Angel Herraez wrote:
>It seems that one of the consequences of latest version of PDB
>(called "remediated" data or wwPDB) is that oxygen atoms in phosphate
>in nucleic acids have changed name, from O1P, O2P to OP1, OP2
>
>
>
fixed for 11.3.33 and 11.2.15
>If needed, I can do further research into this and confirm it is in
>fact a general change of rules in PDB, but with this file the change
>is indeed so:
>
>
Please check also the following if you can:
> "H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P
> "O5T", // 46 - 5' terminus oxygen which replaces P + O1P + O2P
> "O4'", // 49 - sugar ring 4' oxygen ... not present in +T ...
> maybe others
> "O2'", // 50 - sugar 2' oxygen, unique to RNA
// nucleic acid backbone hydrogens
//
"1H5'", // 51 - first equivalent H on sugar 5' carbon
"2H5'", // 52 - second equivalent H on sugar 5' carbon
"H4'", // 53 - H on sugar ring 4' carbon
"H3'", // 54 - H on sugar ring 3' carbon
"1H2'", // 55 - first equivalent H on sugar ring 2' carbon
"2H2'", // 56 - second equivalent H on sugar ring 2' carbon
"2HO'", // 57 - H on sugar 2' oxygen, unique to RNA
"H1'", // 58 - H on sugar ring 1' carbon
//
"H3T", // 59 - 3' terminus hydrogen
thanks.
Bob
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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