5IYJ

Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 resolution

Summary for 5IYJ

• Entry DOI: 10.2210/pdb5iyj/pdb
• Related: 5IYE 5IYG
• Descriptor: DNA (5'-D(*CP*CP*CP*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*G)-3') (2 entities in total)
• Functional Keywords: a-dna duplex, tetragonal space group, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 8565.54

Authors

Karthik, S.,Thirugnanasambandam, A.,Mandal, P.K.,Gautham, N. (deposition date: 2016-03-24, release date: 2017-03-29, Last modification date: 2023-11-08)

Primary citation

Karthik, S.,Thirugnanasambandam, A.,Mandal, P.K.,Gautham, N.
Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 angstrom resolution.
Nucleosides Nucleotides Nucleic Acids, 36:343-354, 2017

PubMed Abstract: We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG) all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P422 to P4. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.

PubMed: 28387634
DOI: 10.1080/15257770.2017.1287378

Experimental method

X-RAY DIFFRACTION (1.701 Å)