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<div dir="ltr">Hi Alex,</div>
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<div dir="ltr">Too small and too thick for porphyrin.</div>
<div dir="ltr">It looks octahedral.</div>
<div dir="ltr">Surrounded by pos charged AA.</div>
<div dir="ltr">Complex 6-coordinated metal ion?</div>
<div dir="ltr"><a rel="noreferrer noopener" href="https://urldefense.com/v3/__https://www.chemguide.co.uk/inorganic/complexions/shapes.html__;!!Mih3wA!HJjVr4vJXKxksPZjaBBP7djvCXQffkeVWEEoIdQk82u6WnSQlY5FrbGJEQMP3jAic8DXJhfvdpSt44ojLbtyV4TAn3s$">https://www.chemguide.co.uk/inorganic/complexions/shapes.html</a><br>
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<div dir="ltr">AlF6?</div>
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<div dir="ltr">Can you get rid of it with EDTA?</div>
<div dir="ltr">Use ICP-MS to identify!</div>
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<div dir="ltr">Good luck,</div>
<div dir="ltr"> Matthias</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Dr. Alexander Belyy <alexander.belyy@mpi-dortmund.mpg.de><br>
<b>Sent:</b> Tuesday, January 17, 2023 7:17:25 PM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> [3dem] A strong density in the cryo-EM map</font>
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<p style="">Dear community of structural biologists,<br>
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In a 3.5 Å cryo-EM reconstruction, we have discovered a large density of 10-12 Å diameter that we are having difficulty identifying (see attachment). This density is surrounded by 5 arginines, 3 asparagines, 2 glutamines, 1 aspartate, and 1 glutamate coming
from 4 different regions of the protein. Functionally, the density is needed to hold the protein together. This density appears at higher thresholds than the protein itself and is visible even at the 2D class level. After local refinement and sharpening, the
density becomes pyramid-like with a series of smaller spheres with pseudosymmetry (or C3?).<br>
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We would be grateful for any suggestions as to what this might be.<br>
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Thank you!<br>
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Best regards from Dortmund,<br>
Alexander<font size="2" style="color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:12pt"><br>
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