3UXP

Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP

Structural Biology Knowledgebase: 3UXP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3UXP

Classification: TRANSFERASE LYASE / DNA

Total Structure Weight: 87624.08


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase beta A, B 335 Rattus norvegicus EC#: 2.7.7.7 IUBMB 4.2.99 IUBMB
Mutation: I260Q
Gene Name(s): Polb
Macromolecule Entities
Molecule Chains Length Organism Details
DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3' D, P 7 synthetic Primer DNA Strand
DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3' E, T 9 synthetic Template DNA Strand

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
D3T
Query on D3T

A, B 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.218
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 100.32 α = 90.00
b = 56.61 β = 102.04
c = 93.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-05
  • Released Date: 2012-12-05
  • Deposition author(s): Gridley, C.L., Jaeger, J.

Revision History

  • 2013-08-28
    Type: Citation | Details: Citation update