3) Let’s explore BPG binding by hemoglobin a bit further! Download the PDB file for hemoglobin bound to BPG (PDB: 1B86) and open it up in PyMOL. Hint:…

3) Let’s explore BPG binding by hemoglobin a bit further! Download the PDB file for hemoglobin

bound to BPG (PDB: 1B86) and open it up in PyMOL. Hint: You can color the individual subunits

differently in order to most easily visualize the quaternary structure of hemoglobin. One way to do

this is to click on the selection line for the PDB (1B86), then click on menu button C (for color) and

select ‘by chain’.

a) In this particular structure, how many binding sites are bound to O2? Hint: you can create a selection

for oxygen by typing in the following command at the prompt: select oxygen, resn OXY

*now you’ll have a selectable line for oxygen on the right side of the window, from which you can

choose how to display oxygen (spheres or dots, etc., with any coloring you like). You can repeat this

command for other non-protein molecules, such as the heme (resn code HEM) or BPG (resn code

DG2).

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