1.0 CA A:ASP115 5.0 25.7 1.0 CB A:ARG100 5.0 26.8 1.0

Sodium binding site 2 out of 2 in the Structure of Editosome Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Editosome Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:20.6 occ:1.00 O B:GLU113 2.3 26.5 1.0 OD1 B:ASP99 2.4 22.6 1.0 OD2 B:ASP115 2.5 26.4 1.0 O B:HOH327 2.5 37.2 1.0 OD1 B:ASP115 2.6 29.5 1.0 CG B:ASP115 2.9 27.5 1.0 C B:GLU113 3.5 26.4 1.0 CG B:ASP99 3.5 22.5 1.0 N B:ARG100 4.1 23.1 1.0 O B:HOH302 4.1 25.3 1.0 CA B:GLU113 4.2 27.8 1.0 OD2 B:ASP99 4.2 23.4 1.0 N B:PHE101 4.4 21.8 1.0 CB B:ASP115 4.4 26.8 1.0 CB B:GLU113 4.5 26.5 1.0 N B:TYR114 4.5 27.3 1.0 CA B:ASP99 4.6 22.4 1.0 CB B:ASP99 4.6 21.7 1.0 N B:ASP115 4.6 25.6 1.0 CA B:TYR114 4.7 25.5 1.0 C B:TYR114 4.7 26.4 1.0 C B:ASP99 4.8 22.9 1.0 CB B:PHE101 4.9 21.9 1.0 CA B:ARG100 4.9 23.5 1.0 CB B:ARG100 5.0 25.1 1.0 CA B:ASP115 5.0 26.6 1.0

Y.J.Park, T.Budiarto, M.Wu, E.Pardon, J.Steyaert, W.G.Hol. The Structure of the C-Terminal Domain of the Largest Editosome Interaction Protein and Its Role in Promoting Rna Binding By Rna-Editing Ligase L2. Nucleic Acids Res. V. 40 6966 2012.
ISSN: ISSN 0305-1048
PubMed: 22561373
DOI: 10.1093/NAR/GKS369