3I8D | pdb_00003i8d

The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 

Literature

Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography.

Pallan, P.S., Egli, M.

(2009) J Am Chem Soc 131: 12548-12549

  • DOI: https://doi.org/10.1021/ja905739j
  • Primary Citation Related Structures: 
    3I8D

  • PubMed Abstract: 

    Certain DNA polymerases (pols) were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analogue is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F.

    • Organizational Affiliation: 
    • Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.

Macromolecule Content 

  • Total Structure Weight: 38.19 kDa 
  • Atom Count: 2,895 
  • Modeled Residue Count: 288 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease H
A, C
132Halalkalibacterium haloduransMutation(s): 1 
Gene Names: BACILLUS HALODURANS, BH0863, RNase-H D132N mutant, rnhA
EC: 3.1.26.4
UniProt
Find proteins for Q9KEI9 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9KEI9 
Go to UniProtKB:  Q9KEI9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KEI9
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'
B, D
12N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.178α = 90
b = 66.714β = 121.04
c = 77.571γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.3: 2021-10-13
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description