# This Rasmol script is for display of Zif268, a eukaryotic transcription 
# factor containing 3 Zinc-finger DNA-binding motifs.  Structure by
# Pavletich and Pabo, since refined further by Pabo's group.
# (M. Elrod-Erickson, M.A. Rould, L. Nekludova, C.O. Pabo, in
# Structure, 1996, vol. 4, p. 1171
# Rasmol command file by Hannah Chen and Jason Kahn
# If you haven't loaded the molecule...
#zap
#load 1aay.pdb
#Script starts here:
#
# Overall view of the complex, showing the three zinc fingers wrapping
# around in the DNA major groove
#
define g_major (G and (*.N7 or *.O6 or *.C5 or *.C6 or *.C8 or *.H8))
define a_major (A and (*.N6 or *.N7 or *.C5 or *.C6 or *.2H6 or *.C8 or *.H8)) 
define t_major (T and (*.C5 or *.O4 or *.C4 or *.C5M or *.1H5M or *.2H5M or *.3H5M))
define c_major (C and (*.C5 or *.N4 or *.C4 or *.1H4 or *.2H4 or *.H5))
define g_minor (G and (*.N3 or *.C4 or *.C2 or *.N2 or *.1H2 or *.2H2))
define a_minor (A and (*.N3 or *.C4 or *.C2 or *.H2))
define c_minor (C and (*.C2 or *.O2))
define t_minor (T and (*.C2 or *.O2))
define major_groove (g_major or a_major or c_major or t_major)
define minor_groove (g_minor or a_minor or c_minor or t_minor)
reset
rotate z 46
rotate x 176
translate x -3
translate y -9
zoom 131
select dna
wireframe 150
select major_groove
color red
select minor_groove
color violet
select DNA and (not major_groove) and (not minor_groove) and (not *.P)
color white
select protein
wireframe off
structure
cartoons
select protein
color [0,255,0]
select protein and resno>133
color [0,255,255]
select protein and resno>160
color [0,0,255]
select Zn
color yellow
spacefill 300
set fontsize 14
select arg103 and *.CA
label N-term
select arg187 and *.CA
label C-term
set specular on
set shadow on
#
#--------------------------------------------------------------------------
# Now highlight the Arg's (and one His) which make specific major groove
# contacts to G's.  Note that all of the recognized G's are on one strand.
#
set specular off
set shadow off
reset
rotate z 163
rotate y -69
rotate x -102
zoom 131
select zn
color [100,100,100]
select dna and not *.P
color white
wireframe 120
backbone 200
select protein
color [143,255,143]
select g2,g4,g6,g7,g8,g10
color cyan
select (g.o6 or g.n7) and (g2,g4,g6,g7,g8,g10)
color red
spacefill 300
select arg180,arg174,arg146,arg124,arg118
color yellow
wireframe 150
select (arg.NH1 or arg.NH2) and (arg180,arg174,arg146,arg124,arg118)
color blue
spacefill 300
select his149
color violet
wireframe 150
select his149.NE2
color green
spacefill 300
set specular on
set shadow on
#
#--------------------------------------------------------------------------
# Highlight the zinc ligands
reset
rotate z -85
rotate y 75
rotate x -117
translate y 5
zoom 128
select cys168,cys165,cys140,cys137,cys112,cys107
color orange
wireframe 100
select cys.sg and (cys168,cys165,cys140,cys137,cys112,cys107)
spacefill 200
select his185,his181,his157,his153,his129,his125
color violet
wireframe 100
select his.ne2 and (his185,his181,his157,his153,his129,his125)
spacefill 200
select Zn202
set fontsize 16
label Zn
#
#-------------------------------------------------------------------------
# Highlight the butressing Aspartates
select asp176,asp148,asp120
color redorange
wireframe 150
#
#-------------------------------------------------------------------------
reset
restrict arg118,asp120,g10,c53
ribbon off
zoom 230
rotate z 4
rotate y 13
rotate x -109
translate x 26
wireframe 200
select (arg118,asp120,g10,c53) and not carbon
color cpk
select arg118.nh1, arg118.nh2, arg118.ne
spacefill 250
color blue
select asp120.od1, asp120.od2
spacefill 250
color magenta
select g10.n7, g10.o6, g10.n1, g10.n2
spacefill 250
select g10.o6
color magenta
select g10.n7, g10.n1, g10.n2
color blue
select c53.o2, c53.n3, c53.n4
spacefill 250
select c53.o2
color magenta
select c53.n3, c53.n4
color blue

set fontsize 16
select g10.o5*
label G10
select c53.p
label C53
select arg118.nh2
label Arg118
select asp120.od2
label Asp120
center atomno=938
select all
monitors off
set monitors off
monitor 938 144
monitor 935 143
monitor 158 144
monitor 141 157
color monitors green
select arg118,asp120,g10,c53
hbonds
hbonds 40
color hbonds green
#--------------------------------------------------------------------------