5OXJ

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

PDB DOI: https://doi.org/10.2210/pdb5OXJ/pdb
NAKB: 5OXJ

Classification: TRANSFERASE
Organism(s): Thermus aquaticus, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-09-06 Released: 2017-11-29
Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.257
R-Value Work: 0.196
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 29136072 Search on PubMed
DOI: https://doi.org/10.1039/c7cc07173f
Primary Citation of Related Structures:
5O7T, 5OXJ

PubMed Abstract:
The possibility to sequence cytotoxic O ⁶-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.

Macromolecule Content

Total Structure Weight: 70.36 kDa
Atom Count: 4,946
Modelled Residue Count: 560
Deposited Residue Count: 568
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	540	Thermus aquaticus	Mutation(s): 1 Gene Names: polA, pol1 EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821 Go to UniProtKB: P19821
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19821
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA primer	B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA template	C	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NZI Query on NZI Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth 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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C]	G [auth A], H [auth A], K [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B]	I [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.257
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.347	α = 90
b = 109.347	β = 90
c = 90.636	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-11-29

Deposition Author(s):

Betz, K.

Diederichs, K.

Marx, A.

Revision History (Full details and data files)

Version 1.0: 2017-11-29
Type: Initial release
Version 1.1: 2017-12-06
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description