Sodium in PDB 8c61: Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa

The structure of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa, PDB code: 8c61 was solved by K.Wendrich, M.Gersch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.28 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.743, 126.559, 144.167, 90, 90, 90
R / Rfree (%)	20 / 24.3

The structure of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa also contains other interesting chemical elements:

Zinc	(Zn)	12 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa (pdb code 8c61). 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 USP54 in Complex with LYS63-Linked Diubiquitin-Pa, PDB code: 8c61:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:75.2 occ:1.00 OD2 C:ASP52 2.5 83.0 1.0 OD2 F:ASP52 2.5 98.5 1.0 OE1 F:GLU24 2.5 101.8 1.0 OE2 C:GLU24 2.7 106.2 1.0 CG C:ASP52 3.6 90.2 1.0 CD F:GLU24 3.6 105.9 1.0 CG F:ASP52 3.6 101.2 1.0 CD C:GLU24 3.6 102.0 1.0 CG C:GLU24 3.9 92.8 1.0 OE2 F:GLU24 4.0 100.8 1.0 CB F:ASP52 4.1 107.8 1.0 CB C:ASP52 4.2 79.0 1.0 NZ F:LYS27 4.3 109.1 1.0 OD1 C:ASP52 4.5 83.3 1.0 OD1 F:ASP52 4.7 104.8 1.0 OE1 C:GLU24 4.7 97.2 1.0 CG F:GLU24 4.9 106.4 1.0 CB F:PRO38 4.9 106.8 1.0 O F:PRO38 4.9 100.5 1.0 CE F:LYS27 5.0 109.7 1.0

Sodium binding site 2 out of 2 in the Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of USP54 in Complex with LYS63-Linked Diubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ G:Na805 b:120.4 occ:1.00 O G:LEU292 3.6 79.0 1.0 CD2 G:PHE308 4.0 111.9 1.0 CE2 G:PHE308 4.1 117.0 1.0 CG G:PHE308 4.2 101.2 1.0 CB G:TYR291 4.3 87.1 1.0 CZ G:PHE308 4.4 114.6 1.0 CD1 G:PHE308 4.5 99.0 1.0 CE1 G:PHE308 4.7 106.3 1.0 C G:LEU292 4.7 76.3 1.0 CB G:PHE308 4.8 93.4 1.0 CD1 G:TYR291 4.8 89.4 1.0 CG G:TYR291 4.9 93.6 1.0 CZ2 G:TRP315 4.9 80.3 1.0 N G:LEU292 5.0 78.2 1.0

K.Wendrich, M.Gersch. Structure of USP54 in Complex with LYS63 Linked Diubiquitin-Pa To Be Published.