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

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Subject: Re: Mg++ binding to N7 of G
From: Martin Hallberg Martin {- dot -} Hallberg {- at -} KI {- dot -} SE
Date: 2008-04-03

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Subject: Re: Mg++ binding to N7 of G
From: Pirkko Heikinheimo Pirkko {- dot -} Heikinheimo {- at -} HELSINKI {- dot -} FI
Date: 2008-04-03

William,
it is not clear from your message why you think this is a Mg++, not Mn++
which has been observed in this site before? Mn++ would be visible in
anomalous data from a home source, but not Mg++. The only way to
distinguish Mg++ and water is the number of coordination which should be
very clearly organized around a Mg++. You could propably also tell by
the bond lengts as the Mg-O coordination should be 2.1-2.2, water
hydrohgen bonding around 2.7 Å

Could the atom be Zn++ or Na+ ?

Pirkko Heikinheimo

Martin Hallberg wrote:
> Hi Bill,
>
> On Apr 2, 2008, at 10:58 PM, William G. Scott wrote:
>>
>> 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 would also be hesitant.
>>
>> 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.
>>
>
> One can often see magnesium ions in anomalous-difference fouriers with
> good home-source data. Since you appear to have very good diffraction
> and your magnesium is most definitely relatively well ordered (if it
> is a magnesium..) I think it is worth a try to carefully collect a
> data set using a wavelength around 1.5-1.6 Å (or simply your home
> source depending on how good it is).
>
> Cheers,
>
> Martin
>
> .
> B. Martin Hallberg, PhD
> Assistant professor
> Department of Cell and Molecular Biology
> Medical Nobel Institute
> Karolinska Institutet
> Nobels väg 3
> SE-171 77 Stockholm
> Sweden
>

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Pirkko Heikinheimo

Structural Biology and Biophysics,
Institute of Biotechnology,
P. O. Box 65,
FIN-00014 University of Helsinki, Finland

Visit address:
Biocenter 3, room 4320
Viikinkaari 3, 00790 Helsinki, Finland

http://www.biocenter.helsinki.fi/bi/xray/pirkko
e-mail: pirkko.heikinheimo@helsinki.fi
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CCP4bb <-- 2008 <-- April 2008 <-- 03 April 2008

Previous message:
Subject: Re: Mg++ binding to N7 of G
From: Martin Hallberg Martin {- dot -} Hallberg {- at -} KI {- dot -} SE
Date: 2008-04-03

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Subject: Re: twinned?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-03