Final answer:
The positions of sidechain atoms are not included in the representation of the protein in Dali, so the correct answer is b) No. Amino acids carry ionic charges based on their side chain's chemical properties; positively charged ones include arginine and lysine, while aspartate and glutamate can carry negative charges.
Step-by-step explanation:
The positions of sidechain atoms are not included in the representation of the protein in Dali; thus the answer to the student's question is b) No. Dali is used for protein 3D structure comparison, where the main focus is on the backbone conformation, specifically the α-carbon positions. The side chains are often not represented to simplify the comparison across different proteins. To draw structures for all amino acid side chains at an active site, one would have to refer to individual residue information, which is obtainable from detailed x-ray crystallography data or from a model that includes side chain positions.
For the amino acid side chains that carry an ionic charge, one would identify these based on their chemical properties; commonly charged side chains include arginine and lysine for positive charges and aspartate and glutamate for negative charges.