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- PDB-2mco: Structural studies on dinuclear ruthenium(II) complexes that bind... -

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Basic information

Entry
Database: PDB / ID: 2mco
TitleStructural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an anti-parallel folded human telomere sequence
Componentshuman telomere quadruplex
KeywordsDNA / quadruplex / complex / ruthenium
Function / homologyChem-2FJ / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsWilliamson, M.P. / Wilson, T. / Thomas, J.A. / Felix, V. / Costa, P.J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural Studies on Dinuclear Ruthenium(II) Complexes That Bind Diastereoselectively to an Antiparallel Folded Human Telomere Sequence.
Authors: Wilson, T. / Costa, P.J. / Felix, V. / Williamson, M.P. / Thomas, J.A.
History
DepositionAug 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: human telomere quadruplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2414
Polymers6,9831
Non-polymers1,2573
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 5all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: DNA chain human telomere quadruplex


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: standard solid phase synthesis, hplc purified
#2: Chemical ChemComp-2FJ / tetrakis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)(mu-tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~13~,N~14~)diruthenium(4+) L enantiomer


Mass: 1211.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C64H44N14Ru2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Complex of LL-[{Ru(bipy)2}2tppz]4+ bound to human telomere sequence quadruplex DNA (basket). Structures used NMR intermolecular restraints followed by unrestrained MD. The 5 structures in ...Details: Complex of LL-[{Ru(bipy)2}2tppz]4+ bound to human telomere sequence quadruplex DNA (basket). Structures used NMR intermolecular restraints followed by unrestrained MD. The 5 structures in the ensemble are representatives of the 5 most populated clusters from a 50 ns simulation. Simulation had explicit solvent plus counterions, which are removed in these files except for two sodiums in the middle of the quadruplex.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-31P HSQC

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Sample preparation

DetailsContents: 0.3 mM human telomere quadruplex, 0.3 mM LL-(Ru[bipy]2)tppz4+, 50 mM sodium chloride, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.3 mMhuman telomere quadruplex-11
0.3 mMLL-(Ru[bipy]2)tppz4+-21
50 mMsodium chloride-31
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 13 / NOE intraresidue total count: 0 / NOE long range total count: 0 / NOE medium range total count: 0 / NOE sequential total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 5 / Conformers submitted total number: 5 / Maximum lower distance constraint violation: 0.5 Å / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.1 Å / Distance rms dev error: 0.05 Å

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