PDBsum entry 1dnx

DNA-RNA hybrid

PDB id: 1dnx

Contents

DNA/RNA

Metals

_MG

Waters ×84

PDB id:

1dnx

Name:

DNA-RNA hybrid

Title:

RNA/DNA dodecamer r(g)d(cgtatacgc) with magnesium binding sites

Structure:

DNA/RNA (5'-r( Gp)-d( Cp Gp Tp Ap Tp Ap Cp Gp C)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.195 R-free: 0.243

Authors:

H.Robinson,Y.-G.Gao,R.Sanishvili,A.Joachimiak,A.H.-J.Wang

Key ref:

H.Robinson et al. (2000). Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes. Nucleic Acids Res, 28, 1760-1766. PubMed id: 10734195 DOI: 10.1093/nar/28.8.1760

Date:

16-Dec-99 Release date: 10-Apr-00

DNA/RNA chains

G-C-G-T-A-T-A-C-G-C 10 bases

G-C-G-T-A-T-A-C-G-C 10 bases

DOI no: 10.1093/nar/28.8.1760

Nucleic Acids Res 28:1760-1766 (2000)

PubMed id: 10734195

Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.

H.Robinson, Y.G.Gao, R.Sanishvili, A.Joachimiak, A.H.Wang.

ABSTRACT

Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.