Well....just to add, it has been our contention that many of the metal ions have been modelled as waters in several structures- due perhaps to the lack of sufficiently high resolution data. We published some of the potential metal binding sites in many structures a few years ago:
Proteins. 2008 Mar;70(4):1206-18. Shekhar On Thu, Mar 8, 2012 at 9:42 AM, Parthasarathy Sampathkumar < [email protected]> wrote: > Dear Uma, > > The water pictured in W12-1.jpg: could this be a potential metal ion? If > you flip the side chain on Asn at 3.08Angstrom, then this has 3 or 4 > coordination with oxygen atoms. So, provided your crystallization condition > or buffer contains metal ion(s), you could attempt to see if it fits better > with a refinement cycle. > > May be a similar situation with the water described in W11-1.jpg as well? > Difficult to say from these figures. > > COOT within the "validate" wizard has an option to search for > "hihgly-coordinated waters" like the one you have pictured. > > Hope this helps, > Partha > > On Wed, Mar 7, 2012 at 4:21 PM, Uma Ratu <[email protected]> wrote: > >> Dear Roger: >> >> Thank you very much for your comments. I use them as guideline and remove >> many 'false waters". >> >> Still, I am not clear of some of these 'waters' are real or not. I have >> the pic attached. >> >> In Pic-W11-1, the 'water' is connected to the adjust residues with 4 >> contacts, which are 'N' or 'O' atoms. I would consider this 'water' is >> false. My question is: if these 4 contacts include "C" from residues, will >> it be a polar contact or not? >> >> In Pic-W12-1, the 'water' is connected to the adjust residues with 3 >> contacts. The 4th is to another 'water'. >> Will this 'water' is true or not? Similar case is seen in Pic-W190-1 >> >> In Pic-W109-1, some 'waters' are connected to adjust residues, some not. >> Are these 'water' true or not? >> >> Further more, >> > and the b-factors are not way out of line, >> >> I am not clear on how to define "out of line". >> How to find b-factor of individual residue in Coot? I search the web, but >> find no answer. >> >> Thank you for advice >> >> Uma >> >> On Wed, Mar 7, 2012 at 11:44 AM, Roger Rowlett <[email protected]>wrote: >> >>> Uma, >>> >>> Remember that your structure, ultimately, is a model. A model is your >>> best judgment of the true representation of the protein structure in your >>> crystal. Your model should make chemical sense. Coot is pretty good at >>> placing waters, but it cannot substitute entirely for the experimentalist. >>> Coot will miss some waters, and mis-assign others into weak, unmodeled or >>> alternate side- or main-chain density, or into density that might be >>> attributable to cations and anions or other crystallization materials. Your >>> waters should be subjected to inspection and verification. It is really >>> helpful to turn on environment distances in Coot when you do this. Even in >>> a large protein model, it is possible to inspect all waters for >>> reasonableness pretty quickly. If you have no significant positive or >>> negative difference density, and the b-factors are not way out of line, and >>> hydrogen bonding partners are reasonable, then modeling a water is probably >>> a good call. >>> >>> Waters should have hydrogen bonding partners with side chains or >>> main-chain polar atoms, within reasonable distances, or be withing hydrogen >>> bonding distance of other waters that are (chains of waters). If a "water" >>> has strong electron density and more than 4 polar contacts, you might >>> consider anion or cation occupancy. Most anions and cations will have >>> higher electron density, and appropriately different types of polar >>> contacts. (e.g. you might find sulfates near a cluster of basic residues). >>> Low occupancy anions can often look a lot like water. PEGs can create ugly >>> "snakes" of variable density that may be challenging to model. Modeling >>> non-protein structural bits is endlessly entertaining for the protein >>> crystallographer. ;) >>> >>> Cheers, >>> >>> _______________________________________ >>> Roger S. Rowlett >>> Gordon & Dorothy Kline Professor >>> Department of Chemistry >>> Colgate University >>> 13 Oak Drive >>> Hamilton, NY 13346 >>> >>> tel: (315)-228-7245 >>> ofc: (315)-228-7395 >>> fax: (315)-228-7935 >>> email: [email protected] >>> >>> >>> On 3/7/2012 11:20 AM, Uma Ratu wrote: >>> >>> Dear All: >>> >>> I try to add water to my model. >>> >>> Here is how I did: >>> Coot: Find Wates >>> Map: FWT PHWT; 1.8 rmsd; Distances to protein atoms: >>> 2.4 min/3.2 max >>> >>> Coot found 270 water molecules. >>> >>> I then examed these waters. Most of them had ball shape. Some had two or >>> more balls together. Some had irregular shape (not glabol shape). >>> >>> I run Water Check. The program did not find any mis-matched water. >>> >>> Here is my question: how could I tell the waters are real? Or something >>> else? >>> >>> Thank you for advice >>> >>> Ros >>> >>> >>> >>> >>> >> > -- Shekhar C. Mande (शेखर चिं मांडे) Director, National Centre for Cell Science Ganeshkhind, Pune 411 007 Email: [email protected], [email protected] Phone: +91-20-25708120 Fax:+91-20-25692259
