1en9: Difference between revisions

Revision as of 13:29, 21 February 2008

1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.

OverviewOverview

The 1 A resolution X-ray crystal structures of Mg(2+) and Ca(2+) salts of the B-DNA decamers CCAACGTTGG and CCAGCGCTGG reveal sequence-specific binding of Mg(2+) and Ca(2+) to the major and minor grooves of DNA, as well as non-specific binding to backbone phosphate oxygen atoms. Minor groove binding involves H-bond interactions between cross-strand DNA base atoms of adjacent base-pairs and the cations' water ligands. In the major groove the cations' water ligands can interact through H-bonds with O and N atoms from either one base or adjacent bases, and in addition the softer Ca(2+) can form polar covalent bonds bridging adjacent N7 and O6 atoms at GG bases. For reasons outlined earlier, localized monovalent cations are neither expected nor found.Ultra-high atomic resolution gives an unprecedented view of hydration in both grooves of DNA, permits an analysis of individual anisotropic displacement parameters, and reveals up to 22 divalent cations per DNA duplex. Each DNA helix is quite anisotropic, and alternate conformations, with motion in the direction of opening and closing the minor groove, are observed for the sugar-phosphate backbone. Taking into consideration the variability of experimental parameters and crystal packing environments among these four helices, and 24 other Mg(2+) and Ca(2+) bound B-DNA structures, we conclude that sequence-specific and strand-specific binding of Mg(2+) and Ca(2+) to the major groove causes DNA bending by base-roll compression towards the major groove, while sequence-specific binding of Mg(2+) and Ca(2+) in the minor groove has a negligible effect on helix curvature. The minor groove opens and closes to accommodate Mg(2+) and Ca(2+) without the necessity for significant bending of the overall helix.The program Shelxdna was written to facilitate refinement and analysis of X-ray crystal structures by Shelxl-97 and to plot and analyze one or more Curves and Freehelix output files.

About this StructureAbout this Structure

1EN9 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium., Chiu TK, Dickerson RE, J Mol Biol. 2000 Aug 25;301(4):915-45. PMID:10966796

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 '''1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.'''<br />
 ==Overview==
-The 1 A resolution X-ray crystal structures of Mg(2+) and Ca(2+) salts of, the B-DNA decamers CCAACGTTGG and CCAGCGCTGG reveal sequence-specific, binding of Mg(2+) and Ca(2+) to the major and minor grooves of DNA, as, well as non-specific binding to backbone phosphate oxygen atoms. Minor, groove binding involves H-bond interactions between cross-strand DNA base, atoms of adjacent base-pairs and the cations' water ligands. In the major, groove the cations' water ligands can interact through H-bonds with O and, N atoms from either one base or adjacent bases, and in addition the softer, Ca(2+) can form polar covalent bonds bridging adjacent N7 and O6 atoms at, GG bases. For reasons outlined earlier, localized monovalent cations are, neither expected nor found.Ultra-high atomic resolution gives an, unprecedented view of hydration in both grooves of DNA, permits an, analysis of individual anisotropic displacement parameters, and reveals up, to 22 divalent cations per DNA duplex. Each DNA helix is quite, anisotropic, and alternate conformations, with motion in the direction of, opening and closing the minor groove, are observed for the sugar-phosphate, backbone. Taking into consideration the variability of experimental, parameters and crystal packing environments among these four helices, and, 24 other Mg(2+) and Ca(2+) bound B-DNA structures, we conclude that, sequence-specific and strand-specific binding of Mg(2+) and Ca(2+) to the, major groove causes DNA bending by base-roll compression towards the major, groove, while sequence-specific binding of Mg(2+) and Ca(2+) in the minor, groove has a negligible effect on helix curvature. The minor groove opens, and closes to accommodate Mg(2+) and Ca(2+) without the necessity for, significant bending of the overall helix.The program Shelxdna was written, to facilitate refinement and analysis of X-ray crystal structures by, Shelxl-97 and to plot and analyze one or more Curves and Freehelix output, files.
+The 1 A resolution X-ray crystal structures of Mg(2+) and Ca(2+) salts of the B-DNA decamers CCAACGTTGG and CCAGCGCTGG reveal sequence-specific binding of Mg(2+) and Ca(2+) to the major and minor grooves of DNA, as well as non-specific binding to backbone phosphate oxygen atoms. Minor groove binding involves H-bond interactions between cross-strand DNA base atoms of adjacent base-pairs and the cations' water ligands. In the major groove the cations' water ligands can interact through H-bonds with O and N atoms from either one base or adjacent bases, and in addition the softer Ca(2+) can form polar covalent bonds bridging adjacent N7 and O6 atoms at GG bases. For reasons outlined earlier, localized monovalent cations are neither expected nor found.Ultra-high atomic resolution gives an unprecedented view of hydration in both grooves of DNA, permits an analysis of individual anisotropic displacement parameters, and reveals up to 22 divalent cations per DNA duplex. Each DNA helix is quite anisotropic, and alternate conformations, with motion in the direction of opening and closing the minor groove, are observed for the sugar-phosphate backbone. Taking into consideration the variability of experimental parameters and crystal packing environments among these four helices, and 24 other Mg(2+) and Ca(2+) bound B-DNA structures, we conclude that sequence-specific and strand-specific binding of Mg(2+) and Ca(2+) to the major groove causes DNA bending by base-roll compression towards the major groove, while sequence-specific binding of Mg(2+) and Ca(2+) in the minor groove has a negligible effect on helix curvature. The minor groove opens and closes to accommodate Mg(2+) and Ca(2+) without the necessity for significant bending of the overall helix.The program Shelxdna was written to facilitate refinement and analysis of X-ray crystal structures by Shelxl-97 and to plot and analyze one or more Curves and Freehelix output files.
 ==About this Structure==
-EN9 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EN9 OCA].
+EN9 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EN9 OCA].
 ==Reference==
 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium., Chiu TK, Dickerson RE, J Mol Biol. 2000 Aug 25;301(4):915-45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10966796 10966796]
 [[Category: Protein complex]]
-[[Category: Chiu, T.K.]]
+[[Category: Chiu, T K.]]
-[[Category: Dickerson, R.E.]]
+[[Category: Dickerson, R E.]]
 [[Category: MG]]
 [[Category: b-dna]]
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 [[Category: shelxdna]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:33:39 2007''
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