Re: [ccp4bb] Mg++ binding to N7 of G

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Mg++ binding to N7 of G
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-04-02

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Subject: Re: Mg++ binding to N7 of G
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-04-02

Sorry, I should have been less cryptic:

On Apr 2, 2008, at 2:13 PM, Jacob Keller wrote:

> Forgive the naive questions:
>
> To what do the terms "hard" and "soft" refer here?

In inorganic chemistry, "hard" refers to bonding where the Coulomb
potential dominates, and "soft" where orbital terms dominate. If one
partner prefers electrostatic interactions and the other more covalent-
like interactions, the interaction is less probable. So Mg++ likes
oxygen, Mn++ likes Nitrogen.

>
>
> And "G", I assume, is glycine,

Guanine

> but what is "N7?"

Purine numbering...

>
>
> JPK
>
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: j-keller2@northwestern.edu
> *******************************************
>
> ----- Original Message ----- From: "William G. Scott"
> >
> To:
> Sent: Wednesday, April 02, 2008 3:58 PM
> Subject: [ccp4bb] Mg++ binding to N7 of G
>
>
> Howdie folks:
>
> I've got what appears to be an inner-sphere interaction between Mg++
> and the N7 of a G. The mode of binding is the same as what is observed
> at this site for Mn++, confirmed with anomalous data. Our resolution
> is 1.6 Å, so I am reasonably confident this is right. However, my
> chemist's viewpoint is that Mg++ is too hard and N is too soft for
> this to happen.
>
> I looked in a database called http://merna.lbl.gov for Mg++ binding
> sites, and a bunch pop up for inner-sphere N7 interactions with Mg++.
> However, if I restrict the search to structures having 1.8 Å
> resolution or better, the number goes to zero.
>
> Since Mg++ has the same number of electrons as water and no useful
> absorbance, it seems assigning them based on hydration geometry and
> bond distances is the only hope.
>
> Does anyone have anything more definitive I can refer to?
>
> Thanks.
>
> Bill Scott
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Mg++ binding to N7 of G
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-04-02

Next message:
Subject: Re: 3D model in glass
From: Mike Lawrence lawrence {- at -} WEHI {- dot -} EDU {- dot -} AU
Date: 2008-04-02