1I0F

1.6 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-AMINOOXYETHYL THYMINE IN PLACE OF T6, BA-FORM

Summary for 1I0F

• Entry DOI: 10.2210/pdb1i0f/pdb
• Descriptor: 5'-D(*GP*CP*GP*TP*AP*(127)P*AP*CP*GP*C)-3', BARIUM ION (3 entities in total)
• Functional Keywords: a-form double helix, modified sugar, dna
• Total number of polymer chains: 2
• Total formula weight: 6377.47

Authors

Tereshko, V.,Wilds, C.J.,Minasov, G.,Prakash, T.P.,Maier, M.A.,Howard, A.,Wawrzak, Z.,Manoharan, M.,Egli, M. (deposition date: 2001-01-29, release date: 2001-04-04, Last modification date: 2024-02-07)

Primary citation

Tereshko, V.,Wilds, C.J.,Minasov, G.,Prakash, T.P.,Maier, M.A.,Howard, A.,Wawrzak, Z.,Manoharan, M.,Egli, M.
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
Nucleic Acids Res., 29:1208-1215, 2001

PubMed Abstract: The observation of light metal ions in nucleic acids crystals is generally a fortuitous event. Sodium ions in particular are notoriously difficult to detect because their X-ray scattering contributions are virtually identical to those of water and Na(+.)O distances are only slightly shorter than strong hydrogen bonds between well-ordered water molecules. We demonstrate here that replacement of Na(+) by K(+), Rb(+) or Cs(+) and precise measurements of anomalous differences in intensities provide a particularly sensitive method for detecting alkali metal ion-binding sites in nucleic acid crystals. Not only can alkali metal ions be readily located in such structures, but the presence of Rb(+) or Cs(+) also allows structure determination by the single wavelength anomalous diffraction technique. Besides allowing identification of high occupancy binding sites, the combination of high resolution and anomalous diffraction data established here can also pinpoint binding sites that feature only partial occupancy. Conversely, high resolution of the data alone does not necessarily allow differentiation between water and partially ordered metal ions, as demonstrated with the crystal structure of a DNA duplex determined to a resolution of 0.6 A.

PubMed: 11222771
DOI: 10.1093/nar/29.5.1208

Experimental method

X-RAY DIFFRACTION (1.6 Å)