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- PDB-1qsx: SOLUTION NMR STRUCTURE OF THE 2:1 HOECHST 33258-D(CTTTTGCAAAAG)2 ... -

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Basic information

Entry
Database: PDB / ID: 1qsx
TitleSOLUTION NMR STRUCTURE OF THE 2:1 HOECHST 33258-D(CTTTTGCAAAAG)2 COMPLEX
Components5'-D(CP*TP*TP*TP*TP*GP*CP*AP*AP*AP*AP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / HOECHST 33258 / DEOXYRIBONUCLEIC ACID / MINOR GROOVE RECOGNITION / DOUBLE HELIX / NMR SPECTROSCOPY
Function / homologyChem-HT / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / 1NS RESTRAINED MOLECULAR DYNAMICS
AuthorsGavathiotis, E. / Sharman, G.J. / Searle, M.S.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2).
Authors: Gavathiotis, E. / Sharman, G.J. / Searle, M.S.
#1: Journal: Nucleic Acids Res. / Year: 1990
Title: Sequence-Specific Interaction of Hoechst 33258 with the Minor Groove of an Adenine-Tract DNA Duplex Studied in Solution by 1H NMR Spectroscopy
Authors: Searle, M.S. / Embrey, K.J.
History
DepositionJun 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 5'-D(CP*TP*TP*TP*TP*GP*CP*AP*AP*AP*AP*G)-3'
B: 5'-D(CP*TP*TP*TP*TP*GP*CP*AP*AP*AP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,60923
Polymers7,3232
Non-polymers1,28621
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 / -
Representative

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Components

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


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SOLID PHASE SYNTHESIS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HT / 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33258


Mass: 424.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24N6O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 1.5mM Hoechst 33258-D(CTTTTGCAAAAG)2 100mM NaCl, 10mM NaH2PO4 buffer
Solvent system: D2O and 90% H20 10% D20
Sample conditionspH: 7 / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

RefinementMethod: 1NS RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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