Posted: September 8th, 2022

using your structure, write a PyMol script to display a) protein secondary structure hydrogen bonding and 2) polar contacts between the protein and DNA. You will need to use the “select” and “distance” commands. What types of secondary structure does your protein exhibit?

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using your structure, write a PyMol script to display a) protein secondary structure
hydrogen bonding and 2) polar contacts between the protein and DNA. You will need to use the “select”
and “distance” commands. What types of secondary structure does your protein exhibit? Are there any
protein side chains that may be in an incorrect rotamer (i.e. would an alternative rotamer further stabilize the protein-RNA interaction)? Does the experimental model include sodium (NA), potassium (K),
magnesium (MG), or chloride (CL) counter-ions (hint – use Pymol to select atoms with the names NA, K,
MG or CL)? Determine the total charge of your complex and explain your reasoning (hint – use can Pymol
to select charged amino acids, select charged nucleic acid bases, and/or counter-ions). Include your PyMol
script and a ray-traced image of the complex in your answer. ***my PDB structure is 5Z1G***

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