101d

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{{STRUCTURE_101d| PDB=101d | SCENE= }}
{{STRUCTURE_101d| PDB=101d | SCENE= }}
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'''REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION'''
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===REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION===
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==Overview==
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The X-ray crystal structure of the complex of the B-DNA dodecamer CGCGAATTCGCG with the antitumor drug netropsin has been reexamined to locate the drug accurately for computer-based drug design. The optimum solution is with the drug centered in the AATT region of the minor groove, making three good bifurcated hydrogen bonds with adenine N3 and thymine O2 atoms along the floor of the groove. Pyrrole rings of netropsin are packed against the C2 positions of adenines, leaving no room for the amine group of guanine and, hence, providing a structural rationale for the A.T specificity of netropsin. An alternative positioning in which the drug is shifted along the minor groove by ca. one-half base pair step is rejected on the basis of free R factor calculations and the appearance of the original drug-free difference maps. Final omit maps, although of more pleasing appearance, are not a dependable means of discriminating between right and wrong structures. The shifted alternative drug position ignores potential hydrogen bonding along the floor of the groove, provides no explanation for netropsin's observed A.T specificity, and is contradicted by NMR results [Patel, D. J. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6424].
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(as it appears on PubMed at http://www.pubmed.gov), where 7711020 is the PubMed ID number.
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{{ABSTRACT_PUBMED_7711020}}
==About this Structure==
==About this Structure==
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[[Category: Double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:24:19 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:06:06 2008''

Revision as of 12:06, 30 June 2008

Image:101d.png

Template:STRUCTURE 101d

REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION

Template:ABSTRACT PUBMED 7711020

About this Structure

Full crystallographic information is available from OCA.

Reference

Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation., Goodsell DS, Kopka ML, Dickerson RE, Biochemistry. 1995 Apr 18;34(15):4983-93. PMID:7711020

Page seeded by OCA on Mon Jun 30 15:06:06 2008

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