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.


1i0f

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:31, 7 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1i0f.gif|left|200px]]
 
-
{{Structure
+
==1.6 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-AMINOOXYETHYL THYMINE IN PLACE OF T6, BA-FORM==
-
|PDB= 1i0f |SIZE=350|CAPTION= <scene name='initialview01'>1i0f</scene>, resolution 1.6&Aring;
+
<StructureSection load='1i0f' size='340' side='right'caption='[[1i0f]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=127:2&#39;-O-AMINOOXY-ETHYL-5-METHYL-URIDINE-5&#39;-MONOPHOSPHATE'>127</scene>, <scene name='pdbligand=BA:BARIUM+ION'>BA</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>
+
<table><tr><td colspan='2'>[[1i0f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I0F 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]] 1.6&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=127:2-O-AMINOOXY-ETHYL-5-METHYL-URIDINE-5-MONOPHOSPHATE'>127</scene>, <scene name='pdbligand=BA:BARIUM+ION'>BA</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=1i0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i0f OCA], [https://pdbe.org/1i0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i0f RCSB], [https://www.ebi.ac.uk/pdbsum/1i0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i0f ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i0f OCA], [http://www.ebi.ac.uk/pdbsum/1i0f PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1i0f RCSB]</span>
+
__TOC__
-
}}
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
'''1.6 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-AMINOOXYETHYL THYMINE IN PLACE OF T6, BA-FORM'''
+
[[Category: Egli M]]
-
 
+
[[Category: Howard A]]
-
 
+
[[Category: Maier MA]]
-
==Overview==
+
[[Category: Manoharan M]]
-
The observation of light metal ions in nucleic acids crystals is generally a fortuitous event. Sodium ions in particular are notoriously difficult to detect because their X-ray scattering contributions are virtually identical to those of water and Na(+.)O distances are only slightly shorter than strong hydrogen bonds between well-ordered water molecules. We demonstrate here that replacement of Na(+) by K(+), Rb(+) or Cs(+) and precise measurements of anomalous differences in intensities provide a particularly sensitive method for detecting alkali metal ion-binding sites in nucleic acid crystals. Not only can alkali metal ions be readily located in such structures, but the presence of Rb(+) or Cs(+) also allows structure determination by the single wavelength anomalous diffraction technique. Besides allowing identification of high occupancy binding sites, the combination of high resolution and anomalous diffraction data established here can also pinpoint binding sites that feature only partial occupancy. Conversely, high resolution of the data alone does not necessarily allow differentiation between water and partially ordered metal ions, as demonstrated with the crystal structure of a DNA duplex determined to a resolution of 0.6 A.
+
[[Category: Minasov G]]
-
 
+
[[Category: Prakash TP]]
-
==About this Structure==
+
[[Category: Tereshko V]]
-
1I0F 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=1I0F OCA].
+
[[Category: Wawrzak Z]]
-
 
+
[[Category: Wilds CJ]]
-
==Reference==
+
-
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments., Tereshko V, Wilds CJ, Minasov G, Prakash TP, Maier MA, Howard A, Wawrzak Z, Manoharan M, Egli M, Nucleic Acids Res. 2001 Mar 1;29(5):1208-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11222771 11222771]
+
-
[[Category: Protein complex]]
+
-
[[Category: Egli, M.]]
+
-
[[Category: Howard, A.]]
+
-
[[Category: Maier, M A.]]
+
-
[[Category: Manoharan, M.]]
+
-
[[Category: Minasov, G.]]
+
-
[[Category: Prakash, T P.]]
+
-
[[Category: Tereshko, V.]]
+
-
[[Category: Wawrzak, Z.]]
+
-
[[Category: Wilds, C J.]]
+
-
[[Category: a-form double helix]]
+
-
[[Category: modified sugar]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:12:51 2008''
+

Current revision

1.6 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-AMINOOXYETHYL THYMINE IN PLACE OF T6, BA-FORM

PDB ID 1i0f

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/1i0f"
Personal tools