Sodium in PDB 2oni: Catalytic Domain of the Human NEDD4-Like E3 Ligase

The structure of Catalytic Domain of the Human NEDD4-Like E3 Ligase, PDB code: 2oni was solved by J.R.Walker, G.V.Avvakumov, S.Xue, C.Butler-Cole, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 2.20
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.058, 103.058, 182.214, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 25.9

The binding sites of Sodium atom in the Catalytic Domain of the Human NEDD4-Like E3 Ligase (pdb code 2oni). 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 Catalytic Domain of the Human NEDD4-Like E3 Ligase, PDB code: 2oni:

Sodium binding site 1 out of 1 in the Catalytic Domain of the Human NEDD4-Like E3 Ligase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catalytic Domain of the Human NEDD4-Like E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1000 b:45.7 occ:1.00 O A:THR883 2.4 39.8 1.0 OD1 A:ASN924 2.5 41.0 1.0 O A:THR921 2.7 44.8 1.0 C A:THR883 3.5 39.4 1.0 CG A:ASN924 3.6 41.0 1.0 O A:TYR897 3.7 51.8 1.0 C A:THR921 3.9 46.9 1.0 CA A:THR883 3.9 39.1 1.0 CA A:GLY898 4.0 60.4 1.0 CB A:THR883 4.0 38.6 1.0 ND2 A:ASN924 4.2 39.8 1.0 O A:HOH63 4.3 45.7 1.0 O A:HOH101 4.5 57.6 1.0 N A:ASN924 4.6 43.7 1.0 C A:GLY898 4.6 67.3 1.0 C A:TYR897 4.6 52.7 1.0 N A:GLY884 4.7 37.2 1.0 CA A:CYS922 4.7 56.0 1.0 N A:CYS922 4.7 50.8 1.0 CA A:THR921 4.8 45.1 1.0 N A:GLY898 4.8 56.3 1.0 C A:CYS922 4.8 54.7 1.0 CB A:ASN924 4.8 39.0 1.0 O A:CYS922 4.8 56.7 1.0 CA A:ASN924 4.9 41.3 1.0 OG1 A:THR883 4.9 39.3 1.0 CB A:THR921 5.0 47.1 1.0

J.R.Walker, G.V.Avvakumov, S.Xue, C.Butler-Cole, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. NEDD4-Like E3 Ubiquitin-Protein Ligase To Be Published.