Zinc in PDB 2y5b: Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde

All present enzymatic activity of Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde:
3.1.2.15; 3.4.19.12;

The structure of Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde, PDB code: 2y5b was solved by Y.Ye, M.Akutsu, F.Reyes-Turcu, R.I.Enchev, K.D.Wilkinson, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.870, 102.200, 86.800, 90.00, 99.82, 90.00
R / Rfree (%)	21.58 / 27.859

The binding sites of Zinc atom in the Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde (pdb code 2y5b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde, PDB code: 2y5b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:18.6 occ:1.00 SG A:CYS387 2.3 18.5 1.0 SG A:CYS440 2.3 21.9 1.0 SG A:CYS384 2.3 17.9 1.0 SG A:CYS437 2.3 19.9 1.0 CB A:CYS437 3.3 20.6 1.0 CB A:CYS387 3.3 18.2 1.0 CB A:CYS384 3.4 18.3 1.0 CB A:CYS440 3.4 23.0 1.0 N A:CYS387 3.6 17.7 1.0 N A:CYS440 3.8 24.0 1.0 CA A:CYS387 4.0 17.8 1.0 CA A:CYS440 4.2 24.3 1.0 CB A:ALA386 4.6 17.7 1.0 CB A:ARG439 4.7 23.6 1.0 C A:CYS387 4.7 17.9 1.0 CA A:CYS437 4.7 21.6 1.0 C A:ALA386 4.7 17.7 1.0 N A:GLY388 4.7 17.6 1.0 CA A:CYS384 4.8 18.7 1.0 C A:CYS440 5.0 25.4 1.0 C A:ARG439 5.0 24.0 1.0 O A:GLN442 5.0 30.1 1.0 CA A:ALA386 5.0 18.0 1.0

Zinc binding site 2 out of 2 in the Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of USP21 in Complex with Linear Diubiquitin-Aldehyde within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1000 b:19.9 occ:1.00 SG E:CYS437 2.3 19.8 1.0 SG E:CYS387 2.3 18.5 1.0 SG E:CYS440 2.3 20.7 1.0 SG E:CYS384 2.3 20.3 1.0 CB E:CYS437 3.3 20.1 1.0 CB E:CYS387 3.3 18.8 1.0 CB E:CYS440 3.3 20.5 1.0 CB E:CYS384 3.4 20.3 1.0 N E:CYS387 3.7 19.0 1.0 N E:CYS440 3.9 20.7 1.0 CA E:CYS387 4.0 18.8 1.0 CA E:CYS440 4.2 20.5 1.0 CB E:ALA386 4.6 19.9 1.0 CA E:CYS437 4.7 20.4 1.0 CA E:CYS384 4.8 20.7 1.0 C E:ALA386 4.8 19.2 1.0 C E:CYS387 4.8 18.9 1.0 N E:GLY388 4.8 18.7 1.0 OG1 E:THR444 4.9 20.7 1.0 CB E:TYR389 5.0 19.6 1.0 C E:ARG439 5.0 21.0 1.0 CB E:ARG439 5.0 21.0 1.0

Y.Ye, M.Akutsu, F.Reyes-Turcu, R.I.Enchev, K.D.Wilkinson, D.Komander. Polyubiquitin Binding and Cross-Reactivity in the Usp Domain Deubiquitinase USP21. Embo Rep. V. 12 350 2011.
ISSN: ISSN 1469-221X
PubMed: 21399617
DOI: 10.1038/EMBOR.2011.17