3TFS

Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CFH)PP in the active site: Stereoselective binding of (S) isomer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 

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Literature

Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta.

Chamberlain, B.T., Batra, V.K., Beard, W.A., Kadina, A.P., Shock, D.D., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

(2012) Chembiochem 13: 528-530

  • DOI: https://doi.org/10.1002/cbic.201100738
  • Primary Citation of Related Structures:  
    3TFR, 3TFS

  • PubMed Abstract: 

    The influence of water: crystallization of (R/S)-α,β-CHF-dATP with the preorganized pol β-DNA complex shows that (S)-α,β-CHF-dATP is preferentially bound to the active site with the C=F fluorine proximal to a structural water bound to Asp276.

    • Organizational Affiliation: 

    Departments of Chemistry and Biology, University of Southern California, Los Angeles, CA 90089, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase beta335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
GTEx:  ENSG00000070501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06746
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')B [auth T]16N/A
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')C [auth P]10N/A
Sequence Annotations
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*GP*G)-3')5N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FHA
Query on FHA
Download Ideal Coordinates CCD File 
E [auth A]2'-deoxy-5'-O-[(S)-{(S)-fluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine
C11 H17 F N5 O11 P3
HAJKJTDYTZCDDL-LLVCWYDASA-N
CL
Query on CL
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J [auth A],
K [auth A],
L [auth A],
M [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
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F [auth A],
G [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
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H [auth A],
I [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.77α = 90
b = 79.58β = 107.75
c = 55.72γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description