473D

NI2+/GUANINE INTERACTIONS AND NETROPSIN/GUANINE STACKING IN D(CGTATATACG)2

Summary for 473D

• Entry DOI: 10.2210/pdb473d/pdb
• Descriptor: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3'), NICKEL (II) ION, NETROPSIN, ... (4 entities in total)
• Functional Keywords: netropsin/guanine stacking, ni2+/guanine interactions, minor groove binding, dna
• Total number of polymer chains: 2
• Total formula weight: 6753.27

Authors

Abrescia, N.G.A.,Malinina, L.,Subirana, J.A. (deposition date: 1999-05-18, release date: 1999-12-02, Last modification date: 2023-12-27)

Primary citation

Abrescia, N.G.,Malinina, L.,Subirana, J.A.
Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2.
J.Mol.Biol., 294:657-666, 1999

PubMed Abstract: We present the structure of the decanucleotide d(CGTATATACG) determined by single crystal X-ray diffraction at 1.58 A resolution. A netropsin drug is found in the minor groove with guanine stacked on a pyrrole ring of the drug, a feature described here for the first time. The stacked guanine is an extra-helical base coming from the end of a neighbour oligonucleotide. This observation may open the way to the development of minor groove binding drugs with a higher sequence selectivity. The oligonucleotide is in the B-conformation, but the terminal base-pairs are disrupted: the cytosine residues are disordered while the guanine residues penetrate into the minor groove of neighbouring duplexes. Four hydrated Ni ions with octahedral co-ordination are found associated with the N7 atoms of each guanine. The high affinity of these ions with guanine suggests that they may be used as probes for specific guanine residues.

PubMed: 10610787
DOI: 10.1006/jmbi.1999.3280

Experimental method

X-RAY DIFFRACTION (1.58 Å)