ArticleBiochemistry2011
Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma.Journal of chemical theory and computation · 2025Article
- Crystal structures of monomeric BsmI restriction endonuclease reveal coordinated sequential cleavage of two DNA strands.Communications biology · 2025Article
- Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA.The Biochemical journal · 2025Review
- Innovative nucleic acid detection ofFrontiers in cellular and infection microbiology · 2025Article
- Structural Insights into Binding of Remdesivir Triphosphate within the Replication-Transcription Complex of SARS-CoV-2.Biochemistry · 2022Article
- Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion.Frontiers in molecular biosciences · 2022Review
- Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability.Frontiers in molecular biosciences · 2022Article
- Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69.Frontiers in molecular biosciences · 2021Article
- Manganese-Induced Substrate Promiscuity in the Reaction Catalyzed by Phosphoglutamine Cytidylyltransferase from Campylobacter jejuni.Biochemistry · 2019Article
- Crystallographic evidence for two-metal-ion catalysis in human pol η.Protein science : a publication of the Protein Society · 2019Article
- The effect of different divalent cations on the kinetics and fidelity ofAIMS biophysics · 2018Article
- Calcium-driven DNA synthesis by a high-fidelity DNA polymerase.Nucleic acids research · 2017Article
- Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases.The Journal of biological chemistry · 2016Review
- Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase ι.The Journal of biological chemistry · 2016Article
- Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase.Nucleic acids research · 2016Article
- Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase.Biochemistry · 2016Article
- Fluorescence resonance energy transfer studies of DNA polymerase β: the critical role of fingers domain movements and a novel non-covalent step during nucleotide selection.The Journal of biological chemistry · 2014Article
- RB69 DNA polymerase structure, kinetics, and fidelity.Biochemistry · 2014Review
- Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization.Advances in protein chemistry and structural biology · 2014Review
- Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.Nucleic acids research · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-α,β-substituted triphosphate, dUpXpp, where X is either NH or CH(2), opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca(2+) and four other structures with catalytically competent Mn(2+) or Mg(2+). These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the α-phosphorus atom (Pα) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's α-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach Pα. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to Pα to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to Pα. This geometric relationship appears to be conserved among DNA polymerases of known structure.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.