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Zinc in PDB 3wup: Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta

Enzymatic activity of Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta

All present enzymatic activity of Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta, PDB code: 3wup was solved by N.Suzuki, S.Wakatsuki, S.Kawasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.78 / 1.60
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 49.188, 49.188, 49.188, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22.6

Other elements in 3wup:

The structure of Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta (pdb code 3wup). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta, PDB code: 3wup:

Zinc binding site 1 out of 1 in 3wup

Go back to Zinc Binding Sites List in 3wup
Zinc binding site 1 out of 1 in the Crystal Structure of the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta


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 the Ubiquitin-Binding Zinc Finger (Ubz) Domain of the Human Dna Polymerase Eta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:16.4
occ:1.00
 NE2 A:HIS654 2.0 13.8 1.0
NE2 A:HIS650 2.0 15.4 1.0
SG A:CYS635 2.3 18.1 1.0
SG A:CYS638 2.3 15.1 1.0
CD2 A:HIS650 2.9 13.2 1.0
CE1 A:HIS654 3.0 15.4 1.0
CD2 A:HIS654 3.0 16.8 1.0
CB A:CYS635 3.0 16.9 1.0
CE1 A:HIS650 3.1 14.3 1.0
CB A:CYS638 3.4 17.0 1.0
N A:CYS638 3.7 19.1 1.0
O A:HOH812 4.0 16.5 1.0
CA A:CYS638 4.1 17.5 1.0
CG A:HIS650 4.1 13.7 1.0
ND1 A:HIS650 4.1 13.6 1.0
ND1 A:HIS654 4.1 17.3 1.0
CG A:HIS654 4.2 18.3 1.0
CB A:LYS637 4.4 21.9 1.0
CA A:CYS635 4.6 17.6 1.0
C A:LYS637 4.7 20.5 1.0
C A:CYS638 4.8 16.8 1.0
N A:GLY639 4.8 16.3 1.0
CB A:SER640 4.8 15.8 1.0
N A:LYS637 4.9 20.9 1.0
CA A:LYS637 4.9 21.2 1.0
OG A:SER640 4.9 15.8 1.0
SD A:MET651 4.9 21.3 1.0
N A:SER640 5.0 15.2 1.0

Reference:

N.Suzuki, A.Rohaim, R.Kato, I.Dikic, S.Wakatsuki, M.Kawasaki. A Novel Mode of Ubiquitin Recognition By the Ubiquitin-Binding Zinc Finger Domain of WRNIP1. Febs J. 2016.
ISSN: ISSN 1742-464X
PubMed: 27062441
DOI: 10.1111/FEBS.13734
Page generated: Wed Aug 20 15:24:37 2025

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