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PDBsum entry 2gq7
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References listed in PDB file
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Key reference
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Title
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The first crystal structure of an RNA racemate.
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Authors
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W.Rypniewski,
M.Vallazza,
M.Perbandt,
S.Klussmann,
L.J.Delucas,
C.Betzel,
V.A.Erdmann.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2006,
62,
659-664.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 2.
Figure 2 A hydrated calcium ion capping the terminal sugar
moiety of G86. The contours correspond to the 2F[o] - F[c]
electron density at one r.m.s. level. Water molecules are
labelled W.
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2006,
62,
659-664)
copyright 2006.
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Headers
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