1m77
From Proteopedia
(New page: 200px<br /><applet load="1m77" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m77, resolution 1.25Å" /> '''Near Atomic Resoluti...) |
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| - | [[Image:1m77.gif|left|200px]]<br /><applet load="1m77" size=" | + | [[Image:1m77.gif|left|200px]]<br /><applet load="1m77" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1m77, resolution 1.25Å" /> | caption="1m77, resolution 1.25Å" /> | ||
'''Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA'''<br /> | '''Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25 | + | The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25 A resolution. The decamer crystallized in the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 44.3, c = 24.8 A and one strand in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to R(work) and R(free) values of 16.3 and 18.5%, respectively, for 5969 reflections. The decamer forms the A-form DNA duplex, with the abutting crystal packing typical of A-DNA. The crystal packing interactions seem to distort the local conformation: A5 adopts the trans/trans conformation for the torsion angles alpha and gamma instead of the usual gauche(-)/gauche(+) conformations, yielding G*(G.C) base triplets. The highly hydrated [Co(NH(3))(6)](3+) ion adopts a novel binding mode to the DNA duplex, binding directly to phosphate groups and connecting to N7 and O6 atoms of guanines by water bridges. Analysis of thermal parameters (B factors) shows that the nucleotides involved in abutting crystal packing are thermally more stable than other nucleotides in the duplex. |
==About this Structure== | ==About this Structure== | ||
| - | 1M77 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NCO as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1M77 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M77 OCA]. |
==Reference== | ==Reference== | ||
Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA., Ramakrishnan B, Sekharudu C, Pan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):67-72. Epub 2002, Dec 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12499541 12499541] | Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA., Ramakrishnan B, Sekharudu C, Pan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):67-72. Epub 2002, Dec 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12499541 12499541] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Pan, B | + | [[Category: Pan, B C.]] |
[[Category: Ramakrishnan, B.]] | [[Category: Ramakrishnan, B.]] | ||
[[Category: Sekharudu, C.]] | [[Category: Sekharudu, C.]] | ||
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[[Category: cobalt hexammine]] | [[Category: cobalt hexammine]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:52:20 2008'' |
Revision as of 11:52, 21 February 2008
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Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA
Overview
The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25 A resolution. The decamer crystallized in the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 44.3, c = 24.8 A and one strand in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to R(work) and R(free) values of 16.3 and 18.5%, respectively, for 5969 reflections. The decamer forms the A-form DNA duplex, with the abutting crystal packing typical of A-DNA. The crystal packing interactions seem to distort the local conformation: A5 adopts the trans/trans conformation for the torsion angles alpha and gamma instead of the usual gauche(-)/gauche(+) conformations, yielding G*(G.C) base triplets. The highly hydrated [Co(NH(3))(6)](3+) ion adopts a novel binding mode to the DNA duplex, binding directly to phosphate groups and connecting to N7 and O6 atoms of guanines by water bridges. Analysis of thermal parameters (B factors) shows that the nucleotides involved in abutting crystal packing are thermally more stable than other nucleotides in the duplex.
About this Structure
1M77 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA., Ramakrishnan B, Sekharudu C, Pan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):67-72. Epub 2002, Dec 19. PMID:12499541
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