Chloride coordination spheres are typically tetrahedral (CN=4) or square pyramidal (CN=5), and occasionally octahedral (CN=6). Arg and His and well as amide nitrogens are common protein ligands, and it is possible but not common to see carboxylates in the coordination sphere.
Roger Rowlett On Wed, Mar 4, 2020, 1:05 PM Jessica Besaw <jbesaw1...@gmail.com> wrote: > > Hey Roger, > > I believe the Chloride spot is a negatively changed anion because it has > more density that water and it is close to an arginine. Does this chloride > binding coordination look reasonable? > > All of the other water are coordinated to two other side-chains, and do > not depend on the partially occupied water > > Cheers! > > Jessica > > > > On Wed, 4 Mar 2020 at 12:27, Roger Rowlett <rrowl...@colgate.edu> wrote: > >> In addition, one should carefully consider the chemistry and coordination >> geometry around the putative chloride ion. Not only do candidates have to >> be consistent with the observed omit density, but they must also make >> chemical interaction and geometry sense. I suspect a partial occupancy >> water may make the most sense from the limited data provided, but only if >> all the other placed solvent molecules have clearly defined interactions >> that do not depend solely on the partially occupied water. What does the >> chloride coordination geometry look like? Is it clearly a chloride ion and >> not a cation? >> >> Roger Rowlett >> Gordon & Dorothy Kline Professor, Emeritus >> Colgate University >> >> On Wed, Mar 4, 2020, 12:20 PM Nukri Sanishvili <sannu...@gmail.com> >> wrote: >> >>> Hi Jessica, >>> You do not say how well is the rest of the structure refined. >>> First, you should refine the structure best you can, without placing >>> anything in the unclear blob of your interest so to obtain the best >>> possible phases and hopefully improve the blob density as well. >>> Then you should let the BB see what that density looks like. Looking at >>> only the list of possibilities has very little value without seeing the >>> density itself. >>> Best wishes, >>> Nukri >>> >>> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw <jbesaw1...@gmail.com> >>> wrote: >>> >>>> Hello friends, >>>> >>>> I have a "blob" of density in an active site of my protein. >>>> >>>> I am struggling to determine if I should place a water in this spot, if >>>> I should model it as a disordered water, if the density may be a ligand >>>> that I have not considered, or if it should be left as unaccounted for >>>> density. I would like to publish this structure without compromising the >>>> science. >>>> >>>> I have attached several possibilities that I have considered below. >>>> >>>> Any suggestions would be appreciated. >>>> >>>> Cheers! >>>> >>>> Jessica Besaw >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
