PDB file 5CYT
This structure of cytochrome c from tuna was determined by Takano et al. 1988.
Suggested display options:
1. With the protein displayed as wireframe, color chain.
Select hetero-ligand to choose the heme, display as ball & stick and color CPK.
You can select atom-Fe & display as spacefill, to make the iron more prominent.
Drag to rotate. Note the planar nature of the porphyrin ring.
View also with the protein displayed as spacefill.
Question: What part of the heme is exposed at the protein surface?
2. To visualize axial ligands of the heme, first select and display the protein as ribbons or cartoon.
Use the command line to select met80, his18, and display as sticks or ball & stick.
Question: Which atoms of histidine and methionine interact with the heme iron?
3. Visualize the cysteine residues that covalently link to the porphyrin ring. (See diagram of heme c).
4. Positively charged lysine residues on cyt c form ionic bonds with anionic residues on respiratory chain complexes to which cyt c binds during electron transfer.
With the protein displayed as spacefill, change the color of Lys residues.
Identify Lys13 which is thought to form a salt bridge to an Asp residue of complex IV.
on Electron Transfer
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