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.


400d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:35, 1 March 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:400d.gif|left|200px]]
 
-
{{Structure
+
==THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA==
-
|PDB= 400d |SIZE=350|CAPTION= <scene name='initialview01'>400d</scene>, resolution 1.650&Aring;
+
<StructureSection load='400d' size='340' side='right'caption='[[400d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=5CM:5-METHYL-2&#39;-DEOXY-CYTIDINE-5&#39;-MONOPHOSPHATE'>5CM</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>
+
<table><tr><td colspan='2'>[[400d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=400D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=400D 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]] 1.65&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=400d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=400d OCA], [https://pdbe.org/400d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=400d RCSB], [https://www.ebi.ac.uk/pdbsum/400d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=400d ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=400d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=400d OCA], [http://www.ebi.ac.uk/pdbsum/400d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=400d RCSB]</span>
+
-
}}
+
-
'''THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA'''
+
==See Also==
-
 
+
*[[Z-DNA|Z-DNA]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Alternating pyrimidine-purine sequences typically form Z-DNA, with the pyrimidines in the anti and purines in the syn conformations. The observation that dC and dT nucleotides can also adopt the syn conformation (i.e. the nucleotides are out-of-alternation) extends the range of sequences that can convert to this left-handed form of DNA. Here, we study the effects of placing two adjacent d(G*C) base pairs as opposed to a single d(G*C) base pair or two d(A*T) base pairs out-of-alternation by comparing the structure of d(m5CGGCm5CG)2with the previously published structures of d(m5CGGGm5CG)*d(m5CGCCm5CG) and d(m5CGATm5CG)2. A high buckle and loss of stacking interactions are observed as intrinsic properties of the out-of-alternation base pairs regardless of sequence and the context of the dinucleotide. From solution titrations, we find that the destabilizing effect of out-of-alternation d(G*C) base pairs are identical whether these base pairs are adjacent or isolated. We can therefore conclude that it is these intrinsic distortions in the structure of the base pairs and not neighboring effects that account for the inability of out-of-alternation base pairs to adopt the left-handed Z conformation.
+
[[Category: Large Structures]]
-
 
+
[[Category: Synthetic construct]]
-
==About this Structure==
+
[[Category: Basham B]]
-
400D 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=400D OCA].
+
[[Category: Eichman BF]]
-
 
+
[[Category: Ho PS]]
-
==Reference==
+
[[Category: Schroth GP]]
-
The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA., Eichman BF, Schroth GP, Basham BE, Ho PS, Nucleic Acids Res. 1999 Jan 15;27(2):543-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9862978 9862978]
+
-
[[Category: Protein complex]]
+
-
[[Category: Basham, B.]]
+
-
[[Category: Eichman, P S.Ho B F.]]
+
-
[[Category: Schroth, G P.]]
+
-
[[Category: z-dna double helix]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:46 2008''
+

Current revision

THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA

PDB ID 400d

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/400d"
Personal tools