Zinc in PDB 3i3t: Crystal Structure of Covalent Ubiquitin-USP21 Complex

All present enzymatic activity of Crystal Structure of Covalent Ubiquitin-USP21 Complex:
3.1.2.15;

The structure of Crystal Structure of Covalent Ubiquitin-USP21 Complex, PDB code: 3i3t was solved by D.Neculai, G.V.Avvakumov, J.R.Walker, S.Xue, C.Butler-Cole, J.Weigelt, C.Bountra, A.M.Edwards, C.H.Arrowsmith, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.37 / 2.59
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.428, 83.663, 118.792, 88.71, 75.73, 85.11
R / Rfree (%)	18.6 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Covalent Ubiquitin-USP21 Complex (pdb code 3i3t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Covalent Ubiquitin-USP21 Complex, PDB code: 3i3t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Covalent Ubiquitin-USP21 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Covalent Ubiquitin-USP21 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:74.3 occ:1.00 SG A:CYS437 2.3 70.7 1.0 SG A:CYS384 2.3 67.2 1.0 SG A:CYS440 2.3 76.2 1.0 SG A:CYS387 2.4 67.4 1.0 CB A:CYS437 3.1 66.9 1.0 CB A:CYS384 3.2 62.4 1.0 CB A:CYS440 3.4 73.5 1.0 CB A:CYS387 3.5 64.5 1.0 N A:CYS440 3.8 72.4 1.0 N A:CYS387 3.8 64.8 1.0 CA A:CYS440 4.2 73.7 1.0 CA A:CYS387 4.2 64.1 1.0 CA A:CYS437 4.5 66.8 1.0 CA A:CYS384 4.6 61.9 1.0 CB A:ARG439 4.6 70.3 1.0 CB A:TYR389 4.7 58.9 1.0 CB A:ALA386 4.7 65.5 1.0 C A:ARG439 4.9 71.2 1.0 C A:ALA386 4.9 65.3 1.0 N A:ARG439 5.0 70.2 1.0 N A:ALA386 5.0 64.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Covalent Ubiquitin-USP21 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Covalent Ubiquitin-USP21 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn700 b:71.2 occ:1.00 SG C:CYS387 2.3 67.0 1.0 SG C:CYS440 2.3 75.6 1.0 SG C:CYS437 2.3 70.1 1.0 SG C:CYS384 2.3 66.7 1.0 CB C:CYS437 3.2 66.9 1.0 CB C:CYS384 3.2 62.3 1.0 CB C:CYS440 3.3 73.5 1.0 CB C:CYS387 3.4 64.5 1.0 N C:CYS387 3.7 64.7 1.0 N C:CYS440 3.9 72.3 1.0 CA C:CYS387 4.1 64.2 1.0 CA C:CYS440 4.2 73.5 1.0 CB C:ALA386 4.5 65.4 1.0 CA C:CYS384 4.6 61.8 1.0 CA C:CYS437 4.6 66.7 1.0 C C:ALA386 4.7 65.4 1.0 CB C:TYR389 4.8 58.5 1.0 N C:ALA386 4.8 64.8 1.0 CA C:ALA386 4.9 65.2 1.0 C C:CYS384 5.0 61.6 1.0 CB C:ARG439 5.0 69.8 1.0 C C:CYS387 5.0 63.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Covalent Ubiquitin-USP21 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Covalent Ubiquitin-USP21 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn700 b:68.9 occ:1.00 SG E:CYS387 2.3 67.3 1.0 SG E:CYS384 2.3 67.1 1.0 SG E:CYS437 2.4 70.3 1.0 SG E:CYS440 2.4 76.1 1.0 CB E:CYS384 3.1 62.2 1.0 CB E:CYS387 3.3 64.6 1.0 CB E:CYS437 3.3 66.8 1.0 N E:CYS387 3.5 64.7 1.0 CB E:CYS440 3.5 73.4 1.0 CA E:CYS387 3.9 64.2 1.0 N E:CYS440 4.0 72.5 1.0 CA E:CYS440 4.4 73.6 1.0 CB E:ALA386 4.5 65.4 1.0 C E:ALA386 4.5 65.3 1.0 CA E:CYS384 4.5 61.7 1.0 CB E:TYR389 4.7 58.6 1.0 N E:ALA386 4.7 64.8 1.0 CB E:ARG439 4.7 69.4 1.0 CA E:ALA386 4.7 65.3 1.0 C E:CYS387 4.8 63.6 1.0 CA E:CYS437 4.8 66.8 1.0 C E:CYS384 4.8 61.6 1.0 N E:GLY388 4.9 62.7 1.0 N E:TYR389 5.0 59.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Covalent Ubiquitin-USP21 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Covalent Ubiquitin-USP21 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn700 b:74.8 occ:1.00 SG G:CYS437 2.3 70.3 1.0 SG G:CYS440 2.3 75.8 1.0 SG G:CYS384 2.4 67.2 1.0 SG G:CYS387 2.4 67.6 1.0 CB G:CYS437 3.1 67.1 1.0 CB G:CYS440 3.3 73.5 1.0 CB G:CYS384 3.3 62.4 1.0 CB G:CYS387 3.4 64.6 1.0 N G:CYS440 3.6 72.3 1.0 N G:CYS387 3.9 64.8 1.0 CA G:CYS440 4.0 73.6 1.0 CA G:CYS387 4.3 64.2 1.0 CB G:ARG439 4.4 70.3 0.5 CA G:CYS437 4.6 66.8 1.0 CB G:ARG439 4.6 69.9 0.5 CB G:TYR389 4.7 58.9 1.0 C G:ARG439 4.7 71.1 1.0 CB G:ALA386 4.7 65.5 1.0 CA G:CYS384 4.8 61.8 1.0 N G:ARG439 4.9 70.2 1.0 C G:CYS440 4.9 74.3 1.0 CA G:ARG439 4.9 70.5 0.5 CA G:ARG439 4.9 70.3 0.5 N G:ARG441 4.9 74.6 1.0 C G:ALA386 5.0 65.3 1.0 C G:CYS437 5.0 67.3 1.0

A.Ernst, G.Avvakumov, J.Tong, Y.Fan, Y.Zhao, P.Alberts, A.Persaud, J.R.Walker, A.M.Neculai, D.Neculai, A.Vorobyov, P.Garg, L.Beatty, P.K.Chan, Y.C.Juang, M.C.Landry, C.Yeh, E.Zeqiraj, K.Karamboulas, A.Allali-Hassani, M.Vedadi, M.Tyers, J.Moffat, F.Sicheri, L.Pelletier, D.Durocher, B.Raught, D.Rotin, J.Yang, M.F.Moran, S.Dhe-Paganon, S.S.Sidhu. A Strategy For Modulation of Enzymes in the Ubiquitin System. Science V. 339 590 2013.
ISSN: ISSN 0036-8075
PubMed: 23287719
DOI: 10.1126/SCIENCE.1230161