1L3Z

Crystal Structure Analysis of an RNA Heptamer

Summary for 1L3Z

• Entry DOI: 10.2210/pdb1l3z/pdb
• Descriptor: 5'-R(*GP*UP*AP*UP*AP*CP*A)-3', SODIUM ION (3 entities in total)
• Functional Keywords: rna
• Total number of polymer chains: 2
• Total formula weight: 4433.75

Authors

Shi, K.,Pan, B.,Sundaralingam, M. (deposition date: 2002-03-04, release date: 2003-02-25, Last modification date: 2024-02-14)

Primary citation

Shi, K.,Pan, B.,Sundaralingam, M.
The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs
Nucleic Acids Res., 31:1392-1397, 2003

PubMed Abstract: The crystal structure of an alternating RNA heptamer r(GUAUACA) has been determined to 2.0 A resolution and refined to an R(work) of 17.1% and R(free) of 18.5% using 2797 reflections. The heptamer crystallized in the space group C222 with a unit cell of a = 25.74, b = 106.58, c = 30.26 A and two independent strands in the asymmetric unit. Each heptamer forms a duplex with its symmetry-related strand and each duplex contains six Watson-Crick base pairs and 3'-end adenosine overhangs. Therefore, two kinds of duplex (duplex 1 and duplex 2) are formed. Duplexes 1 stack on each other forming a pseudo-continuous column, which is typical of the RNA packing mode, while duplex 2 is typical of A-DNA packing with its termini in abutting interactions. Overhang adenine residues stack within the duplexes with C3'-endo sugar pucker and C2'-endo sugar pucker in duplexes 1 and 2, respectively. A Na+ ion in the crystal lattice is water bridged to two N1 atoms of symmetry-related A7 bases.

PubMed: 12595546
DOI: 10.1093/nar/gkg226

Experimental method

X-RAY DIFFRACTION (2.01 Å)