100d
From Proteopedia
(New page: 200px<br /> <applet load="100d" size="450" color="white" frame="true" align="right" spinBox="true" caption="100d, resolution 1.900Å" /> '''CRYSTAL STRUCTURE ...) |
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caption="100d, resolution 1.900Å" /> | caption="100d, resolution 1.900Å" /> | ||
'''CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING'''<br /> | '''CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the self-complementary chimeric decamer duplex, r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved, at 1.9 A resolution by the molecular replacement method and refined to an, R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the, terminal riboses apparently drive the entire chimeric duplex into an A-DNA, conformation, in contrast to the B-DNA conformation adopted by the, all-deoxy decamer of the same sequence. Five symmetry related duplexes, encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and, hydrogen bonding interactions. The spermine interaction severely bends the, duplexes by 31 degrees into the major groove at the fourth base ... | + | The crystal structure of the self-complementary chimeric decamer duplex, r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved, at 1.9 A resolution by the molecular replacement method and refined to an, R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the, terminal riboses apparently drive the entire chimeric duplex into an A-DNA, conformation, in contrast to the B-DNA conformation adopted by the, all-deoxy decamer of the same sequence. Five symmetry related duplexes, encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and, hydrogen bonding interactions. The spermine interaction severely bends the, duplexes by 31 degrees into the major groove at the fourth base pair, G(4).C(17), jolts it and slides the 'base plate' into the minor groove., This base pair, together with the adjacent base pair in the top half and, the corresponding pseudo two-fold related base pairs in the bottom half, form four minor groove base-paired multiples with the terminal base pairs, of two neighboring duplexes. |
==About this Structure== | ==About this Structure== | ||
| - | 100D is a | + | 100D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SPM:'>SPM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=100D OCA]. |
==Reference== | ==Reference== | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 15:27:41 2008'' |
Revision as of 13:27, 15 February 2008
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CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING
Overview
The crystal structure of the self-complementary chimeric decamer duplex, r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved, at 1.9 A resolution by the molecular replacement method and refined to an, R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the, terminal riboses apparently drive the entire chimeric duplex into an A-DNA, conformation, in contrast to the B-DNA conformation adopted by the, all-deoxy decamer of the same sequence. Five symmetry related duplexes, encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and, hydrogen bonding interactions. The spermine interaction severely bends the, duplexes by 31 degrees into the major groove at the fourth base pair, G(4).C(17), jolts it and slides the 'base plate' into the minor groove., This base pair, together with the adjacent base pair in the top half and, the corresponding pseudo two-fold related base pairs in the bottom half, form four minor groove base-paired multiples with the terminal base pairs, of two neighboring duplexes.
About this Structure
100D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing., Ban C, Ramakrishnan B, Sundaralingam M, Nucleic Acids Res. 1994 Dec 11;22(24):5466-76. PMID:7816639
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