5OXJ

Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase.

Betz, K.Nilforoushan, A.Wyss, L.A.Diederichs, K.Sturla, S.J.Marx, A.

(2017) Chem. Commun. (Camb.) 53: 12704-12707

  • DOI: 10.1039/c7cc07173f
  • Primary Citation of Related Structures:  5O7T

  • PubMed Abstract: 
  • The possibility to sequence cytotoxic O6-alkylG DNA adducts would greatly benefit research. Recently we reported a benzimidazole-derived nucleotide that is selectively incorporated opposite the damaged site by a mutated DNA polymerase. Here we provid ...

    The possibility to sequence cytotoxic O6-alkylG DNA adducts would greatly benefit research. Recently we reported a benzimidazole-derived nucleotide that is selectively incorporated opposite the damaged site by a mutated DNA polymerase. Here we provide the structural basis for this reaction which may spur future developments in DNA damage sequencing.


    Organizational Affiliation

    Department of Chemistry & Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany. andreas.marx@uni-konstanz.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I, thermostable
A
540Thermus aquaticusGene Names: polA (pol1)
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Go to UniProtKB:  P19821
Entity ID: 2
MoleculeChainsLengthOrganism
DNA primerB12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA templateC16synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NZI
Query on NZI

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Download CCD File 
A
[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate
C12 H17 N2 O13 P3
OMCWLYQAPHJDBD-HBNTYKKESA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DDG
Query on DDG
B
DNA LINKINGC10 H14 N5 O6 PDG
6OG
Query on 6OG
C
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.347α = 90.00
b = 109.347β = 90.00
c = 90.636γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references