Myoglobin - Heme Interactions (Jmol exercise)
The interaction between the myoglobin polypeptide chain and the heme group can be explored further by using the command box in the right frame to issue Jmol commands for selectively modifying the molecular image. The following series of commands generates a magnified view of the heme group interacting with the contact residues from the Mb polypeptide chain. The original image can always be restored "manually" or by pressing the browser's "Reload" button.
Examine the structure anywhere along the way using the mouse pointer and button. Mouse Moves
 
Starting instructions:
Click the "Clear Input" button.
(This button may be pressed at any time without affecting commands already entered.)
Move the mouse pointer into the "Console Box" and click the mouse button.
After typing a command, press the Enter key.
Highlight heme group of Mb
JMol command  
Comments
  1. select *
    select entire image
  2. hbonds off
    turns off hbonds
  3. restrict hem
    restrict image to the heme group including porphyrin ring, Fe, & chelated O2
  4. center hem
    center rotations on the heme group
  5. zoom 300
    magnify by an arbitrary factor of "300"
  6. select hem.o1,hem.o2 (note that these are the letter o, not the number 0).
    selects the two oxygens in O2 chelated to heme iron
  7. color magenta
    colors O2 magenta
  8. rotate y 100
    rotates the heme group around the Y-axis bringing the oxygen atoms into view
Highlight heme contact residues of Mb
JMol command  
Comments
  1. select within(8.0,hem) and not hem
    select all atoms within 8.0 Å of heme atoms but not heme atoms themselves ("not hem")
  2. spacefill
    spacefill contact atoms
  3. restrict selected
    restricts the image to the selected atoms
  4. spacefill off
    spacefill off
  5. wireframe 100
    view contact atoms with a wireframe size of "100" (relative size)
Reset structure image
JMol command 
Comments
  1. select *
    select all atoms
  2. spacefill
    spacefill contact atoms
  3. color CPK
    color all atoms in CPK colors
  4. reset
    reset structure to original coordinates ("undoes" rotations, translations, and zooms)
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©
August 2, 2012