1g6d
From Proteopedia
(New page: 200px<br /><applet load="1g6d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g6d, resolution 2.9Å" /> '''STRUCTURE OF PEPTIDYL...) |
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| - | [[Image:1g6d.gif|left|200px]]<br /><applet load="1g6d" size=" | + | [[Image:1g6d.gif|left|200px]]<br /><applet load="1g6d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1g6d, resolution 2.9Å" /> | caption="1g6d, resolution 2.9Å" /> | ||
'''STRUCTURE OF PEPTIDYL-D(CGCAATTGCG) IN THE PRESENCE OF ZINC IONS'''<br /> | '''STRUCTURE OF PEPTIDYL-D(CGCAATTGCG) IN THE PRESENCE OF ZINC IONS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have synthesized and crystallized in the presence of Zn(2+) ions the | + | We have synthesized and crystallized in the presence of Zn(2+) ions the peptidyl-oligonucleotide adduct CH(3)CO-(Arg)(4)-NH-(CH(2))(6)-NH-p-d(CGCAATTGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 A resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn(2+) ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn(2+) ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form. |
==About this Structure== | ==About this Structure== | ||
| - | 1G6D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1G6D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G6D OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Malinina, L.]] | [[Category: Malinina, L.]] | ||
[[Category: Soler-Lopez, M.]] | [[Category: Soler-Lopez, M.]] | ||
| - | [[Category: Subirana, J | + | [[Category: Subirana, J A.]] |
[[Category: Tereshko, V.]] | [[Category: Tereshko, V.]] | ||
[[Category: Zarytova, V.]] | [[Category: Zarytova, V.]] | ||
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[[Category: zn ions]] | [[Category: zn ions]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:46:35 2008'' |
Revision as of 10:46, 21 February 2008
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STRUCTURE OF PEPTIDYL-D(CGCAATTGCG) IN THE PRESENCE OF ZINC IONS
Overview
We have synthesized and crystallized in the presence of Zn(2+) ions the peptidyl-oligonucleotide adduct CH(3)CO-(Arg)(4)-NH-(CH(2))(6)-NH-p-d(CGCAATTGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 A resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn(2+) ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn(2+) ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.
About this Structure
1G6D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 A resolution X-ray structure., Soler-Lopez M, Malinina L, Tereshko V, Zarytova V, Subirana JA, J Biol Inorg Chem. 2002 Apr;7(4-5):533-8. Epub 2002 Feb 7. PMID:11941511
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