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Zinc in PDB 3mtn: USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor

Enzymatic activity of USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor

All present enzymatic activity of USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor:
3.1.2.15;

Protein crystallography data

The structure of USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor, PDB code: 3mtn was solved by J.R.Walker, G.V.Avvakumov, S.Xue, Y.Li, A.Ernst, S.Sidhu, 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) 19.61 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.065, 58.235, 133.596, 90.00, 121.19, 90.00
R / Rfree (%) 21.8 / 27.3

Other elements in 3mtn:

The structure of USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor (pdb code 3mtn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor, PDB code: 3mtn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3mtn

Go back to Zinc Binding Sites List in 3mtn
Zinc binding site 1 out of 2 in the USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:83.8
occ:1.00
SG A:CYS384 2.4 77.7 1.0
SG A:CYS387 2.4 84.6 1.0
SG A:CYS440 2.4 89.3 1.0
SG A:CYS437 2.4 84.7 1.0
CB A:CYS437 2.9 84.5 1.0
CB A:CYS384 3.2 74.5 1.0
CB A:CYS440 3.4 93.4 1.0
N A:CYS387 3.4 84.6 1.0
CB A:CYS387 3.5 87.0 1.0
N A:CYS440 4.0 92.2 1.0
CA A:CYS387 4.0 86.0 1.0
CB A:ALA386 4.1 84.9 1.0
CA A:CYS440 4.3 94.2 1.0
CA A:CYS437 4.4 83.0 1.0
N A:GLY388 4.4 81.4 1.0
C A:ALA386 4.5 85.1 1.0
CA A:ALA386 4.7 84.0 1.0
CA A:CYS384 4.7 72.4 1.0
C A:CYS387 4.7 84.2 1.0
N A:ALA386 4.7 80.8 1.0
CB A:TYR389 4.8 79.7 1.0
N A:TYR389 4.9 78.8 1.0
CB A:ARG439 4.9 90.2 1.0
N A:ARG441 4.9 92.0 1.0
C A:CYS440 5.0 94.4 1.0
C A:CYS384 5.0 74.0 1.0

Zinc binding site 2 out of 2 in 3mtn

Go back to Zinc Binding Sites List in 3mtn
Zinc binding site 2 out of 2 in the USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of USP21 in Complex with A Ubiquitin-Based, USP21-Specific Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn700

b:0.2
occ:1.00
SG C:CYS440 2.4 0.4 1.0
SG C:CYS387 2.4 0.9 1.0
SG C:CYS437 2.4 0.5 1.0
SG C:CYS384 2.4 0.2 1.0
CB C:CYS437 3.0 0.2 1.0
CB C:CYS440 3.1 0.9 1.0
CB C:CYS384 3.3 97.9 1.0
N C:CYS440 3.5 0.7 1.0
CB C:CYS387 3.6 0.9 1.0
CA C:CYS440 3.9 0.6 1.0
N C:CYS387 3.9 0.9 1.0
CA C:CYS387 4.3 0.3 1.0
CB C:ARG439 4.5 0.3 0.5
CA C:CYS437 4.5 0.6 1.0
CB C:ARG439 4.5 0.6 0.5
C C:ARG439 4.7 0.7 0.5
C C:ARG439 4.7 0.8 0.5
CA C:CYS384 4.7 96.6 1.0
N C:ARG441 4.7 0.9 1.0
C C:CYS387 4.8 0.1 1.0
C C:CYS440 4.8 0.3 1.0
CB C:ALA386 4.8 0.8 1.0
CB C:TYR389 4.8 0.3 1.0
N C:GLY388 4.8 0.2 1.0
N C:ARG439 4.9 0.6 0.5
N C:ARG439 4.9 0.4 0.5
CA C:ARG439 4.9 1.0 0.5
CA C:ARG439 4.9 0.2 0.5

Reference:

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
Page generated: Wed Dec 16 04:36:07 2020

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