(Q34801870)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

title

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism (English)

1 reference

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11 January 2020

1

1 reference

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11 January 2020

author name string

Matteo Dal Peraro

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

Michael L Klein

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

language of work or name

English

0 references

publication date

29 July 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

Journal of the American Chemical Society

11 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

volume

130

1 reference

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11 January 2020

issue

33

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

page(s)

10955-10962

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD

11 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Proton shuttles and phosphatase activity in soluble epoxide hydrolase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Phosphoryl transfer enzymes and hypervalent phosphorus chemistry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Phosphoryl group transfer: evolution of a catalytic scaffold

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Crystal structure of Argonaute and its implications for RISC slicer activity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Analysis of the substrate specificity loop of the HAD superfamily cap domain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Understanding the transition states of phosphodiester bond cleavage: insights from heavy atom isotope effects

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Two-metal ion mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV RNase H inhibitors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Stereochemical course of Escherichia coli RNase H.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

The role and perspective of ab initio molecular dynamics in the study of biological systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Comparative architecture of transposase and integrase complexes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Catalysis by Escherichia coli ribonuclease HI is facilitated by a phosphate group of the substrate.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Integrating DNA: transposases and retroviral integrases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Unified Approach for Molecular Dynamics and Density-Functional Theory

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Density-functional exchange-energy approximation with correct asymptotic behavior

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Canonical dynamics: Equilibrium phase-space distributions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

RNase H activity of human hepatitis B virus polymerase expressed in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Expression, purification, and characterization of an active RNase H domain of the hepatitis B viral polymerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

A general two-metal-ion mechanism for catalytic RNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Recombining the structures of HIV integrase, RuvC and RNase H.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Chemical confirmation of a pentavalent phosphorane in complex with beta-phosphoglucomutase

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Dissecting the effects of DNA polymerase and ribonuclease H inhibitor combinations on HIV-1 reverse-transcriptase activities

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Water-assisted reaction mechanism of monozinc beta-lactamases

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Density functional study of the enzymatic reaction catalyzed by a cyclin-dependent kinase

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Estimating pKa values for pentaoxyphosphoranes

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2745632

Comment on "The Pentacovalent Phosphorus Intermediate of a Phosphoryl Transfer Reaction"

26 October 2018

1 reference

12 December 2020

Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations

1 reference

12 December 2020

Representative Benchmark Suites for Barrier Heights of Diverse Reaction Types and Assessment of Electronic Structure Methods for Thermochemical Kinetics

1 reference

12 December 2020

Efficient pseudopotentials for plane-wave calculations. II. Operators for fast iterative diagonalization

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA8005786

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18662000%20AND%20SRC:MED&resulttype=core&format=json

11 January 2020

PubMed publication ID

18662000

1 reference