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: [EMAIL PROTECTED]
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----- Original Message ----- From: "William G. Scott" <[EMAIL PROTECTED]
>
To: <[email protected]>
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
