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- PDB-2lo8: Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Reco... -

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Basic information

Entry
Database: PDB / ID: 2lo8
TitleStructural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA
ComponentsDNA_(5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')_
KeywordsDNA / thymine bulge / hairpin / Bifunctional Zn(II) Macrocyclic Complex
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model 1
AuthorsMorrow, J.R. / Fountain, M.A. / del Mundo, I.A. / Siter, K.E.
CitationJournal: Inorg.Chem. / Year: 2012
Title: Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA.
Authors: Del Mundo, I.M. / Siters, K.E. / Fountain, M.A. / Morrow, J.R.
History
DepositionJan 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
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: DNA_(5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')_


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain DNA_(5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')_


Mass: 3045.993 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure determined using NOE distance restraints for the Zn(cy4q)DNA complex. Structure presented without the Zn(cy4q) ligand.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3'), 100% D2O100% D2O
22.0 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3'), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.6 mMDNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')-11
2.0 mMDNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.17.5ambient 293 K
20.17.5ambient 5 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
Sparky3.14Goddardchemical shift assignment
Sparky3.14Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 4 / NA beta-angle constraints total count: 4 / NA chi-angle constraints total count: 8 / NA delta-angle constraints total count: 6 / NA epsilon-angle constraints total count: 4 / NA gamma-angle constraints total count: 4 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 118 / NOE long range total count: 64
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 2.05 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 18 / Maximum lower distance constraint violation: 0.28 Å / Maximum torsion angle constraint violation: 6.6 ° / Maximum upper distance constraint violation: 0.28 Å
NMR ensemble rmsDistance rms dev: 0.0202 Å / Distance rms dev error: 0.0047 Å

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