Zinc 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:

Sodium

(Na)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of USP36 in Complex with Ubiquitin-Pa, PDB code: 8bs9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of USP36 in Complex with Ubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn801 b:36.4 occ:1.00 NE2 A:HIS155 2.0 32.2 1.0 SG A:CYS168 2.3 38.8 1.0 SG A:CYS165 2.3 34.9 1.0 SG A:CYS159 2.4 46.6 1.0 CE1 A:HIS155 2.8 38.1 1.0 CB A:CYS159 3.1 45.6 1.0 CB A:CYS165 3.2 29.9 1.0 CD2 A:HIS155 3.2 39.6 1.0 CB A:CYS168 3.4 31.2 1.0 N A:CYS168 3.5 28.7 1.0 CA A:CYS168 3.9 30.4 1.0 ND1 A:HIS155 4.0 32.6 1.0 O A:HOH936 4.0 58.9 1.0 CG A:HIS155 4.2 46.0 1.0 CB A:LEU167 4.4 33.1 1.0 C A:LEU167 4.5 34.5 1.0 CA A:CYS159 4.5 69.5 1.0 CA A:CYS165 4.5 33.8 1.0 O A:HOH1137 4.7 54.2 1.0 O A:CYS165 4.8 28.8 1.0 C A:CYS165 4.8 35.4 1.0 CA A:LEU167 4.9 30.2 1.0 N A:LEU167 5.0 27.1 1.0

Zinc binding site 2 out of 4 in the Structure of USP36 in Complex with Ubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of USP36 in Complex with Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:43.3 occ:1.00 SG A:CYS255 2.3 42.3 1.0 SG A:CYS302 2.4 46.8 1.0 SG A:CYS305 2.4 48.5 1.0 SG A:CYS258 2.4 48.0 1.0 CB A:CYS255 3.2 38.4 1.0 CB A:CYS258 3.2 44.0 1.0 CB A:CYS305 3.3 51.9 1.0 CB A:CYS302 3.4 44.0 1.0 N A:CYS305 3.7 61.2 1.0 N A:CYS258 3.7 43.5 1.0 CA A:CYS258 4.1 47.4 1.0 CA A:CYS305 4.1 50.3 1.0 CB A:LYS304 4.6 53.1 1.0 CB A:VAL257 4.6 54.0 1.0 CA A:CYS255 4.6 44.5 1.0 C A:LYS304 4.7 52.8 1.0 CG1 A:VAL309 4.7 45.9 1.0 C A:CYS258 4.8 42.8 1.0 CA A:CYS302 4.8 48.6 1.0 C A:VAL257 4.8 54.5 1.0 CG2 A:VAL309 4.9 39.8 1.0 CB A:SER260 5.0 59.0 1.0 N A:VAL257 5.0 44.0 1.0 CD A:LYS304 5.0 70.7 1.0

Zinc binding site 3 out of 4 in the Structure of USP36 in Complex with Ubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of USP36 in Complex with Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:37.3 occ:1.00 NE2 C:HIS155 2.0 32.1 1.0 SG C:CYS159 2.3 46.6 1.0 SG C:CYS168 2.3 37.2 1.0 SG C:CYS165 2.3 35.2 1.0 CE1 C:HIS155 2.8 40.4 1.0 CB C:CYS159 3.1 50.6 1.0 CD2 C:HIS155 3.1 40.3 1.0 CB C:CYS165 3.2 33.7 1.0 CB C:CYS168 3.4 29.3 1.0 N C:CYS168 3.5 27.9 1.0 CA C:CYS168 3.9 28.2 1.0 ND1 C:HIS155 4.0 35.7 1.0 O C:HOH1134 4.1 57.2 1.0 CG C:HIS155 4.1 47.0 1.0 C C:LEU167 4.5 28.2 1.0 CB C:LEU167 4.5 28.1 1.0 CA C:CYS159 4.5 64.8 1.0 CA C:CYS165 4.6 32.5 1.0 O C:CYS165 4.9 32.0 1.0 O C:HOH1081 4.9 67.7 1.0 CA C:LEU167 4.9 28.8 1.0 C C:CYS165 4.9 41.8 1.0 N C:LEU167 5.0 29.3 1.0 O C:HOH1039 5.0 47.9 1.0

Zinc binding site 4 out of 4 in the Structure of USP36 in Complex with Ubiquitin-Pa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of USP36 in Complex with Ubiquitin-Pa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn802 b:42.1 occ:1.00 SG C:CYS255 2.3 41.5 1.0 SG C:CYS258 2.3 46.2 1.0 SG C:CYS302 2.4 48.9 1.0 SG C:CYS305 2.4 46.0 1.0 CB C:CYS255 3.2 34.8 1.0 CB C:CYS258 3.2 43.2 1.0 CB C:CYS305 3.3 48.5 1.0 CB C:CYS302 3.4 47.0 1.0 N C:CYS305 3.7 52.7 1.0 N C:CYS258 3.8 41.0 1.0 CA C:CYS305 4.1 48.8 1.0 CA C:CYS258 4.1 49.8 1.0 CB C:LYS304 4.5 55.0 1.0 CA C:CYS255 4.7 40.5 1.0 C C:LYS304 4.7 51.2 1.0 CB C:VAL257 4.8 51.4 1.0 CA C:CYS302 4.8 45.7 1.0 CG1 C:VAL309 4.8 45.9 1.0 C C:CYS258 4.8 46.8 1.0 CG2 C:VAL309 4.9 42.4 1.0 C C:VAL257 4.9 45.4 1.0 CB C:SER260 4.9 48.7 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