PDB file 1GIA

This structure of the a subunit of an inhibitory G Protein, with bound GTPgS, was solved by D. E. Coleman et al., in 1994.

The analog GTPgS was used in place of the normal ligand GTP.

Recommended display options:

Team up with someone at an adjacent computer. Together explore this structure of Ga-GTP.
Keep the display on one computer while together you display Gabg-
GDP on the other computer.
Compare the position of switch II in the two cases.

Color chain, and display as cartoon.
elect hetero-ligand, display as spacefill, and color CPK.  Note how GTPgS sits in a deep cleft in the protein. Identify the yellow S substituting for an oxygen in the terminal phosphate of GTP.
is GTPgS used in place of GTP during protein crystallization?
Mg++ is required for activation of Ga. What atoms of the protein and the GTP analog coordinate Mg++?

Select protein-sheet and then select-change color to, and specify a color, to highlight the 6-stranded b-sheet adjacent to the nucleotide binding site. 

Enter into the command line select 40-47, and then use the mouse menu to specify a color.
Explore how this "
P-loop" is adjacent to the terminal phosphates of GTP. 

Select 178-184, and color CPK.
This is
Switch I, one of the regions that changes position when GTP substitutes for GDP.
Change display to
ball & stick.
Look for
the invariant threonine that interacts with Mg. 

To visualize Switch II, select 200-215 and display as sticks.
Look for the conserved glutamine residue that helps to position the attacking water molecule at the active site for GTP hydrolysis.

Now change the display for residues 200-215 (Switch II) to cartoon and color magenta (Use this exact color so that you will be able to compare the position of Switch II in Gabg-GDP.)
The a-helix in this domain ends in a region that interacts with Adenylate Cyclase. The helix also interacts with the inhibitory b subunit when Ga has bound GDP. The change in conformation of switch II with GDP/GTP exchange may contribute to altered affinity of Ga for Gb and for Adenyate Cyclase.

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