Tereshko V, Wilds C J, Minasov G, Prakash T P, Maier M A, Howard A, Wawrzak Z, Manoharan M, Egli M
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Nucleic Acids Res. 2001 Mar 1;29(5):1208-15. doi: 10.1093/nar/29.5.1208.
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.
在核酸晶体中观察轻金属离子通常是偶然事件。特别是钠离子，因其X射线散射贡献与水几乎相同，且Na(+)·O距离仅略短于有序水分子间的强氢键，故而极难检测。我们在此证明，用K(+)、Rb(+)或Cs(+)取代Na(+)并精确测量强度的反常差异，为检测核酸晶体中的碱金属离子结合位点提供了一种特别灵敏的方法。不仅碱金属离子能在此类结构中轻易定位，而且Rb(+)或Cs(+)的存在还能通过单波长反常衍射技术确定结构。除了能识别高占有率结合位点外，此处建立的高分辨率和反常衍射数据相结合，还能精确找出仅具有部分占有率的结合位点。相反，仅靠数据的高分辨率并不一定能区分水和部分有序的金属离子，这在分辨率为0.6 Å的DNA双链晶体结构中得到了证明。
