Sodium in PDB 8q00: Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa

The structure of Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa, PDB code: 8q00 was solved by M.Uthoff, T.Hermanns, K.Hofmann, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.22 / 1.62
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.75, 103.75, 191.52, 90, 90, 90
R / Rfree (%)	17.4 / 19.8

The binding sites of Sodium atom in the Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa (pdb code 8q00). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa, PDB code: 8q00:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:28.2 occ:1.00 O A:VAL368 2.3 25.4 1.0 O A:THR365 2.3 27.2 1.0 O A:HOH846 2.4 35.5 1.0 OD1 A:ASP370 2.4 38.1 1.0 O A:ARG363 2.4 26.1 1.0 C A:ARG363 3.4 25.3 1.0 C A:THR365 3.5 28.3 1.0 C A:VAL368 3.5 26.1 1.0 CG A:ASP370 3.6 42.6 1.0 N A:ASP370 3.8 27.2 1.0 C A:PRO369 3.9 25.8 1.0 N A:THR365 4.0 26.3 1.0 CA A:ASP370 4.0 26.9 1.0 C A:ALA364 4.1 31.6 1.0 O A:HOH653 4.1 56.9 1.0 N A:ALA364 4.3 25.4 1.0 N A:VAL368 4.3 26.0 1.0 CA A:ARG363 4.3 25.2 1.0 CA A:ALA364 4.3 29.2 1.0 CB A:ASP370 4.3 30.2 1.0 CA A:PRO369 4.3 25.7 1.0 CA A:THR365 4.4 27.4 1.0 N A:PRO369 4.4 23.5 1.0 N A:PRO366 4.4 27.3 1.0 CA A:VAL368 4.4 23.7 1.0 O A:PRO369 4.4 26.1 1.0 CA A:PRO366 4.4 29.3 1.0 O A:HOH767 4.4 41.7 1.0 O A:PRO366 4.5 28.9 1.0 C A:PRO366 4.5 26.9 1.0 OD2 A:ASP370 4.5 47.2 1.0 O A:ALA364 4.5 31.4 1.0 O A:LEU362 4.6 24.6 1.0 CB A:VAL368 4.8 23.9 1.0 OG1 A:THR365 4.9 24.6 1.0

Sodium binding site 2 out of 2 in the Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tssm-Ub-Pa Complex - A Usp-Like Dub From B. Pseudomallei (193-430) Reacted with Ub-Pa within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:31.1 occ:1.00 O C:HOH803 2.3 35.9 1.0 O C:THR365 2.3 31.9 1.0 O C:VAL368 2.3 30.3 1.0 OD1 C:ASP370 2.4 36.3 1.0 O C:ARG363 2.4 31.9 1.0 O C:HOH608 2.6 52.1 1.0 C C:ARG363 3.5 28.8 1.0 C C:THR365 3.5 27.6 1.0 C C:VAL368 3.5 27.4 1.0 CG C:ASP370 3.6 37.2 1.0 N C:ASP370 3.7 30.5 1.0 C C:PRO369 3.9 31.4 1.0 CA C:ASP370 4.0 30.0 1.0 C C:ALA364 4.1 38.9 1.0 N C:THR365 4.1 34.4 1.0 O C:HOH750 4.2 44.0 1.0 O C:HOH808 4.2 44.5 1.0 N C:VAL368 4.3 30.3 1.0 CA C:PRO366 4.3 33.8 1.0 N C:ALA364 4.3 29.8 1.0 CB C:ASP370 4.3 33.1 1.0 CA C:ARG363 4.3 27.1 1.0 CA C:ALA364 4.4 35.5 1.0 N C:PRO366 4.4 33.4 1.0 O C:PRO369 4.4 28.2 1.0 O C:PRO366 4.4 34.8 1.0 CA C:VAL368 4.4 27.2 1.0 C C:PRO366 4.4 31.3 1.0 CA C:PRO369 4.4 28.0 1.0 N C:PRO369 4.4 28.5 1.0 CA C:THR365 4.5 30.8 1.0 O C:ALA364 4.5 36.2 1.0 OD2 C:ASP370 4.5 42.3 1.0 O C:LEU362 4.7 29.9 1.0 CB C:VAL368 4.8 26.5 1.0 OG1 C:THR365 4.9 31.8 1.0

T.Hermanns, M.Uthoff, U.Baumann, K.Hofmann. The Structural Basis For Deubiquitination By the Fingerless Usp-Type Effector Tssm To Be Published.