331d
From Proteopedia
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|PDB= 331d |SIZE=350|CAPTION= <scene name='initialview01'>331d</scene>, resolution 1.650Å | |PDB= 331d |SIZE=350|CAPTION= <scene name='initialview01'>331d</scene>, resolution 1.650Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NCO:COBALT HEXAMMINE ION'>NCO</scene> | + | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=331d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=331d OCA], [http://www.ebi.ac.uk/pdbsum/331d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=331d RCSB]</span> | ||
}} | }} | ||
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[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
[[Category: Wahl, M.]] | [[Category: Wahl, M.]] | ||
| - | [[Category: NCO]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: flipped-out base]] | [[Category: flipped-out base]] | ||
| Line 31: | Line 33: | ||
[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''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 05:21:28 2008'' |
Revision as of 02:21, 31 March 2008
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| , resolution 1.650Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF D(GCGCGCG) WITH 5'-OVERHANG G'S
Overview
The crystal structure of the DNA heptamer d(GCGCGCG) has been solved at 1.65 A resolution by the molecular replacement method and refined to an R-value of 0.184 for 3598 reflections. The heptamer forms a Z-DNA d(CGCGCG)2 with 5'-overhang G residues instead of an A-DNA d(GCGCGC)2 with 3'-overhang G residues. The overhang G residues from parallel strands of two adjacent duplexes form a trans reverse Hoogsteen G x G basepair that stacks on the six Z-DNA basepairs to produce a pseudocontinuous helix. The reverse Hoogsteen G x G basepair is unusual in that the displacement of one G base relative to the other allows them to participate in a bifurcated (G1)N2 . . . N7(G8) and an enhanced (G8)C8-H . . . O6(G1) hydrogen bond, in addition to the two usual hydrogen bonds. The 5'-overhang G residues are anti and C2'-endo while the 3'-terminal G residues are syn and C2'-endo. The conformations of both G residues are different from the syn/C3'-endo for the guanosine in a standard Z-DNA. The two cobalt hexammine ions bind to the phosphate groups in both GpC and CpG steps in Z(I) and Z(II) conformations. The water structure motif is similar to the other Z-DNA structures.
About this Structure
331D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(GCGCGCG) with 5'-overhang G residues., Pan B, Ban C, Wahl MC, Sundaralingam M, Biophys J. 1997 Sep;73(3):1553-61. PMID:9284322
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