3V9D

Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex

Summary for 3V9D

• Entry DOI: 10.2210/pdb3v9d/pdb
• Related: 3QK4
• Descriptor: DNA (5'-D(*CP*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*GP*G)-3'), MANGANESE (II) ION (3 entities in total)
• Functional Keywords: tetra-decanucleotide, a-dna duplex, crystal packing, a-type double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 8620.47

Authors

Mandal, P.K.,Venkadesh, S.,Gautham, N. (deposition date: 2011-12-26, release date: 2012-04-18, Last modification date: 2024-04-03)

Primary citation

Mandal, P.K.,Venkadesh, S.,Gautham, N.
Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex
Acta Crystallogr.,Sect.F, 68:393-399, 2012

PubMed Abstract: The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.

PubMed: 22505405
DOI: 10.1107/S174430911200869X

Experimental method

X-RAY DIFFRACTION (2.5 Å)