D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND ZINC

Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 19 11:38:50 2011

Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 19 11:40:17 2011

Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 19 11:44:52 2011

Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 19 11:46:10 2011

Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 19 11:48:13 2011

Information obtained from PDB's Chemical Component Dictionary
at http://wwpdb-remediation.rutgers.edu/downloads.html
Downloaded on Tue Jul 19 10:28:58 2011

[(2S,3S,4S,6S)-4,6-dihydroxy-2,4-dimethyl-oxan-3-yl] ethanoate

[(2R,3R,4R,6S)-4,6-dihydroxy-2-methyl-oxan-3-yl] ethanoate

polydeoxyribonucleotide polysaccharide(D)

Internal TSP referenced to external TSP (in a co-axial capillary)
because of susceptibility effects in the sample.
All reported chemical shifts are relative to external TSP.

A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.

The structure of a DNA octamer d(TTGGCCAA)(2) complexed to chromomycin-A(3) and
a single divalent cobalt ion has been solved by using the pseudocontact shifts
due to the unpaired electrons on the cobalt. A protocol was developed and
critically evaluated for using the pseudocontact shifts in structure
determination. The pseudocontact shifts were input as experimental restraints
in molecular dynamics simulations with or without NOE constraints. Both the
magnitude and orientation of the susceptibility anisotropy tensor required for
the shift calculations were determined during the simulations by iterative
refinement. The pseudocontact shifts could be used to define the structure to a
very high precision and accuracy compared with a corresponding NOE-determined
structure. Convergence was obtained from different starting structures and
tensors. A structure determination using both NOE's and pseudocontact shifts
revealed a general agreement between the two data sets. However, some evidence
for a discrepancy between NOE's and pseudocontact shifts was observed in the
backbone and terminal base pairs of the DNA. Violations in shift or NOE
restraints remaining in the final structures were examined and may be a
reflection of motional averaging of the constraints and evidence for
flexibility. This work demonstrates that pseudocontact shifts are a powerful
tool for NMR structure determination.

Journal of the American Chemical Society
Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints.

Average solution structure of d(TTGGCCAA)2 bound to Chromomycin-A3 and zinc

update DNA residue label to two-letter code