Talk:Aconitase

From Proteopedia

Iron-sulphur cluster

I don't want to mess with the existing scenes, but I see problems with the display of Fe-S cluster and also with part of the text. Under "Catalytic mechanism of mitochondrial ACO", the green link "which are bound to three of the four" brings a display with a cluster with too many bonds (i.e. Fe-Fe); maybe this is in the original file? or just calculated by Jmol autobonding [1]. Anyway, not didactic.

Then, the sentence "On activation of the enzyme, a fourth iron atom is included in the cluster" seems to mean an extra Fe atom; there were already 4 and no more will appear... from where? Clicking on this green link brings indeed a new Fe atom from outside, which on its way (animated) binds an oxygen/water until it comes to the 4th position that was made vacant before the animation. I find this wholly unjustifiable.

The next sentence, "This Fe4 is free to bind one, two, or three partners" is rather confusing.

[1] With autobond off, 7ACN form PDB hasn't got the extra bonds. However, the file in Proteopedia has the inconvenient too long Fe-S bonds crossing the center of the cluster (getfrozenstructure?e1bb8cd7fce4df66392858678cc9c439)

The animation is getfrozenstructure?77517829f7cd812292bdfe6b7f6e86e7 This has Fe-Fe bonds.

I think these may all be fixed without changing the model files, by adding

connect 3.0 5.0 ([SF4] and _S) ([SF4] and _Fe) delete;
connect ([SF4] and _Fe) ([SF4] and _Fe) delete;
connect 3.0 5.0 ([F3S] and _S) ([F3S] and _Fe) delete;
connect ([F3S] and _Fe) ([F3S] and _Fe) delete;

to the scenes. --Angel_Herraez 11:48, 9 January 2021 (UTC)