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 11528

Title: STRUCTURE OF METALLO-DNA IN SOLUTION

Authors: Yamaguchi, H.; Sebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.; Kojima, C.; Sychrovsky, V.; Tanaka, Y.

Citation: Yamaguchi, H.; Sebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.; Kojima, C.; Sychrovsky, V.; Tanaka, Y.. "The structure of metallo-DNA with consecutive T-Hg(II)-T base-pairs explains positive entropy for the metallo-base-pair formation"  Not known ., .-..

Assembly members:
5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3', polymer, 10 residues, 3011.991 Da.
5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3', polymer, 10 residues, 3061.029 Da.
MERCURY (II) ION, non-polymer, 200.590 Da.

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

Experimental source:   Production method: chemical synthesis   Host organism: not applicable

Entity Sequences (FASTA):
5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3': CGCGTTGTCC
5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3': GGACTTCGCG

Data sets:
Data typeCount
1H chemical shifts220

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
15'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'1
25'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'2
3MERCURY (II) ION_13
4MERCURY (II) ION_23

Entities:

Entity 1, 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 10 residues - 3011.991 Da.

1   DCDGDCDGDTDTDGDTDCDC

Entity 2, 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 10 residues - 3061.029 Da.

1   DGDGDADCDTDTDCDGDCDG

Entity 3, MERCURY (II) ION_1 - Hg - 200.590 Da.

1   HG

Samples:

sample_1: 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 2.0 mM; 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 2.0 mM; Mercury(II) perchlorate 4.0 mM; Sodium perchlorate 100 mM; D2O, [U-100% 2H], 100%

sample_2: 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 2.0 mM; 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 2.0 mM; Mercury(II) perchlorate 4.0 mM; Sodium perchlorate 100 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_conditions_1: ionic strength: 0.10 M; pH: 6.0; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0.10 M; pH: 6.0; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D DQF-COSYsample_1isotropicsample_conditions_1

Software:

X-PLOR v3.851, A. T. BRUNGER - refinement, structure solution

SPARKY v3.1, Goddard - chemical shift assignment, peak picking, processing

MARDIGRAS, Thomas L. James - structure solution

NMR spectrometers:

  • BRUKER DRX800 800 MHz

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