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146d
From Proteopedia
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| - | [[Image:146d.gif|left|200px]]< | + | [[Image:146d.gif|left|200px]] |
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| - | '''SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX''' | + | {{Structure |
| + | |PDB= 146d |SIZE=350|CAPTION= <scene name='initialview01'>146d</scene> | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CRH:1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE'>CRH</scene> and <scene name='pdbligand=MDA:2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE'>MDA</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 146D is a [ | + | 146D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=146D OCA]. |
==Reference== | ==Reference== | ||
| - | Solution structure of the mithramycin dimer-DNA complex., Sastry M, Patel DJ, Biochemistry. 1993 Jul 6;32(26):6588-604. PMID:[http:// | + | Solution structure of the mithramycin dimer-DNA complex., Sastry M, Patel DJ, Biochemistry. 1993 Jul 6;32(26):6588-604. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8329387 8329387] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 09:49:35 2008'' |
Revision as of 07:49, 20 March 2008
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| Ligands: | , and | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX
Overview
We have characterized the NMR parameters for the complexes formed by the Mg(2+)-coordinated mithramycin dimer with self-complementary d(T-G-G-C-C-A) and d(T-C-G-C-G-A) duplexes. The solution structure of the latter complex has been determined using a combined NMR-molecular dynamics study including relaxation matrix refinement. The Mg(2+)-coordinated mithramycin dimer-d(T-C-G-C-G-A) complex exhibits a 2-fold center of symmetry with the divalent cation coordinated aglycons positioned opposite the central (G3-C4).(G3-C4) segment such that the aglycon C8 hydroxyl oxygens form symmetrical sequence-specific hydrogen bonds to guanine amino protons in the complex. The C-D-E trisaccharide segments of each monomer in the mithramycin dimer adopt extended conformations, are positioned inside the minor groove, and are directed toward either end of the duplex. The C-D saccharide component of one monomer and the aglycon of the other monomer in the mithramycin dimer share a widened minor groove with the hydrophobic edges of the C and D sugars interacting with individual strands of the duplex. The E-sugar ring is positioned in the floor of the minor groove, and its hydroxyl-bearing face interacts with both strands of the duplex through hydrogen-bonding and hydrophobic intermolecular interactions. The A-B disaccharide and the hydrophilic side chain form intermolecular contacts with the sugar-phosphate backbone in the complex. The antiparallel alignment of divalent cation coordinated monomers in the mithramycin dimer results in the two outwardly directed C-D-E trisaccharide segments generating a right-handed continuous hexasaccharide domain that spans six base pairs in the minor groove of the duplex. The solution structure of the mithramycin dimer-DNA complex reported in this study and the solution structure of the chromomycin dimer-DNA complex reported previously [Gao, X., Mirau, P., & Patel, D. J. (1992) J. Mol. Biol. 223, 259-279] show global similarities, as well as local differences that are of interest. All four nucleotides in the tetranucleotide segment of the duplex centered about the sequence-specific (G-C).(G-C) step adopt A-DNA sugar puckers and glycosidic torsion angles in the chromomycin dimer-DNA complex, while only the central cytidine adopts an A-DNA sugar pucker and glycosidic torsion angle in the mithramycin dimer-DNA complex.(ABSTRACT TRUNCATED AT 400 WORDS)
About this Structure
146D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of the mithramycin dimer-DNA complex., Sastry M, Patel DJ, Biochemistry. 1993 Jul 6;32(26):6588-604. PMID:8329387
Page seeded by OCA on Thu Mar 20 09:49:35 2008
Categories: Protein complex | Patel, D J. | Sastry, M. | CRH | MDA | MG | Dna | Mithramycin dimer | Nmr
