There are plenty of Zinc hydrolase enzymes that adopt octahedral geometry around the metal ion when you include a water in the 6th coordination site.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) On Mar 12, 2025, at 6:14 AM, Roger Rowlett <rrowl...@colgate.edu> wrote: External Mail This email originated from outside of UT Southwestern. Please be cautious. <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/MznTZTSvDXGV0Co!W_xDF9UcglqRaZ3BpT3ZJbm5rYAgCnqQhCyVwQS0FlyNAFI43SORjOnFKLQ4-qK3ICddEc-D8JbRVsM8vAA93l9eX6cEhgX6VULMGRiW9H1PpflLS8wuSrc9MzRft9IAPfn7g5TP$> Report Suspicious It would be unusual for a coordinated metal ion to have multiple occupancies. Are you sure your metal is zinc? Zinc coordination sites are typically pseudotetrahedral (occasionally 5-coordinate) with waters filling out the coordination shell in a His-His-Asp/Glu ligand environment, with Zn-N(O) bond distances of 2.0A plus or minus. There are metalloenzymes with fairly plastic metal affinities (e.g. certain carbonic anhydrases) that can naturally accommodate Cd or Fe. The former has coordination geometries similar to Zn with longer bond lengths. The latter will typically be in an octahedral coordination environment. Roger Rowlett Gordon & Dorothy Kline Professor of Chemistry, Emeritus Colgate University On Wed, Mar 12, 2025, 5:45 AM Shikha Gupta <shikha.gupta.01...@gmail.com<mailto:shikha.gupta.01...@gmail.com>> wrote: Dear all, I have a complex structure where zinc <Image_250312_150256.jpeg> metal ion is present in the active site (evidence from several PDBs). However, despite multiple efforts, I am getting lot of positive densities close to the metal ion (please see image attached). I have also tried to place water or two zinc ions but that also doesn’t seem to work. The last and overall best solution I came up with was by positioning three zinc ions with combined occupancy of 1 (0.3+0.2+0.3). Although I still see positive densities around but this is best I have achieved. This was a soaked crystals, any suggestions on this. Is this the right way to do this. The resolution of the structure is 1.7 angs. Thanks, Shikha ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!Fe_k5bPayZQpHxyUIfANBR6rkt--nv1212CVVwzVsJlyQGraHp_nTjcTL2kUiU2CPYYprMNLfazMHK16ubRPICl41HLxMj-g8A$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!MznTZTSvDXGV0Co!Fe_k5bPayZQpHxyUIfANBR6rkt--nv1212CVVwzVsJlyQGraHp_nTjcTL2kUiU2CPYYprMNLfazMHK16ubRPICl41HLxMj-g8A$> ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
