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

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Basic information

Entry
Database: PDB / ID: 2loa
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 / BIFUNCTIONAL ZN(II) MACROCYCLIC COMPLEX / cyclen
Function / homologyChem-C4Q / DNA
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, Docking with energy minimization
Model detailsmost favorable docked structure, 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 20, 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 ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _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: DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4253
Polymers3,0461
Non-polymers3792
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1structures with acceptable covalent geometry
RepresentativeModel #1most favorable docked structure

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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
#2: Chemical ChemComp-C4Q / 4-(1,4,7,10-tetraazacyclododecan-1-ylmethyl)quinoline


Mass: 313.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27N5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure if a thymine bulge with a Zn 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane complex bound
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 278 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
HyperChem6HyperCube, Increfinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, Docking with energy minimization
Software ordinal: 1
Details: One of the structures from PDB 2lo8 was selected and used for docking of of the Zn(cy4q), One conformer was selected from the the cyana calculation above and the Zn(cy4q) docked using energy ...Details: One of the structures from PDB 2lo8 was selected and used for docking of of the Zn(cy4q), One conformer was selected from the the cyana calculation above and the Zn(cy4q) docked using energy minimization and distance restraints obtained from NMR data.
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: most favorable docked structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 1 / Conformers submitted total number: 1

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