Dear Yingjie,
I agree with Ed Berry that I do not believe that nearby binding sites
influence the Km (~Kd) which depend on bound and unbound concentrations.
However, there could be a strong kinetic effect, e.g. these secondary
binding sites could act as stepping stones when the path to the primary
binding site would otherwise be difficult to pass. The crystal structure
of the potassium channel provides a beautiful example of this.
Best regards,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Yingjie Peng
Sent: Monday, February 16, 2009 11:09 AM
To: [email protected]
Subject: [ccp4bb] Off-topic: ligand enrichment
Dear guys,
Sorry for the off-topic question.
After I have solved my strucutre, I have found my target ligand
bound at the potential binding site. Also, I have
found that there are two more ligand molecules bound along the
path from solvent to the binding site. I think this
can enrich the ligand to binding site, enhancing the local
concentration of the ligand, thus reducing the Km of the
ligand.
I am wondering if anybody can give some suggestions on how to
solve this problem clearly. If there is any
similar case, it will be better.
Thank you in advance.
Best wishes,
Yingjie
Yingjie PENG, Ph.D. student
Structural Biology Group
Shanghai Institute of Biochemistry and Cell Biology (SIBCB)
Shanghai Institute of Biological Sciences (SIBS)
Chinese Academy of Sciences (CAS)
320 Yue Yang Road, Shanghai 200031
P. R. China
86-21-54921117
Email: [email protected]
