zap
echo ""
echo ""
echo "The last type of zinc finger protein is typified by the yeast"
echo "activator protein GAL4.  Hit a key:"
pause
load "gal4_DNA.pdb"
rotate z 91
rotate x 4
zoom 157
select dna
color blue
select protein
wireframe off
ribbons
select *:a
color green
select *:b
color yellow
echo ""
echo "GAL4 contains a dimerization domain similar to a leucine zipper; it is"
echo "evident in the center.  However, let's focus on the zinc-binding portion."
echo "Hit a key to highlight the metal ions (which are actually Cd in the crystals):"
pause
select cd
color white
spacefill 250
script "delay1.scr"
script "delay1.scr"
spacefill off
script "delay1.scr"
script "delay1.scr"
spacefill 250
echo ""
echo "These metal ions help to organize the DNA-binding domain."
echo "However, in this case, there are two ions coordinated to 6 Cys residues."
echo "Hit a key for a closer look."
pause
translate x -5
translate y -4
zoom 160
script "delay1.scr"
translate x -10
translate y -8
zoom 170
script "delay1.scr"
translate x -15
translate y -12
zoom 180
script "delay1.scr"
translate x -20
translate y -16
zoom 190
script "delay1.scr"
translate x -25
translate y -20
zoom 200
script "delay1.scr"
translate x -30
zoom 225
script "delay1.scr"
translate x -40
zoom 250
script "delay1.scr"
translate x -45
zoom 275
script "delay1.scr"
translate x -50
zoom 300
script "delay1.scr"
select cd39,cd40
spacefill 250
center selected
echo ""
echo "Hit a key to focus on the metal-binding motif:"
pause
restrict cd39,cd40,(*:b and 8-41)
echo ""
echo "This motif is quite different from the previous two types of zinc fingers."
echo "It contains two metal ions instead of one, and two alpha helices.  One of" 
echo "helices interacts with the DNA, but only the very end of the helix does so."
echo "  Rotate it to see its structure, then hit a key:"
pause
reset
slab off
rotate z 91
rotate x 3
translate x -50
translate y -20
zoom 300
restrict cd39,cd40,(*:b and 8-41)
center selected
echo ""
echo ""
echo "Hit a key to turn on the cysteines that coordinate the metal ions:"
pause
select *:b and 8-41 and cys
color blue 
wireframe 60
select *:b and 8-41 and cys and *.sg
color orange
spacefill 200
echo ""
echo "The sulfur atoms are in orange:"
echo " Hit a key to look at the sulfurs and the metal ions:"
pause
restrict (*:b and 8-41 and cys and *.sg),cd39,cd40
select *.sg and (cys11,cys28) and *:b
color red
echo ""
echo "Two sulfurs are coordinated with both metal ions."
echo "Rotate to see how the metal ions relate to the sulfurs."
echo ""
echo "Then hit a key to restore the view."
pause
reset
slab off
rotate z 91
rotate x 3
translate x -50
translate y -20
zoom 300
echo ""
echo "Hit a key to bring back the protein:"
pause
restrict cd39,cd40,(*:b and 8-41)
wireframe off
ribbons
select *:b and 8-41 and cys
color yellow
spacefill off
echo ""
echo "This protein is unusual, in that the groups that contact the DNA are only"
echo " partly located in an alpha helix; they are at its very end, or in an adjacent"
echo " loop (shown in red). We won't look at their interaction with the DNA."
echo " Rotate the structure if you like."
echo ""
echo "Then hit a key to see the last structural motif:"
select (17,18) and *:b
center selected
color red
wireframe 50
pauseasses\bioc568\Motifs\Fast_rotations\Z90-2.SCR --> 128.196.201.8 /robert/bioweb/Biochemistry/bmbweb/classes/bioc568/Motifs/Fast_rotations Z90-2.SCR