Cadmium in PDB 8oyp: Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic

All present enzymatic activity of Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic:
3.4.19.12;

The structure of Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic, PDB code: 8oyp was solved by S.K.Maurer, S.G.Caulton, S.J.Ward, J.Emsley, I.Dreveny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.44
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.321, 186.102, 75.761, 90, 90, 90
R / Rfree (%)	17 / 23.5

The structure of Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic (pdb code 8oyp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic, PDB code: 8oyp:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:43.3 occ:1.00 SG A:CYS805 2.5 49.8 1.0 SG A:CYS468 2.5 38.5 1.0 SG A:CYS471 2.5 35.6 1.0 SG A:CYS802 2.6 48.0 1.0 CB A:CYS805 3.1 38.1 1.0 CB A:CYS802 3.2 48.0 1.0 CB A:CYS468 3.3 31.2 1.0 CB A:CYS471 3.6 37.4 1.0 N A:CYS805 3.8 51.3 1.0 N A:CYS471 4.0 47.1 1.0 CA A:CYS805 4.0 48.7 1.0 CA A:CYS471 4.4 41.8 1.0 CB A:ASN473 4.4 33.1 1.0 CA A:CYS802 4.6 44.2 1.0 CB A:ASP470 4.6 48.2 1.0 CG A:GLN809 4.6 41.0 1.0 NE2 A:GLN809 4.8 53.1 1.0 CA A:CYS468 4.8 39.3 1.0 C A:SER804 4.8 45.2 1.0 C A:CYS805 4.9 50.1 1.0 CB A:SER804 4.9 45.5 1.0 N A:ASN473 5.0 33.1 1.0 CD A:GLN809 5.0 51.8 1.0 O A:CYS802 5.0 48.4 1.0 C A:CYS802 5.0 46.1 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Ubiquitin Specific Protease 11 (USP11) in Complex with A Substrate Mimetic within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1001 b:37.9 occ:1.00 SG B:CYS471 2.4 36.6 1.0 SG B:CYS805 2.5 59.7 1.0 SG B:CYS468 2.5 33.3 1.0 SG B:CYS802 2.7 46.5 1.0 CB B:CYS802 3.3 43.9 1.0 CB B:CYS805 3.3 49.3 1.0 CB B:CYS468 3.3 35.2 1.0 CB B:CYS471 3.5 37.6 1.0 N B:CYS471 3.8 37.2 1.0 N B:CYS805 3.8 45.9 1.0 CA B:CYS805 4.2 56.1 1.0 CA B:CYS471 4.2 36.3 1.0 CB B:ASN473 4.5 44.4 1.0 CB B:ASP470 4.5 57.1 1.0 CB B:SER804 4.5 52.1 1.0 NE2 B:GLN809 4.6 42.6 1.0 CG B:GLN809 4.6 39.3 1.0 CA B:CYS802 4.7 46.1 1.0 CA B:CYS468 4.8 30.7 1.0 C B:SER804 4.8 46.2 1.0 C B:ASP470 4.9 45.9 1.0 C B:CYS471 4.9 40.9 1.0 CD B:GLN809 4.9 41.0 1.0 N B:ASN473 5.0 34.5 1.0 N B:GLY472 5.0 34.1 1.0

S.K.Maurer, M.P.Mayer, S.J.Ward, S.Boudjema, M.Halawa, J.Zhang, S.G.Caulton, J.Emsley, I.Dreveny. Ubiquitin Specific Protease 11 Structure in Complex with An Engineered Substrate Mimetic Reveals A Molecular Feature For Deubiquitination Selectivity. J.Biol.Chem. 05300 2023.
ISSN: ESSN 1083-351X
PubMed: 37777157
DOI: 10.1016/J.JBC.2023.105300