Sandbox Reserved 426
From Proteopedia
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<font color='red'>Everyone -- note that this is NOT a protein, but a complex with DNA. Edit your text accordingly, eg discussing alpha helices etc does not make sense. </font> | <font color='red'>Everyone -- note that this is NOT a protein, but a complex with DNA. Edit your text accordingly, eg discussing alpha helices etc does not make sense. </font> | ||
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==Overall Structure== | ==Overall Structure== | ||
The 1xcs (model at right) complex is a small, simple globular DNA-peptide complex, and as such lacks secondary beta sheets or alpha helices. The complex consists of two non-identical dimers. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the side chains removed for clarity. The peptide backbones can be followed from N to C termini following along each strand from blue to red. Note that the strands are antiparallel where they are non-covalently bound. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with the side chains displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from N to C terminus. | The 1xcs (model at right) complex is a small, simple globular DNA-peptide complex, and as such lacks secondary beta sheets or alpha helices. The complex consists of two non-identical dimers. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the side chains removed for clarity. The peptide backbones can be followed from N to C termini following along each strand from blue to red. Note that the strands are antiparallel where they are non-covalently bound. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with the side chains displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from N to C terminus. | ||
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==Binding Interactions== | ==Binding Interactions== | ||
<scene name='48/483883/1xcs_binding_site/2'>Click here to see the binding site | <scene name='48/483883/1xcs_binding_site/2'>Click here to see the binding site | ||
1xcs is a complex with DNA and it is a two chain structure. It has ligands A4L, BA and CO. There are strong cation interactions that help form a crystal structure. The complex crystallizes when there is either Co(2+), Ba(2+) and Na(+) ions. </scene> | 1xcs is a complex with DNA and it is a two chain structure. It has ligands A4L, BA and CO. There are strong cation interactions that help form a crystal structure. The complex crystallizes when there is either Co(2+), Ba(2+) and Na(+) ions. </scene> | ||
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==Additional Features== | ==Additional Features== | ||
Click <scene name='48/483883/Protein_between_dna_strands/1'>here</scene> to see that the drug binds directly between strands of DNA. This interrupts the expression of this section of DNA. | Click <scene name='48/483883/Protein_between_dna_strands/1'>here</scene> to see that the drug binds directly between strands of DNA. This interrupts the expression of this section of DNA. | ||
I will then go on to explain how specifically this complex interrupts/changes gene expression. | I will then go on to explain how specifically this complex interrupts/changes gene expression. | ||
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==Quiz Question 1== | ==Quiz Question 1== | ||
Why is it important for the protein to bind <scene name='48/483883/Quiz_question/1'>here</scene>? | Why is it important for the protein to bind <scene name='48/483883/Quiz_question/1'>here</scene>? | ||
| - | + | A unique site is the __ ion found associated with the <scene name='48/483883/O6_atom_of_two_guanines/1'>O6_atom_of_two_guanines</scene>, which gives additional strength to the guanine–Co2+–guanine interaction. A Mg2+ B Co2+ C Ba2+ D Mg2+ | |
==See Also== | ==See Also== | ||
Revision as of 21:45, 2 March 2016
| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
Structure of Oligonucleotide/Drug complex (1xcs)[1]
by Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, and Nathaneal Park
Student Projects for UMass Chemistry 423 Spring 2016
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