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 <[log in to unmask]> on behalf of Reza Khayat <[log in to unmask]>
Reply to: Reza Khayat <[log in to unmask]>
Date: Thursday, 23 July 2020 at 21:13
To: ccp4bb <[log in to unmask]>
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 <[log in to unmask]> on behalf of Jon Cooper <[log in to unmask]>
Sent: Thursday, July 23, 2020 1:07 PM
To: [log in to unmask]
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 < [log in to unmask]> 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
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