.tec3 Thanks very much for your explanation. Now it’s clear to me.
Kai
> Message: 6
> Date: Thu, 17 Mar 2022 03:25:11 +0000
> From: Thomas Cheatham <tec3.utah.edu>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] question about ATP-Mg2+ binding system
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>> My questions are:
>> 1. Assuming if only Mg2+ ions in the simulation, there should be two Mg2+ around ATP (-4).
>> But why only one Mg2+ was found in the PDB file?
>
> Let's explore your assumption ... why do you think two Mg2+ are required to balance the -4 charge and/or that these should be seen in the crystal?
>
> There is a concept of bound vs. mobile ions which can neutralize the charge - the difference between bound vs. mobile is time scale of the interaction. Bound does not mean permanent interaction as ions can exchange. Think of mobile ions as diffuse which means they are moving around and crystallography cannot pick this up. Even though the ion is mobile, it can balance the charge.
>
>> 2. Would the water surrounding ATP hinder the cation ion approach?
>
> Of course. Goes to the timescale - to get the Mg2+ to bind, you have to move water out.
>
>> 3. Is the charge of phosphate group of ATP too negative?
>
> The charge is what it is. I would not recommend a -2 ATP, for example. (p.s. the charge of phosphate group is not -4 since each phosphate can only contribute 0 or -1 charge depending on environment / protonation, ATP has multiple phosphates)
>
> A classic blast from my past is (from the reflector, but our search engine is sub-optimal so I cannot find it, but basically), I'm running a DNA (duplex) simulation and the Na+ ions which were directly chelating between the two phosphates move away so the simulation must be wrong. No, the ions are mobile and on average balance the charge... Manning theory, among many others. Gets even more complicated with bound ions when you consider partial occupancy, etc.
>
> Another way to think about it is that a crystal structure is a static snapshot of the system where if things are not moving too much, you see defined atomic density. In real life, everything is moving. Waters or ions that you see in crystal have long lifetimes (or are persistent even with exchange of water or ion). Thing's you do not see are still there (to balance charge, etc.), you just cannot see them.
>
> —tec3
Dear
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Received on Thu Mar 17 2022 - 19:30:02 PDT
