Standard Residues: Difference between revisions

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Eric Martz, Wayne Decatur

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 * The [[Amino Acids|20 standard amino acids]], plus ambiguous residue codes ASX, GLX, and undetermined UNK. In 2014, the [[PDB]] is in the process of adding [[Amino Acids|SEC (U) and PYL (O)]] making 22 standard amino acids.
-* Twelve standard nucleotides A, C, G, I, U, DA, DC, DG, DI, DT, and DU<ref>In June, 2014, there are over 60 entries in the Protein Data Bank containing deoxyribo-U ("DU"). There are none containing ribo-T ("T").</ref>, plus N for an unknown nucleotide. (I is inosine.) The PDB [http://www.wwpdb.org/documentation/format33/sect4.html#HET provides this list under HET].
+* Twelve standard nucleotides A, C, G, I, U, DA, DC, DG, DI, DT, and DU<ref name="du">In June, 2014, there are over 60 entries in the Protein Data Bank containing deoxyribo-U ("DU"). There are none containing ribo-T ("T").</ref>, plus N for an unknown nucleotide. (I is inosine.) The PDB [http://www.wwpdb.org/documentation/format33/sect4.html#HET provides this list under HET].
-The distinction between ribonucleotides (A, C, G, I, T, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU) was first made when the PDB was remediated, effective August 1, 2007. The unremediated files can still be obtained, see [[Getting Unremediated PDB Files]].
+The distinction between ribonucleotides (A, C, G, I, U) and deoxyribonucleotides (DA, DC, DG, DI, DT, DU<ref name="du" />) was first made when the PDB was remediated, effective August 1, 2007. The unremediated files can still be obtained, see [[Getting Unremediated PDB Files]].
 Note that, in [[Jmol]], A, C, G, I, T, U select nucleotides in either DNA or RNA for backward compatibility, while DA, DC, DG, DI, DT, and DU select only DNA nucleotides. You can select RNA nucleotides with e.g. "(A, U) and RNA".