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.


1d77

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:50, 7 February 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
 +
==CRYSTAL STRUCTURE OF A B-DNA DODECAMER CONTAINING INOSINE, D(CGCIAATTCGCG), AT 2.4 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER B-DNA DODECAMERS==
==CRYSTAL STRUCTURE OF A B-DNA DODECAMER CONTAINING INOSINE, D(CGCIAATTCGCG), AT 2.4 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER B-DNA DODECAMERS==
-
<StructureSection load='1d77' size='340' side='right' caption='[[1d77]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+
<StructureSection load='1d77' size='340' side='right'caption='[[1d77]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1d77]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D77 OCA]. <br>
+
<table><tr><td colspan='2'>[[1d77]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D77 FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=1d77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d77 OCA], [https://pdbe.org/1d77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d77 RCSB], [https://www.ebi.ac.uk/pdbsum/1d77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d77 ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d77 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d77 RCSB], [http://www.ebi.ac.uk/pdbsum/1d77 PDBsum]</span></td></tr>
+
</table>
-
<table>
+
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The crystal structure of the dodecamer, d(CGCIAATTCGCG), has been determined at 2.4 A resolution by molecular replacement, and refined to an R-factor of 0.174. The structure is isomorphous with that of the B-DNA dodecamer, d(CGCGAATTCGCG), in space group P2(1)2(1)2(1) with cell dimensions of a = 24.9, b = 40.4, and c = 66.4 A. The initial difference Fourier maps clearly indicated the presence of inosine instead of guanine. The structure was refined with 44 water molecules, and compared to the parent dodecamer. Overall the two structures are very similar, and the I:C forms Watson-Crick base pairs with similar hydrogen bond geometry to the G:C base pairs. The propeller twist angle is low for I4:C21 and relatively high for the I16:C9 base pair (-3.2 degrees compared to -23.0 degrees), and the buckle angles alter, probably due to differences in the contacts with symmetry related molecules in the crystal lattice. The central base pairs of d(CGCIAATTCGCG) show the large propeller twist angles, and the narrow minor groove that characterize A-tract DNA, although I:C base pairs cannot form the major groove bifurcated hydrogen bonds that are possible for A:T base pairs.
+
-
 
+
-
Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers.,Xuan JC, Weber IT Nucleic Acids Res. 1992 Oct 25;20(20):5457-64. PMID:1437563<ref>PMID:1437563</ref>
+
-
 
+
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Weber, I T.]]
+
[[Category: Large Structures]]
-
[[Category: Xuan, J C.]]
+
[[Category: Weber IT]]
-
[[Category: B-dna]]
+
[[Category: Xuan JC]]
-
[[Category: Dna]]
+
-
[[Category: Double helix]]
+
-
[[Category: Modified]]
+

Current revision

CRYSTAL STRUCTURE OF A B-DNA DODECAMER CONTAINING INOSINE, D(CGCIAATTCGCG), AT 2.4 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER B-DNA DODECAMERS

PDB ID 1d77

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/1d77"
Personal tools