@text
"PROTEIN-DNA  INTERACTIONS  --  A  ZINC  FINGER  PROTEIN"

This zinc finger protein, known as Zif-268, contains three identical zinc finger motifs (also termed 'domains') within a single amino acid chain.  Specifically, each finger contains an alpha-helix, a two-stranded beta-sheet, one zinc ion, and in this case, two cysteine and two histidine metal ligands.  The protein, a transcription factor, regulates certain DNA processes by binding in the major groove.  Structure derived from PDB file, 1ZAA.
@kinemage 1
@caption
Calpha trace of the 3 zinc fingers of Zif-268, with zinc ions and their ligands displayed.  Turn on the 'DNA' to see the way the fingers wrap around the double helix of DNA.  The start-up view is looking down the central axis of DNA; view2 presents a side view of DNA.
@onewidth
@viewid {Top}
@zoom 1.0
@zslab 180
@center 3.063 15.128 50.382
@matrix 
-.605122 .502122 -.617819 .506841 -.355478 -.785333 -.613955 -.788358 -.039389
@2viewid {Side}
@2zoom 0.94 
@2zslab 180 
@2center 3.063 15.128 50.382 
@2matrix 
0.004246 -0.690453 0.723365 -0.183359 -0.711645 -0.678190 0.983037 -0.129757 -0.129621 
@group {Zif/268} 
@subgroup {Alpha C's} dominant
@vectorlist {backbone} color=pinktint
{ca arg c 3}P -13.582 8.064 60.257
{ca pro c 4}-14.45 4.944 62.173
{ca tyr c 5}-10.845 3.825 62.287
{ca ala c 6}-8.66 5.319 64.996
{ca cys c 7}-4.975 5.016 65.521
{ca pro c 8}-4.496 2.926 68.786
{ca val c 9}-1.188 4.545 69.512
{ca glu c 10}-1.858 6.426 72.765
{ca ser c 11}0.169 9.366 71.436
{ca cys c 12}-1.522 9.628 68.063
{ca asp c 13}-4.772 11.353 67.306
{ca arg c 14}-5.649 10.09 63.822
{ca arg c 15}-8.993 8.612 62.484
{ca phe c 16}-9.566 7.185 58.991
{ca ser c 17}-12.387 6.257 56.683
{ca arg c 18}-11.073 2.892 55.486
{ca ser c 19}-9.1 0.144 57.131
{ca asp c 20}-6.285 0.364 54.532
{ca glu c 21}-5.659 4. 55.323
{ca leu c 22}-5.036 2.938 58.938
{ca thr c 23}-2.764 0.075 58.009
{ca arg c 24}-0.751 2.363 55.844
{ca his c 25}-0.651 4.999 58.583
{ca ile c 26}0.54 2.384 61.147
{ca arg c 27}3.91 2.328 59.328
{ca ile c 28}4.827 5.673 60.838
{ca his c 29}4.43 4.046 64.21
{ca thr c 30}6.081 0.736 63.402
{ca gly c 31}8.973 2.049 61.221
{ca gln c 32}8.106 -0.491 58.576
{ca lys c 33}9.525 0.507 55.173
{ca pro c 34}8.542 -2.33 52.841
{ca phe c 35}9.953 -0.915 49.593
{ca gln c 36}13.634 -0.915 48.797
{ca cys c 37}15.248 1.127 46.123
{ca arg c 38}17.017 -1.306 43.841
{ca ile c 39}19.699 1.264 43.203
{ca cys c 40}20.601 2.837 46.481
{ca met c 41}19.016 0.225 48.772
{ca arg c 42}17.168 2.943 50.559
{ca asn c 43}13.874 1.879 52.142
{ca phe c 44}10.517 3.462 51.765
{ca ser c 45}7.209 3.255 53.457
{c ser c 45}6.164 2.992 52.379
{o ser c 45}5.285 2.159 52.603
{c ser c 45}P 6.164 2.992 52.379
{n arg c 46}6.239 3.685 51.224
{ca arg c 46}5.248 3.499 50.179
{ca ser c 47}5.163 2.157 46.617
{ca asp c 48}4.323 5.371 44.994
{ca his c 49}7.046 7.17 46.892
{ca leu c 50}9.572 4.619 45.768
{ca thr c 51}8.655 5.098 42.064
{ca thr c 52}9.118 8.801 42.256
{ca his c 53}12.401 8.561 44.207
{ca ile c 54}13.958 6.209 41.623
{ca arg c 55}13.521 9.049 39.138
{ca thr c 56}16.236 10.885 41.026
{ca his c 57}18.566 8.105 39.965
{ca thr c 58}17.511 7.723 36.377
{ca gly c 59}16.795 11.397 35.662
{ca glu c 60}13.455 10.502 34.104
{ca lys c 61}11.025 13.441 33.948
{ca pro c 62}7.641 12.63 32.682
{ca phe c 63}5.926 16.039 33.207
{ca ala c 64}6.539 19.09 31.087
{ca cys c 65}5.153 22.537 31.441
{ca asp c 66}2.655 23.408 28.713
{ca ile c 67}3.894 27.042 28.473
{ca cys c 68}7.586 26.565 28.487
{ca gly c 69}8.218 22.84 28.134
{ca arg c 70}10.332 22.689 31.302
{ca lys c 71}10.508 19.087 32.597
{ca phe c 72}9.849 17.689 36.054
{ca ala c 73}10.005 14.326 37.773
{c ala c 73}8.613 14.004 38.321
{o ala c 73}8.136 12.882 38.228
{c ala c 73}P 8.613 14.004 38.321
{n arg c 74}7.954 14.994 38.906
{ca arg c 74}6.635 14.815 39.495
{ca ser c 75}3.36 16.353 38.564
{ca asp c 76}3.236 18.337 41.81
{ca glu c 77}6.465 19.858 40.792
{ca arg c 78}4.942 20.748 37.475
{ca lys c 79}1.924 22.239 39.137
{ca arg c 80}3.978 24.351 41.494
{ca his c 81}5.864 25.697 38.422
{ca thr c 82}3.12 26.463 35.836
{ca lys c 83}1.912 29.05 38.313
{ca ile c 84}4.999 31.174 37.782
{ca his c 85}3.744 32.007 34.346
{ca leu c 86}1.092 34.147 35.812
{ca arg c 87}4.125 36.027 37.395
@subgroup {Zn sites}
@balllist {Zn} radius=.4 color=green
{Zn d 201}P -0.992 6.979 64.617
{Zn d 202}P 17.433 5.12 45.495
{Zn d 203}P 6.794 26.714 32.37
@vectorlist {ligands} color=yellow
{ca cys c 7}P -4.975 5.016 65.521
{cb cys c 7}-3.909 5.974 65.01
{sg cys c 7}-2.281 5.326 65.383
{ca cys c 12}P -1.522 9.628 68.063
{cb cys c 12}-1.167 8.63 66.961
{sg cys c 12}-1.822 9.146 65.372
{ca his c 25}P -0.651 4.999 58.583
{cb his c 25}-1.878 5.643 59.217
{cg his c 25}-1.554 6.407 60.457
{nd1 his c 25}-1.221 7.742 60.391
{ce1 his c 25}-0.996 8.143 61.638
{ne2 his c 25}-1.17 7.14 62.493
{ne2 his c 25}P -1.17 7.14 62.493
{ce1 his c 25}-0.996 8.143 61.638
{cg his c 25}P -1.554 6.407 60.457
{cd2 his c 25}-1.524 6.023 61.767
{ne2 his c 25}-1.17 7.14 62.493
{ce1 his c 25}-0.996 8.143 61.638
{ca his c 29}P 4.43 4.046 64.21
{cb his c 29}3.065 3.774 64.848
{cg his c 29}2.295 5.046 64.924
{nd1 his c 29}2.895 6.195 65.398
{ce1 his c 29}1.984 7.156 65.351
{ne2 his c 29}0.841 6.676 64.877
{ne2 his c 29}P 0.841 6.676 64.877
{ce1 his c 29}1.984 7.156 65.351
{cg his c 29}P 2.295 5.046 64.924
{cd2 his c 29}1.011 5.339 64.595
{ne2 his c 29}0.841 6.676 64.877
{ce1 his c 29}1.984 7.156 65.351
{ca cys c 37}P 15.248 1.127 46.123
{cb cys c 37}15.747 2.564 46.217
{sg cys c 37}16.53 3.116 44.696
{ca cys c 40}P 20.601 2.837 46.481
{cb cys c 40}20.478 4.37 46.677
{sg cys c 40}18.828 4.932 47.203
{ca his c 53}P 12.401 8.561 44.207
{cb his c 53}12.618 7.867 45.542
{cg his c 53}14.04 7.443 45.745
{nd1 his c 53}14.961 8.272 46.343
{ce1 his c 53}16.097 7.62 46.379
{ne2 his c 53}15.948 6.42 45.841
{ne2 his c 53}P 15.948 6.42 45.841
{ce1 his c 53}16.097 7.62 46.379
{cg his c 53}P 14.04 7.443 45.745
{cd2 his c 53}14.658 6.277 45.435
{ne2 his c 53}15.948 6.42 45.841
{ce1 his c 53}16.097 7.62 46.379
{ca his c 57}P 18.566 8.105 39.965
{cb his c 57}18.524 6.635 40.383
{cg his c 57}18.599 6.505 41.843
{nd1 his c 57}19.604 7.105 42.541
{ce1 his c 57}19.405 6.819 43.821
{ne2 his c 57}18.319 6.069 43.959
{ne2 his c 57}P 18.319 6.069 43.959
{ce1 his c 57}19.405 6.819 43.821
{cg his c 57}P 18.599 6.505 41.843
{cd2 his c 57}17.788 5.856 42.711
{ne2 his c 57}18.319 6.069 43.959
{ce1 his c 57}19.405 6.819 43.821
{ca cys c 65}P 5.153 22.537 31.441
{cb cys c 65}5.919 23.737 32.033
{sg cys c 65}5.126 25.347 31.797
{ca cys c 68}P 7.586 26.565 28.487
{cb cys c 68}8.39 27.353 29.512
{sg cys c 68}8.505 26.46 31.086
{ca his c 81}P 5.864 25.697 38.422
{cb his c 81}6.955 24.912 37.704
{cg his c 81}7.336 25.51 36.394
{nd1 his c 81}8.463 26.296 36.253
{ce1 his c 81}8.523 26.664 34.98
{ne2 his c 81}7.498 26.161 34.297
{ne2 his c 81}P 7.498 26.161 34.297
{ce1 his c 81}8.523 26.664 34.98
{cg his c 81}P 7.336 25.51 36.394
{cd2 his c 81}6.737 25.421 35.177
{ne2 his c 81}7.498 26.161 34.297
{ce1 his c 81}8.523 26.664 34.98
{ca his c 85}P 3.744 32.007 34.346
{cb his c 85}3.556 31.058 33.168
{cg his c 85}4.727 30.202 32.917
{nd1 his c 85}5.92 30.762 32.54
{ce1 his c 85}6.762 29.741 32.382
{ne2 his c 85}6.155 28.574 32.629
{ne2 his c 85}P 6.155 28.574 32.629
{ce1 his c 85}6.762 29.741 32.382
{cg his c 85}P 4.727 30.202 32.917
{cd2 his c 85}4.854 28.848 32.973
{ne2 his c 85}6.155 28.574 32.629
{ce1 his c 85}6.762 29.741 32.382
@group {dom labels} dominant
@labellist {domains} color=white
{DOMAIN 1}{ ca  arg c 3}P -13.582 8.064 60.257
{DOMAIN 2}{ ca  arg c 46}P 4.748 3.899 50.179
{DOMAIN 3}{ ca  gly c 69}8.218 22.84 28.134
@group {DNA} off dominant
@vectorlist {backbone} color=blue
{c4* a a 1}P 15.009 24.791 40.891
{c1* a a 1}14.535 24.011 43.088
{c4* a a 1}P 15.009 24.791 40.891
{p g a 2}15.586 21.173 39.789
{p g a 2}P 15.586 21.173 39.789
{c4* g a 2}16.278 19.04 42.89
{c4* g a 2}P 16.278 19.04 42.89
{c1* g a 2}14.546 18.875 44.403
{c4* g a 2}P 16.278 19.04 42.89
{p c a 3}15.578 15.237 42.785
{p c a 3}P 15.578 15.237 42.785
{c4* c a 3}14.467 14.766 46.427
{c4* c a 3}P 14.467 14.766 46.427
{c1* c a 3}12.483 15.753 46.807
{c4* c a 3}P 14.467 14.766 46.427
{p g a 4}13.055 11.441 47.405
{p g a 4}P 13.055 11.441 47.405
{c4* g a 4}13.072 11.917 51.21
{c4* g a 4}P 13.072 11.917 51.21
{c1* g a 4}11.109 13.179 51.396
{c4* g a 4}P 13.072 11.917 51.21
{p t a 5}11.331 9.564 53.761
{p t a 5}P 11.331 9.564 53.761
{c4* t a 5}7.97 11.445 54.589
{c4* t a 5}P 7.97 11.445 54.589
{c1* t a 5}6.666 11.964 52.803
{c4* t a 5}P 7.97 11.445 54.589
{p g a 6}5.421 8.944 56.113
{p g a 6}P 5.421 8.944 56.113
{c4* g a 6}2.737 11.358 56.896
{c4* g a 6}P 2.737 11.358 56.896
{c1* g a 6}1.763 11.971 54.89
{c4* g a 6}P 2.737 11.358 56.896
{p g a 7}-0.832 10.367 58.012
{p g a 7}P -0.832 10.367 58.012
{c4* g a 7}-3.304 12.747 56.04
{c4* g a 7}P -3.304 12.747 56.04
{c1* g a 7}-3.449 12.101 53.802
{c4* g a 7}P -3.304 12.747 56.04
{p g a 8}-7.061 12.005 55.866
{p g a 8}P -7.061 12.005 55.866
{c4* g a 8}-8.135 12.724 52.322
{c4* g a 8}P -8.135 12.724 52.322
{c1* g a 8}-7.673 11.089 50.762
{c4* g a 8}P -8.135 12.724 52.322
{p c a 9}-11.678 11.507 51.241
{p c a 9}P -11.678 11.507 51.241
{c4* c a 9}-10.801 9.913 47.923
{c4* c a 9}P -10.801 9.913 47.923
{c1* c a 9}-9.439 8.136 47.832
{c4* c a 9}P -10.801 9.913 47.923
{p g a 10}-13.468 8.08 45.991
{p g a 10}P -13.468 8.08 45.991
{c4* g a 10}-12.063 7.743 42.422
{c4* g a 10}P -12.063 7.743 42.422
{c1* g a 10}-10.885 5.732 42.923
{c4* g a 10}P -12.063 7.743 42.422
{p t a 11}-13.5 5.347 39.864
{p t a 11}P -13.5 5.347 39.864
{c4* t a 11}-10.603 2.763 39.733
{c4* t a 11}P -10.603 2.763 39.733
{c1* t a 11}-10.283 1.515 41.583
{c4* t b 1}P -4.743 -5.868 53.086
{c1* t b 1}-6.24 -5.623 51.358
{c4* t b 1}P -4.743 -5.868 53.086
{p a b 2}-1.748 -4.382 51.367
{p a b 2}P -1.748 -4.382 51.367
{c4* a b 2}-1.797 -5.114 47.693
{c4* a b 2}P -1.797 -5.114 47.693
{c1* a b 2}-3.068 -3.159 47.242
{c4* a b 2}P -1.797 -5.114 47.693
{p c b 3}0.964 -2.599 46.539
{p c b 3}P 0.964 -2.599 46.539
{c4* c b 3}-0.579 -1.639 43.157
{c4* c b 3}P -0.579 -1.639 43.157
{c1* c b 3}-1.783 0.265 43.86
{c4* c b 3}P -0.579 -1.639 43.157
{p g b 4}1.442 0.505 40.639
{p g b 4}P 1.442 0.505 40.639
{c4* g b 4}-0.863 3.508 40.229
{c4* g b 4}P -0.863 3.508 40.229
{c1* g b 4}-1.121 4.629 42.18
{c4* g b 4}P -0.863 3.508 40.229
{p c b 5}0.594 6.202 38.204
{p c b 5}P 0.594 6.202 38.204
{c4* c b 5}-1.699 8.914 39.459
{c4* c b 5}P -1.699 8.914 39.459
{c1* c b 5}-2.781 8.985 41.526
{c4* c b 5}P -1.699 8.914 39.459
{p c b 6}-1.381 12.795 38.992
{p c b 6}P -1.381 12.795 38.992
{c4* c b 6}-4.302 14.062 41.183
{c4* c b 6}P -4.302 14.062 41.183
{c1* c b 6}-3.465 14.014 43.321
{c4* c b 6}P -4.302 14.062 41.183
{p c b 7}-4.479 17.969 41.864
{p c b 7}P -4.479 17.969 41.864
{c4* c b 7}-4.512 17.925 45.669
{c4* c b 7}P -4.512 17.925 45.669
{c1* c b 7}-2.611 17.127 46.625
{c4* c b 7}P -4.512 17.925 45.669
{p a b 8}-3.248 21.574 46.704
{p a b 8}P -3.248 21.574 46.704
{c4* a b 8}-2.223 20.22 50.079
{c4* a b 8}P -2.223 20.22 50.079
{c1* a b 8}-0.051 19.427 50.111
{c4* a b 8}P -2.223 20.22 50.079
{p c b 9}-0.549 23.208 52.042
{p c b 9}P -0.549 23.208 52.042
{c4* c b 9}1.599 21.195 54.463
{c4* c b 9}P 1.599 21.195 54.463
{c1* c b 9}3.579 20.494 53.531
{c4* c b 9}P 1.599 21.195 54.463
{p g b 10}3.925 22.97 56.927
{p g b 10}P 3.925 22.97 56.927
{c4* g b 10}7.148 20.705 56.895
{c4* g b 10}P 7.148 20.705 56.895
{c1* g b 10}8.343 20.859 54.919
{c4* g b 10}P 7.148 20.705 56.895
{p c b 11}10.25 22.303 58.626
{p c b 11}P 10.25 22.303 58.626
{c4* c b 11}13.199 20.877 56.588
{c4* c b 11}P 13.199 20.877 56.588
{c1* c b 11}13.194 21.421 54.389
<end of file>