1d83

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
[[Image:1d83.gif|left|200px]]
[[Image:1d83.gif|left|200px]]
-
{{Structure
+
<!--
-
|PDB= 1d83 |SIZE=350|CAPTION= <scene name='initialview01'>1d83</scene>
+
The line below this paragraph, containing "STRUCTURE_1d83", creates the "Structure Box" on the page.
-
|SITE=
+
You may change the PDB parameter (which sets the PDB file loaded into the applet)
-
|LIGAND= <scene name='pdbligand=1GL:4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE'>1GL</scene>, <scene name='pdbligand=ARI:[O4]-ACETOXY-2,3-DIDEOXYFUCOSE'>ARI</scene>, <scene name='pdbligand=CDR:2,3-DIDEOXYFUCOSE'>CDR</scene>, <scene name='pdbligand=CPH:1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO-PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE'>CPH</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=ERI:4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE'>ERI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-
|ACTIVITY=
+
or leave the SCENE parameter empty for the default display.
-
|GENE=
+
-->
-
|DOMAIN=
+
{{STRUCTURE_1d83| PDB=1d83 | SCENE= }}
-
|RELATEDENTRY=
+
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d83 OCA], [http://www.ebi.ac.uk/pdbsum/1d83 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d83 RCSB]</span>
+
-
}}
+
'''STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION'''
'''STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION'''
Line 19: Line 16:
==About this Structure==
==About this Structure==
-
1D83 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=1D83 OCA].
+
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D83 OCA].
==Reference==
==Reference==
Structure refinement of the chromomycin dimer-DNA oligomer complex in solution., Gao XL, Mirau P, Patel DJ, J Mol Biol. 1992 Jan 5;223(1):259-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1731073 1731073]
Structure refinement of the chromomycin dimer-DNA oligomer complex in solution., Gao XL, Mirau P, Patel DJ, J Mol Biol. 1992 Jan 5;223(1):259-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1731073 1731073]
-
[[Category: Protein complex]]
 
[[Category: Gao, X.]]
[[Category: Gao, X.]]
[[Category: Mirau, P.]]
[[Category: Mirau, P.]]
[[Category: Patel, D J.]]
[[Category: Patel, D J.]]
-
[[Category: chromomycin]]
+
[[Category: Chromomycin]]
-
[[Category: dna]]
+
[[Category: Dna]]
-
[[Category: double helix]]
+
[[Category: Double helix]]
-
[[Category: nmr]]
+
[[Category: Nmr]]
-
 
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:33:21 2008''
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:36:39 2008''
+

Revision as of 10:33, 2 May 2008

Image:1d83.gif

Template:STRUCTURE 1d83

STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN SOLUTION


Overview

We have refined the initial docking model of the Mg(II)-co-ordinated chromomycin-d(A2G2C2T2) complex (2 drug equivalents per duplex) by a complete relaxation matrix analysis simulation of the two-dimensional nuclear Overhauser effect (NOESY) spectrum of the complex in 2H2O solution. This relaxation matrix refined structure of the complex exhibits the following characteristics. (1) We observe an unwound and elongated duplex that exhibits characteristics distinct from the A and B-DNA family of helices at the central (G-G-C-C).(G-G-C-C) chromomycin dimer binding and flanking sites. On the other hand sugar puckers, glycosidic torsion angles, displacement of the base-pairs from the helix axis and the minor groove width for this central tetranucleotide segment all fall within the A-family of helical parameters. (2) The chromomycin monomers are aligned in a head-to-tail orientation in the Mg(II)-co-ordinated dimer in the complex. The chromophores are aligned with a slight tilt relative to each other and make an angle of 75 degrees between their planes. The C-D-E trisaccharide segments from individual monomers adopt an extended conformation that projects in opposite directions in the dimer. The divalent metal cation is co-ordinated to the O(1) carbonyl and O(9) enolate atoms of the chromophores and aligns them such that the O(9)-Mg-O(9) angle is 170 degrees while all other O-Mg-O angles are in the 95(+/- 15)degrees range. (3) The sequence specificity of the chromomycin dimer for the widened and shallower (G3-G4-C5-C6).(G3-G4-C5-C6) minor groove binding site is associated with intermolecular hydrogen bonds formed between the OH group at C(8) of the chromophore and the minor groove NH2 group at position 2 and N(3) groups of G4 and between the O(1) oxygen of the E-sugar and the minor groove NH2 group at position 2 of G3 in the complex. (4) Additional intermolecular interactions are primarily van der Waals contacts between anomeric and adjacent CH2 protons on each sugar in the C-D-E trisaccharide segments of the chromomycin dimer and the minor groove surface of the DNA. These results provide insights into the induced conformational transitions required to generate a complementary match between the drug dimer and its DNA binding site on complex formation.

About this Structure

Full crystallographic information is available from OCA.

Reference

Structure refinement of the chromomycin dimer-DNA oligomer complex in solution., Gao XL, Mirau P, Patel DJ, J Mol Biol. 1992 Jan 5;223(1):259-79. PMID:1731073 Page seeded by OCA on Fri May 2 13:33:21 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d83"
Personal tools