zinc fingre

From: Rajesh kumar
Date: 3 April 2012 16:07

Dear All,

I am trying to crystallize a protein, so far I got no diffraction though I have large crystals.

It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only).

Is there a way if I could check using bioinformatic tools if  my protein has Zinc finger or zinc finger-like motif?  If so, is it possible assume it would bind some sort of DNA and could I check that as well?

I appreciate any suggestions to this BROAD question and some references would be helpful.

I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. 

I appreciate your time.

Thanks,

Rajesh

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From: Debasish Chattopadhyay

Read a book.

If you can't find a book then ask the all knowing Google.

 

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From: Rajesh kumar

Thanks...... I will.

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From: Pius Padayatti


Hi Rajesh,
First of all you did the right thing to ask people here about our doubts.
There is nothing wrong in asking questions.

The board is for asking questions realted to crystallography
(all aspects).

Padayatti

--
Pius S Padayatti,PhD,


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From: Debasish Chattopadhyay


Yes, Rajesh, I completely agree with Pius.  There is absolutely nothing wrong in asking a question on ccp4bb.
The suggestion 'read a book and search on-line information sources' is a good one on any subject.

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From: Peter Hsu


Hi Rajesh,

Have you looked at how well conserved these Cys/His residues are? Is the spacing similar to known zinc fingers? Might be good things to consider if you suspect a zinc finger in your protein, of course you probably know this already.

Best,
Peter

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From: Rajesh kumar

Dear All,

Thanks everyone for the suggestions. I did go to library to look up some chapters in books which gave me lot of information about conserved zinc finger domain. My protein  has Cx4C and Cx3C and with very large spacing, so I suspect it could be zinc finger like protein (though no software showed any indication) but I am looking forward to do some experiments to confirm this. I was looking for some examples other than known domains (TFIIS, LIM, ring finger ref:encyclopedia of Mol Biol and Mol Med vol 6) which have C2H2 or C3H but doesn't follow the rules zinc finger but still bind to DNA and has been crystallized. I guess I will do more reading.

Thanks again

Rajesh