3UK3

Crystal structure of ZNF217 bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb3UK3/pdb
• NAKB: 3UK3

• Classification: DNA/METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-08 Released: 2012-12-05 
• Deposition Author(s): Vandevenne, M.S., Jacques, D.A., Guss, J.M., Mackay, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Rediscovering DNA recognition by classical Zinc Fingers.

Vandevenne, M.S., Jacques, D.A., Guss, J.M., Mackay, J.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.52 kDa 
• Atom Count: 1,796 
• Modelled Residue Count: 146 
• Deposited Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein 217	C, D	57	Homo sapiens	Mutation(s): 0  Gene Names: ZNF217, ZABC1
UniProt & NIH Common Fund Data Resources
Find proteins for O75362 (Homo sapiens) Explore O75362  Go to UniProtKB:  O75362
PHAROS:  O75362 GTEx:  ENSG00000171940

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'	A	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'	B	20	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth B], F [auth B], G [auth C], H [auth C], I [auth C], K [auth D], L [auth D], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.67	α = 90
b = 40.98	β = 97.21
c = 52.04	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Vandevenne, M.S., Jacques, D.A., Guss, J.M., Mackay, J.P.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations