1QSL

KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment

Brautigam, C.A.Aschheim, K.Steitz, T.A.

(1999) Chem Biol 6: 901-908

  • DOI: 10.1016/s1074-5521(00)80009-5
  • Primary Citation of Related Structures:  
    1QSL

  • PubMed Abstract: 
  • Biochemical and biophysical experiments have shown that two catalytically essential divalent metal ions (termed 'A' and 'B') bind to the 3'-5' exonuclease active site of the Klenow fragment (KF) of Escherichia coli DNA polymerase I. X-ray crystallographic studies have established the normal positions in the KF 3'-5' exonuclease (KF exo) active site of the two cations and the single-stranded DNA substrate ...

    Biochemical and biophysical experiments have shown that two catalytically essential divalent metal ions (termed 'A' and 'B') bind to the 3'-5' exonuclease active site of the Klenow fragment (KF) of Escherichia coli DNA polymerase I. X-ray crystallographic studies have established the normal positions in the KF 3'-5' exonuclease (KF exo) active site of the two cations and the single-stranded DNA substrate. Lanthanide (III) luminescence studies have demonstrated, however, that only a single europium (III) ion (Eu3+) binds to the KF exo active site. Furthermore, Eu3+ does not support catalysis by KF exo or several other two-metal-ion phosphoryl-transfer enzymes.


    Related Citations: 
    • Structural Principles for the Inhibition of the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I by Phosphorothioates
      Brautigam, C.A., Steitz, T.A.
      (1998) J Mol Biol 277: 363
    • Structural Basis for the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism
      Beese, L.S., Steitz, T.A.
      (1991) EMBO J 10: 25

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE IB [auth A]605Escherichia coliMutation(s): 1 
EC: 2.7.7.7
UniProt
Find proteins for P00582 (Escherichia coli (strain K12))
Explore P00582 
Go to UniProtKB:  P00582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00582
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*TP*TP*AP*CP*GP*C)-3'A [auth B]8N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EU
Query on EU

Download Ideal Coordinates CCD File 
C [auth A]EUROPIUM ION
Eu
MGVUQZZTJGLWJV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.3α = 90
b = 103.3β = 90
c = 86.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations