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PDB molecules Molecular Modelling

AMP: This file contains 35 atoms, 37 bonds

Here's an adenosine monophosphate rotation gif animation. The gif animations and movie files are made small for the web. Mac/PC Molecule, IsisDraw, Chime, and RasMol can all rotate molecules in 3D space in real timeand at full screen resolution, especially with the fast cpu's that are in the new computers. Animations and the novelty of being able to click and rotate a molecule on the computer screen are fun and interesting. But the relationship and similarities betwen different molecules is also something which can be done by the molecular modelling applications such as Mac/PC molecule, etc.

This is adenosine which is just an adenosine monophosphate without the phosphate.

The end view of the AMP molecule is not clearly demonstrative of the ring stuctures.

Perspective one shows the five and six membered nitrogen containing rings clearly but the remaining five membered ring containing one oxygen and four carbons is not distinguishable.

Perspective two shows the converse of perspective one.

Perspective three shows the phosphate group clearly in the foreground.

Zooming in on perspective three clarifies the relationship of the three rings.

Zooming further in makes it possible to more fully discern the rings and their spacial relationship. The hydrogen in the foreground obscures somewhat the full appreciation of the carbon-oxygen ring but in actual useage of the Mac/PC Molecula application, the hydrogen could be selected and rendered invisible.

The ADP molecule with its two phosphates.

The ATP molecule with its three phosphates is shown for further comparison.

If one of the phosphates is moved, using computer magic, to a carbon in the ring with four carbons and one oxygen, we get a part of a molecule which looks like this.

The other part of the molecule is shown here. It is a long chain with carbons, oxygens, nitrogens, and a phosphate near its end.

acetyl-CoA

Combining these two parts we can see a complete acetyl-Coenzyme A molecule.

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