BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30335

Title: NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence

Authors: Harika, N.; Boykin, D.

Citation: Harika, N.; Boykin, D.. "NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence"  . ., .-..

Assembly members:
DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'), polymer, 9 residues, 2748.838 Da.
DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'), polymer, 9 residues, 2721.796 Da.

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'): CCAAGATAG
DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'): CTATCTTGG

Data sets:
Data typeCount
1H chemical shifts131

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 9 residues - 2748.838 Da.

1   DCDCDADADGDADTDADG

Entity 2, entity_2 9 residues - 2721.796 Da.

1   DCDTDADTDCDTDTDGDG

Samples:

sample_1: DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3') 0.54 mM; DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3') 0.54 mM; DSS 0.4 mM; EDTA 0.14 mM; Tris-d11 buffer 10 mM; sodium chloride 10 mM

sample_conditions_1: ionic strength: 0.5 mM; pH: 6.3 pH*; pressure: 1 atm; temperature: 285 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESY 100MSsample_1isotropicsample_conditions_1
2D 1H-1H NOESY 100MSsample_1isotropicsample_conditions_1
2D 1H-1H NOESY 50MSsample_1isotropicsample_conditions_1
2D 1H-1H NOESY 50MSsample_1isotropicsample_conditions_1
2D 1H-1H NOESY 150MSsample_1isotropicsample_conditions_1
2D 1H-1H NOESY 300MSsample_1isotropicsample_conditions_1
2D 1H-1H CONSTANT TIME NOESYsample_1isotropicsample_conditions_1
1D 31Psample_1isotropicsample_conditions_1
1H, 31P-correlated 2D spectra (HPCOR)sample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

SPARKY, Goddard,T.D.; Kneller,D.G. - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker AvanceIII 850 MHz

Related Database Links: