This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1n5c

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:52, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1n5c.gif|left|200px]]
 
-
{{Structure
+
==Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG==
-
|PDB= 1n5c |SIZE=350|CAPTION= <scene name='initialview01'>1n5c</scene>, resolution 1.79&Aring;
+
<StructureSection load='1n5c' size='340' side='right'caption='[[1n5c]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
+
<table><tr><td colspan='2'>[[1n5c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N5C FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.79&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n5c OCA], [https://pdbe.org/1n5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n5c RCSB], [https://www.ebi.ac.uk/pdbsum/1n5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n5c ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Fernandes A]]
-
Exocyclic DNA adducts are formed from metabolites of chemical carcinogens and have also been detected as endogenous lesions in human DNA. The exocyclic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilon dC), positioned opposite deoxyguanosine in the B-form duplex of the dodecanucleotide d(CGCGAATTepsilonCGCG), has been crystallographically characterized at 1.8A resolution. This self-complementary oligomer crystallizes in space group P3(2)12, containing a single strand in the asymmetric unit. The crystal structure was solved by isomorphous replacement with the corresponding unmodified dodecamer structure. Exposure of both structures to identical crystal packing forces allows a detailed investigation of the influence of the exocyclic base adduct on the overall helical structure and local geometry. Structural changes are limited to the epsilon C:G and adjacent T:A and G:C base-pairs. The standard Watson-Crick base-pairing scheme, retained in the T:A and G:C base-pairs, is blocked by the etheno bridge in the epsilon C:G pair. In its place, a hydrogen bond involving O2 of epsilon C and N1 of G is present. Comparison with an epsilon dC-containing NMR structure confirms the general conformation reported for epsilon C:G, including the hydrogen bonding features. Superposition with the crystal structure of a DNA duplex containing a T:G wobble pair shows similar structural changes imposed by both mismatches. Evaluation of the hydration shell of the duplex with bond valence calculations reveals two sodium ions in the crystal.
+
[[Category: Freisinger E]]
-
 
+
[[Category: Grollman AP]]
-
==About this Structure==
+
[[Category: Kisker CF]]
-
1N5C 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=1N5C OCA].
+
-
 
+
-
==Reference==
+
-
Crystallographic characterization of an exocyclic DNA adduct: 3,N4-etheno-2'-deoxycytidine in the dodecamer 5'-CGCGAATTepsilonCGCG-3'., Freisinger E, Fernandes A, Grollman AP, Kisker C, J Mol Biol. 2003 Jun 13;329(4):685-97. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12787670 12787670]
+
-
[[Category: Protein complex]]
+
-
[[Category: Fernandes, A.]]
+
-
[[Category: Freisinger, E.]]
+
-
[[Category: Grollman, A P.]]
+
-
[[Category: Kisker, C F.]]
+
-
[[Category: NA]]
+
-
[[Category: 3]]
+
-
[[Category: b form double helix]]
+
-
[[Category: n4-etheno-2'-cytidine modification opposite g]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:52:27 2008''
+

Current revision

Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG

PDB ID 1n5c

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1n5c"
Personal tools