Dear Reza, We had a case when two phosphate ions and magnesium ion have been bound to the ATP-binding site (300mM sodium phosphate in the crystallisations conditions). However, your ATP/ADP may not have full occupancy and therefore electron density might be lower. You may consider calculation of a blurred map (bring up contributions from low-resolution terms) and see whether there is any density for the nucleotide. But first of all I would calculate omit map (without ligand) and would start to worry if there is no density for nucleotide part.
All the best, Oleg -- Dr Oleg Kovalevskiy CCP4 team UKRI Science and Technology Facilities Council Rutherford Appleton Laboratory Harwell Campus Didcot, Oxfordshire OX11 0QX UK From: CCP4 bulletin board <[email protected]> on behalf of Reza Khayat <[email protected]> Reply to: Reza Khayat <[email protected]> Date: Thursday, 23 July 2020 at 21:13 To: ccp4bb <[email protected]> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP Tried the homologues thing. There are homologues and I've done the fitting, but this is what I consider to be subjective. I'm certain the referee will ask: Given the quality of density for the nucleotide, how certain are the authors that a different fit is not possible? Have other fit poses been considered? Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Jon Cooper <[email protected]> Sent: Thursday, July 23, 2020 1:07 PM To: [email protected] Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? Coot is pretty good at fitting known ligands, and unknown ones, too! -------- Original Message -------- On 23 Jul 2020, 17:53, Reza Khayat < [email protected]> wrote: Hi, Can folks suggest programs for objectively docking ATP/ADP molecules into density? Our density is not so good, probably because of occupancy, and we'd like a less subjecting approach for modeling. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ 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.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=NCJxuuXUzKYpS2Tc2Ny_3kYinX8Cg20Y5D9elTGcnRE&s=cyXoGwvleVJhuJ6PhFggTxLK0WJTnvvxFxlc-U1A0iQ&e=> ________________________________ 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.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=NCJxuuXUzKYpS2Tc2Ny_3kYinX8Cg20Y5D9elTGcnRE&s=cyXoGwvleVJhuJ6PhFggTxLK0WJTnvvxFxlc-U1A0iQ&e=> ________________________________ 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 email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI. ######################################################################## 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/
