Sandbox Reserved 426
From Proteopedia
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The 1xcs (model at right) complex is a small, simple globular DNA-drug complex, and as such lacks any traditional protein structures such as secondary beta sheets or alpha helices. The complex consists of two complimentary strands of DNA. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the nitrogenous bases removed for clarity. The deoxyribose backbones can be followed from 5' to 3' following along each strand from blue to red. Note that the strands are antiparallel where they are (hydrogen) bonded. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with its hydrogen bonding regions displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from 5' to 3' ends. | The 1xcs (model at right) complex is a small, simple globular DNA-drug complex, and as such lacks any traditional protein structures such as secondary beta sheets or alpha helices. The complex consists of two complimentary strands of DNA. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the nitrogenous bases removed for clarity. The deoxyribose backbones can be followed from 5' to 3' following along each strand from blue to red. Note that the strands are antiparallel where they are (hydrogen) bonded. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with its hydrogen bonding regions displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from 5' to 3' ends. | ||
| - | The 1xcs complex also binds to metal ions in more than one location, which have been shown to be important to the drug's binding ability. Different metal ions may be present, including Na(+) and Co(2+). These metal ions sites are colored pink in <scene name='48/483883/1xcs_with_pink_metal_ions/2'>this</scene> scene. One other metal binding site was noted, which had the ability to bind Ba(2+) | + | The 1xcs complex also binds to metal ions in more than one location, which have been shown to be important to the drug's binding ability. Different metal ions may be present, including Na(+) and Co(2+). These metal ions sites are colored pink in <scene name='48/483883/1xcs_with_pink_metal_ions/2'>this</scene> scene. One other metal binding site was noted, which had the ability to bind <scene name='48/483883/Barium_binding_site/1'>Ba(2+)</scene>. This barium binding site is believed to strengthen the ability of the O6 site to bind cobalt. This ability to strongly bind metal ions was also important for x-ray crystallographic purposes, as it enabled researchers to form crystals of the complex by relying on interactions between neighboring molecules' binding sites. |
==Binding Interactions== | ==Binding Interactions== | ||
Revision as of 21:12, 4 April 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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