PDBsum entry 1vtf

DNA

PDB id: 1vtf

Contents

DNA/RNA

Ligands

PRL ×6

Waters ×1

PDB id:

1vtf

Name:

DNA

Title:

Structure of 5'-d( (Bro)cp Gp (Bro)cp G)-3' in complex with proflavine

Structure:

DNA (5'-d( (Bro)cp Gp (Bro)cp G)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.00Å R-factor: 0.269

Authors:

E.Westhof,M.V.Hosur,M.Sundaralingam

Key ref:

E.Westhof et al. (1988). Nonintercalative binding of proflavin to Z-DNA: structure of a complex between d(5BrC-G-5BrC-G) and proflavin. Biochemistry, 27, 5742-5747. PubMed id: 3179273

Date:

13-Dec-88 Release date: 13-Jul-11

DNA/RNA chains

CBR-G-CBR-G 4 bases

CBR-G-CBR-G 4 bases

Biochemistry 27:5742-5747 (1988)

PubMed id: 3179273

Nonintercalative binding of proflavin to Z-DNA: structure of a complex between d(5BrC-G-5BrC-G) and proflavin.

E.Westhof, M.V.Hosur, M.Sundaralingam.

ABSTRACT

The crystal structure of a disordered 1:1 complex between the tetradeoxyoligomer d(5BrC-G-5BrC-G) and proflavin has been determined and refined to an R factor of 26.9% for 474 reflections initially in space group P6(5) and to an R factor of 22.2% for 475 reflections in space group P2(1), both at 2-A resolution with Fobsd greater than or equal to 4.0. The unit cell constants are a = b = 17.9 A, c = 44.5 A, and gamma = 120 degrees. The final models are essentially the same in the two space groups with greater disorder in space group P6(5). In space group P2(1), the asymmetric unit is a tetranucleotide duplex, two sandwiched proflavin molecules, and four "outside-bound" proflavins. The tetranucleotide duplex is in the Z conformation and is located at the origin of the unit cell with a pair of proflavins sandwiched between the tetranucleotides. Thus, the tetranucleotides and proflavin dimers stack alternatively forming a quasi-continuous helix with the helix axis coincident with the c axis. The structure analysis revealed the presence of outside-bound proflavins as well. It is interesting that one type of outside-bound proflavins occupies a similar environment as the cobalt hexaammines in their complex with the decadeoxyoligomer d(CGTACGTACG) [Brennan, R. G., Westhof, E., & Sundaralingam, M. (1986) J. Biomol. Struct. Dyn. 3, 649]. Crystals of the latter are isomorphous to the present complex. The outside-bound proflavins penetrate the deep minor groove, thereby closing it off, and provide a visualization of a quasi-internal mode of binding of proflavin to a nucleic acid.