2GQ5: Crystal Structure Of An Rna Racemate

The racemate of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) from Thermus flavus 5S rRNA has been crystallized and examined by X-ray crystallography. The space group is P1(_) with approximate unit-cell parameters a = 26.5, b = 38.0, c = 45.4 Angstrom, alpha = 113.1, beta = 100.5, gamma = 93.3 degrees. The structure was solved by molecular replacement. There are four RNA duplexes in the unit cell. The crystal lattice consists of columns of RNA duplexes. The duplexes are stacked end-to-end and are stabilized by intermolecular base-stacking interactions. Within each column the L-duplexes and D-duplexes are stacked alternately. Every other duplex in each stack has two alternative conformations, approximately equally occupied, corresponding to molecules oriented in opposite directions. Neighbouring columns are related by the crystallographic centre of symmetry. The unit cell also contains approximately 250 ordered water molecules and six ordered calcium ions. A glycerol molecule is visible in the minor groove interacting with a guanosine residue.
PDB ID: 2GQ5Download
MMDB ID: 98437
PDB Deposition Date: 2006/4/20
Updated in MMDB: 2012/03
Experimental Method:
x-ray diffraction
Resolution: 1.4  Å
Source Organism:
Biological Unit for 2GQ5: dimeric; determined by author
Molecular Components in 2GQ5
Label Count Molecule
Nucleotides(2 molecules)
RNA (5'-r(*(0c)p*(0u)p*(0g)p*(0g)p*(0g)p*(0c)p*(0g)p*(0g))- 3')
Molecule annotation
RNA (5'-r(*(0c)p*(0c)p*(0g)p*(0c)p*(0c)p*(0u)p*(0g)p*(0g))- 3')
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

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