| Abstract: |
Crystal structures of nucleic acids often reveal multiple metal ions. Whether a certain ion is specific to the structural motif or the result of the crystal lattice and/or crystallization conditions is usually not obvious. Five Mg2+ ions per asymmetric unit were observed in the crystal structure of the B-form DNA duplex with sequence CGCGAATTCGCG. One of them binds at a GpC step, adjacent to a kink into the major groove near one end of the duplex. Two others link phosphate groups across the minor groove, resulting in a marked narrowing at one border of the AATT-tract. However, none of the ions binds to only a single duplex. Instead they mediate contacts between symmetry-related DNA dodecamers. Moreover, all Mg2+ ions exhibit either inner- or outer-sphere coordination to phosphate groups. Although some of the Mg2+ ions accentuate conformational features of the DNA duplex in the lattice, their particular locations and coordination modes indicate that ion binding to the dodecamer is primarily a consequence of the crystal packing and, to a lesser degree, of the sequence. |
