Sodium in PDB 7nbb: Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3, PDB code: 7nbb was solved by S.M.Lange, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.95 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.389, 97.615, 74.967, 90, 109.96, 90
R / Rfree (%)	17.5 / 21.2

The structure of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Sodium atom in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 (pdb code 7nbb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3, PDB code: 7nbb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:49.6 occ:1.00 O C:HOH232 2.6 50.4 1.0 OE1 C:GLN31 2.8 47.6 1.0 O C:ALA28 3.0 43.8 1.0 OD1 C:ASP32 3.2 57.8 1.0 CD C:GLN31 3.6 45.1 1.0 CA C:ALA28 3.7 41.8 1.0 C C:ALA28 3.7 40.6 1.0 CB C:ALA28 3.9 47.3 1.0 CG C:GLN31 3.9 44.1 1.0 CB C:GLN31 4.0 41.3 1.0 CG C:ASP32 4.0 56.4 1.0 OD2 C:ASP32 4.3 60.4 1.0 N C:ASP32 4.6 41.2 1.0 NE2 C:GLN31 4.7 42.8 1.0 N C:LYS29 5.0 37.4 1.0

Sodium binding site 2 out of 2 in the Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na201 b:42.7 occ:1.00 O F:HOH360 2.5 37.4 1.0 OH H:TYR108 2.7 27.2 0.5 OD1 H:ASP102 2.7 41.2 1.0 CE2 H:TYR108 3.1 21.8 0.5 CZ H:TYR108 3.2 23.9 0.5 CG G:GLN49 3.3 34.2 1.0 N H:ASP102 3.4 28.0 1.0 CG H:ASP102 3.5 41.7 1.0 CD2 F:LEU8 3.6 26.6 1.0 CD G:GLN49 3.7 43.7 1.0 CB G:GLN49 3.7 27.6 1.0 CG F:LEU8 3.7 25.3 1.0 CB H:ASP102 3.8 37.0 1.0 CD1 F:LEU8 3.9 23.3 1.0 CA H:GLY101 4.0 27.0 1.0 OE1 G:GLN49 4.1 49.5 1.0 CZ H:TYR108 4.1 23.1 0.5 OH H:TYR108 4.1 27.2 0.5 C H:GLY101 4.2 26.0 1.0 NE2 G:GLN49 4.2 48.6 1.0 CE2 H:TYR108 4.2 21.6 0.5 CA H:ASP102 4.3 28.8 1.0 O F:HOH315 4.3 29.7 1.0 CD2 H:TYR108 4.3 19.0 0.5 CE1 H:TYR108 4.5 20.9 0.5 OD2 H:ASP102 4.5 48.2 1.0 CE1 H:TYR108 4.7 18.2 0.5 CD2 H:TYR108 4.9 19.5 0.5 CA G:GLN49 5.0 20.0 1.0

S.M.Lange, Y.Kulathu. Branched LYS48- and LYS63-Linked Tri-Ubiquitin (K48-K63-UB3) in Complex with Synthetic Nanobody NBSL3 To Be Published.