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Properties of proteins: Difference between revisions
→Ideal metal bond distances
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== Ideal metal bond distances == | == Ideal metal coordination and bond distances == | ||
* classic | * classic papers: Harding, M.M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]; (2004) [https://doi.org/10.1107/S0907444904004081 The architecture of metal coordination groups in proteins]. The latter has supporting information: zip archive of the website on architecture of metal coordination groups in proteins, and PDFs containing additional tables. | ||
* | * [http://web.archive.org/web/20161031170012/http://tanna.bch.ed.ac.uk/ 2016 archive of original website set up by M. Harding]; MESPEUS database (successor website but also now offline:) [http://web.archive.org/web/20160901002225/http://mespeus.bch.ed.ac.uk/MESPEUS_10/ 2016 archive of website] | ||
* [http://metalweb.cerm.unifi.it/ MetalPDB] | |||
* [https://csgid.org/metal_sites Check my metal] | |||
== Distinguishing ions from waters == | == Distinguishing ions from waters == | ||
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that are close to each other should not have an occupancy sum greater | that are close to each other should not have an occupancy sum greater | ||
than unity. | than unity. | ||
Further possibilities: | |||
* From the Phenix package, try: mmtbx.water_screen model.pdb data.mtz elements=NA,K | |||
* WASP analyse water molecules in high-resolution protein structure to check if some of those could be metal ions. WASP could be run as a part of STAN server. STAN - the STructure ANalysis server from USF (http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl ) | |||
== Melting point == | == Melting point == | ||