Literature reference for the structure:
J.Mol.Biol. 365, 1005-1016, 2007

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Presentation by Craig Martin
Last updated: October 15, 2007

(JmolShell last updated: Apr 2, 2013)

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This JmolShell presentation made possible by Jmol, an open-source project, using a set of JavaScript functions provided in the library Jmol.js

Developed using JmolShell, by Craig Martin, cmartin@chem.umass.edu, Department of Chemistry, University of Massachusetts, Amherst, MA

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Molecule info:

Please wait...

Enter a multi-line Jmol script here (Help):

      Insert Jmol command - Current view Sticks & Labels

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This JmolShell presentation made possible by Jmol, an open-source project. Scripting commands follow those of Rasmol/CHIME. (see also the Jmol Wiki).

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The Jmol mouse gestures are designed to function with single-button mice on the Mac. All references to 'left' get translated to 'only'

rotate X and Y axes	left drag
zoom + rotate Z axis	shift left drag OR middle button drag
rotate Z axis only	shift right drag
translate X and Y axes	shift double left drag OR double middle drag
reset to center	shift double left click OR double middle click
wheel - zoom	a wheel is also a middle button if clicked/dragged
popup menu	right click OR ctrl left click

To measure distances and angles

Double click, optionally single click 0, 1, or 2 times, Double click

After your first double-click the cursor will change and then you can'hover' over several different atoms to get different distances.

Move outside the applet to cancel the measurement.

For a distance measurment:

double click to drop an anchor
double click on the destination

For an angle measurement:

double click to drop an anchor
single click on an intermediate point
double click on the final point

For a torsion measurement:

double click to drop anchor
single click
single click
double click

Selection examples

Select:

:G	Chain G
145:G	Residue 145 of Chain G
45-50:G	Residues 45 to 50 of Chain G
*.CA	all c-alphas
[Cys].CA	all Cys c-alphas
[Cys]:A.CA	all Cys c-alphas in Chain A

Use the following to execute Jmol commands:

Select:   aa:AsnGlnAspGluArgLysGlyAlaValIleLeuThrPheTyrTrpProMetSerThrCysHisCystine-----HydrophobicNeutralPolarChargedAcidicBasicAminoAromaticAliphaticHydrogenwhere:BondedLigandSurfaceBuried2ndry:HelixSheetTurn   BB:BackboneSidechainType:AllProteinNucleicSolventWaterHeteroIonsDNA:ATCGACGTUPyrimidinePurine
   Chain    Res No    Atom No

  Find within Å of the above selection
  

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Apply:    Wireframe       Color:cpkRedOrangeYellowGreenBlueCyanVioletBrownMagentaPinkLightGreenLightBlueLightYellowGrayBlackWhitePurple
Rocket          Cartoon    Transluc
Backbone    Ribbon
Spacefill    Dots    Halos    

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Show:    Show secondary struct H-bonds
Show all H-bonds

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Global:
   Stereo:
     None  Off  cross-eyed  wall-eyed
   Bkgrnd Color:cpkRedOrangeYellowGreenBlueCyanVioletBrownMagentaPinkLightGreenLightBlueLightYellowGrayBlackWhitePurple   HBonds
Rotate to current view

Backbone views: Backbone Wireframe

Rockets Ribbons Cartoon

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Show how this protein bends the DNA. Note that Pro64 intercalates between bases, to allow a sharp kink in the DNA. Such a sharp kink would expose the hydrophobic base faces to water, but Pro juts into to fill the void.

Try again. Zoom in on a kink. Why the kink?