PDBsum entry 1xcs

DNA

PDB id

1xcs

Loading ...

Contents

			DNA/RNA

			Ligands

					A4L

			Metals

					_BA


					_CO ×2

			Waters ×44

PDB id:

1xcs

Links

Name:

DNA

Title:

Structure of oligonucleotide/drug complex

Structure:

5'-d( Cp Gp Tp Ap Cp G)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Tetramer (from PQS)

Resolution:

1.40Å

R-factor:

0.199

R-free:

0.251

Authors:

N.Valls,R.A.Steiner,G.Wright,G.N.Murshudov,J.A.Subirana

Key ref:

N.Valls et al. (2005). Variable role of ions in two drug intercalation complexes of DNA. J Biol Inorg Chem, 10, 476-482. PubMed id: 15926069

Date:

03-Sep-04

Release date:

19-Jul-05

	Headers

	References

DNA/RNA chains

		C-G-T-A-C-G 6 bases
		C-G-T-A-C-G 6 bases

	J Biol Inorg Chem 10:476-482 (2005)
PubMed id: 15926069

Variable role of ions in two drug intercalation complexes of DNA.
N.Valls, R.A.Steiner, G.Wright, G.N.Murshudov, J.A.Subirana.

ABSTRACT

The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-A resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co(2+), Ba(2+) and Na(+) ions. They reveal at least two different types of coordination environments: (1) specific sites for Co(2+) interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21431128

M.Ferraroni, C.Bazzicalupi, A.R.Bilia, and P.Gratteri (2011).
X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG).

Chem Commun (Camb), 47, 4917-4919.

PDB codes:

3np6 3nx5

17145714

N.H.Hopcroft, A.L.Brogden, M.Searcey, and C.J.Cardin (2006).
X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative.

Nucleic Acids Res, 34, 6663-6672.

PDB code:

2gb9

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.