2arg
From Proteopedia
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|PDB= 2arg |SIZE=350|CAPTION= <scene name='initialview01'>2arg</scene> | |PDB= 2arg |SIZE=350|CAPTION= <scene name='initialview01'>2arg</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ARM:DEOXY-METHYL-ARGININE'>ARM</scene> | + | |LIGAND= <scene name='pdbligand=ARM:DEOXY-METHYL-ARGININE'>ARM</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2arg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2arg OCA], [http://www.ebi.ac.uk/pdbsum/2arg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2arg RCSB]</span> | ||
}} | }} | ||
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[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
[[Category: Wang, W.]] | [[Category: Wang, W.]] | ||
| - | [[Category: ARM]] | ||
[[Category: adaptive dna structural transition]] | [[Category: adaptive dna structural transition]] | ||
[[Category: base encapsulation within minor groove]] | [[Category: base encapsulation within minor groove]] | ||
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[[Category: molecular recognition of an amino acid]] | [[Category: molecular recognition of an amino acid]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:56:18 2008'' |
Revision as of 22:56, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES
Overview
BACKGROUND: In vitro selection has identified DNA aptamers that target cofactors, amino acids, peptides and proteins. Structure determination of such ligand-DNA aptamer complexes should elucidate the details of adaptive DNA structural transitions, binding-pocket architectures and ligand recognition. We have determined the solution structure of the complex of a DNA aptamer containing a guanine-rich 18-residue hairpin loop that binds L-argininamide with approximately 100 microM affinity. RESULTS: The DNA aptamer generates its L-argininamide-binding pocket by adaptive zippering up the 18-residue loop through formation of Watson-Crick pairs, mismatch pairs and base triples, while maximizing stacking interactions. Three of the four base triples involve minor-groove recognition through sheared G.A mismatch formation. The unique fold is also achieved through positioning of an adenine residue deep within the minor groove and through nestling of a smaller loop within the larger loop on complex formation. The accessibility to the unique L-argininamide-binding pocket is restricted by a base pair that bridges across one side of the major-groove-binding site. The guanidinium group of the bound L-argininamide aligns through intermolecular hydrogen-bond formation with the base edges of nonadjacent guanine and cytosine residues while being sandwiched between the planes of nonadjacent guanine residues. CONCLUSIONS: The available structures of L-arginine/L-argininamide bound to their DNA and RNA targets define the common principles and patterns associated with molecular recognition, as well as the diversity of intermolecular hydrogen-bonding alignments associated with the distinct binding pockets.
About this Structure
2ARG is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop., Lin CH, Wang W, Jones RA, Patel DJ, Chem Biol. 1998 Oct;5(10):555-72. PMID:9818148
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