Sodium in PDB 8bs9: Structure of USP36 in Complex with Ubiquitin-Pa

All present enzymatic activity of Structure of USP36 in Complex with Ubiquitin-Pa:
3.4.19.12;

The structure of Structure of USP36 in Complex with Ubiquitin-Pa, PDB code: 8bs9 was solved by R.O'dea, M.Gersch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.24 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.743, 65.307, 103.411, 90, 93.27, 90
R / Rfree (%)	17.1 / 20.9

The structure of Structure of USP36 in Complex with Ubiquitin-Pa also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Structure of USP36 in Complex with Ubiquitin-Pa (pdb code 8bs9). 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 USP36 in Complex with Ubiquitin-Pa, PDB code: 8bs9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of USP36 in Complex with Ubiquitin-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 USP36 in Complex with Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:63.3 occ:1.00 CG A:TYR248 4.1 31.7 1.0 CD2 A:TYR248 4.2 26.9 1.0 CD2 A:HIS318 4.2 36.1 1.0 O A:HOH1160 4.3 59.5 1.0 CD1 A:TYR248 4.4 26.4 1.0 CD1 A:TYR265 4.4 32.1 1.0 CG A:ARG319 4.5 37.1 1.0 CG A:TYR265 4.5 28.7 1.0 CE2 A:TYR248 4.5 33.1 1.0 CB A:TYR265 4.6 28.2 1.0 CB A:TYR248 4.6 27.3 1.0 CE1 A:TYR248 4.7 32.8 1.0 CZ A:TYR248 4.7 37.3 1.0 NH1 A:ARG319 4.8 81.4 1.0 NE2 A:HIS318 4.9 33.5 1.0 CD A:ARG319 4.9 51.5 1.0

Sodium binding site 2 out of 2 in the Structure of USP36 in Complex with Ubiquitin-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 USP36 in Complex with Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ C:Na804 b:64.8 occ:1.00 O C:HOH1152 4.0 61.2 1.0 CE2 C:TYR248 4.3 27.1 1.0 OE1 C:GLN234 4.4 65.5 1.0 CB C:TYR265 4.4 32.6 1.0 CD2 C:TYR248 4.4 28.6 1.0 CZ C:TYR248 4.4 37.9 1.0 CG C:TYR265 4.5 32.3 1.0 O C:HOH1162 4.6 57.7 1.0 O C:HOH1114 4.6 70.3 1.0 CG C:TYR248 4.7 35.2 1.0 CE1 C:TYR248 4.7 38.4 1.0 CD1 C:TYR248 4.8 32.6 1.0 CD1 C:TYR265 4.9 30.5 1.0 OH C:TYR248 4.9 32.0 1.0

R.O'dea, M.Gersch. Molecular Basis For Ubiquitin/Fubi Cross-Reactivity in USP16 and USP36 Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01388-1