In our acetone carboxylase structure, the active metal site contains a octahedral Mn coordinated with two His, one Asp, and one Glu residues. It looks very similar.
https://www.nature.com/articles/s41598-017-06973-8 The protein may have a metal in the active site, is there any background information? Or the metal has bound adventitiously, to find out more anomalous data collection is required, like other people said. Burak ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Goldman, Adrian <adrian.gold...@helsinki.fi> Sent: 29 December 2017 20:32:34 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance All true, I did my undergraduate thesis (at cambridge about 10**6 years ago it feels) on the formation of carboxylate-pairs in the gas phase…. But I agree with the thread: there is a metal there; it’s almost certainly not Mg, but it’s hard to say without further data whether its Mn, Fe, Cu, Zn - those being the most likely culprits. Someone suggested that scanning the edges might tell, and I agree. But what he might find is a mixture, as the metal is probably adventitious and has just been picked up, possibly from whatever is present in solution. We’ve had that experience. Adrian On 29 Dec 2017, at 17:31, Tristan Croll <ti...@cam.ac.uk<mailto:ti...@cam.ac.uk>> wrote: In this case, yes - there’s clearly a metal ion coordinated there. But for the record, it is entirely possible (if somewhat rare) to get acidic side chains directly contacting each other. Look up “carboxyl-carboxylate pair”. They’re typically found at low pH and/or in quite protected environments. Think of it as having one carboxyl group protonated and H-bonding to the other, except that the proton is more-or-less equally shared. Their most common role is as pH-dependent conformational switches - very stably bonded below the pKa, wanting nothing to with each other above. Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY On 29 Dec 2017, at 14:18, Robbie Joosten <robbie_joos...@hotmail.com<mailto:robbie_joos...@hotmail.com>> wrote: Hi Anurag, There is a metal in the middle there. You need to figure out which one. Have a look at the crystallization conditions. If can also have a look at anomalous signal. Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anurag Misra Sent: Friday, December 29, 2017 14:55 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance Dear all, I have solved a protein structure at 2.8 A resolution with Rfree 26%. In this structure catalytic His interacts with non catalytic Asp. This His-Asp pair (Chain A) is facing another identical His-Asp pair (in Chain B) which are related with 2-fold ncs (pics are attached) (The molecule exists as a dimer). There is another His-Asp pair in chain C (not shown in attached pic) which faces to the identical pair related to crystallographic 2-fold. (min distance Asp-Asp 2.58 A, His-His 3.6 A and His1-Asp1/His1-Asp2 ~3.0 A) How to explain Asp-Asp head on pairs in close proximity? Is there a role of His in making such pairs. Is there any role of change in pKa to allow such interactions? Kindly suggest a few references where similar Asp-Asp pairs have been seen. I appreciate your kind attention. Thank you so much for helping me. Best regards, Anurag <image001.png> <image002.png>
