Dear All,
pentagons of water are one of the old myths from the past millennium:
everyone talks about them, nobody has seen them. How many cases do you
have in your structure, how many have you analyzed in the PDB? In other
words, anecdotal evidence is fine, but what is their statistical
significance?
The first shell of waters around biomolecules is ordered, in proteins as
well as nucleic acids. The positions of these waters are a function of
the local geometry of the amino acid or nucleotide which is however
significantly modulated by the neighboring residues. The geometry of the
above mentioned first hydration shell of waters around say guanosine
phosphate is different in the B and A forms of DNA. Another example,
asparagine has different hydration sites in the alpha-helical or beta
sheet environments, of course on top on differences depending on the
asparagine conformation. You may look at
https://www.dnatco.org/watAA/atlas.html for more examples.
I believe that in your case, Vijaykumar, the meaning of the pentagon(s)
is that you see five waters at the interface as other people see three,
four or seven.
Best regards,
Bohdan, bs.structbio.org
On 2019-09-27 14:28, Jon Cooper wrote:
Pentagons of water are quite common in ordered water structure. Is it
isolated or do the waters H-bond to other waters?The dimer interface
looks, if I may say, a bit borderline to me. How does it fare in Pisa?
Best wishes.
On 27 Sep 2019 12:33, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com>
wrote:
Dear Community,
I solved the structure of a protein from vibrio. There are two
molecules in the asymmetric unit of this protein. At the dimer
interface, the C-termini of both the chains interact with each other
with the help of five water molecules that form a pentagon. I have
attached an image showing both the chains and stereo image of dimer
interface in the inset. I was wondering if there is any significance
to this or if there is any relevant literature that explains this
behavior.
Thank you
Vijaykumar Pillalamarri
C/O: Dr. Anthony Addlagatta
Principal Scientist
CSIR-IICT, Tarnaka
Hyderabad, India-500007
Mobile: +918886922975
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