Protein Data Bank

26 APPENDIX B - ATOM NAMES A.Amino Acids These atom names follow the IUPAC-IUB rules 1 except: (i)Greek letter remoteness codes are transliterated as follows:α−Α, β−Β, γ−G, δ−D, ε−Ε, ζ− Ζ, η−Η (ii)Atoms for which some ambiguity exists in the crystallographic results are desig- nated A. This will usually apply only to the terminal atoms of asparagine and glutamine and to the ring atoms of histidine. Within each residue the atoms occur in the order specified by the superscripts (fol- lowing figure). The extra oxygen atom of the carboxy terminal amino acid is designated OXT. Four characters are reserved for these atom names. They are assigned as follows: 1-2Chemical symbol - right justified 3Remoteness indicator (alphabetic) 4Branch designator (numeric) (iii)For protein coordinate sets containing hydrogen atoms, the IUPAC-IUB rules 1 have been followed. Recommendation rule number 4.4 has been modified as follows: When more than one hydrogen atom is bonded to a single non-hydrogen atom, the hydrogen atom number designation is given as the first character of the atom name rather than as the last character (e.g. H β1 is denoted as 1HB). Exceptions to these rules may occur in certain data sets at the depositors’ request. Any such exceptions will be delineated clearly in FTNOTE and REMARK records. 1 IUPAC-IUB Commission on Biochemical Nomenclature. "Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains. Tentative Rules (1969)", J. Biol. Chem.245, 6489 (1970). The 1974 recommendations on the "Nomenclature ofα−Amino Acids (Biochemistry, 14, 449 (1975)) provides a scheme based on normal rules for organic compounds, but this scheme will not be used here. 28 B.Nucleic Acids Atom names employed for polynucleotides generally follow the precedents set for mononucle- otides. The following points are worthy of note. (i)The prime character (& 39;) commonly used to denote atoms of the ribose originally was avoided because of non-uniformity of its external representation. An asterisk ( ) therefore was used in its place, in entries released through January 1992. (ii)Of the four characters reserved for atom names the leftmost two are reserved for the chemical symbol (right justified) and the remaining two denote the atom& 39;s position. (iii)Atoms exocyclic to the ring systems have the same position identifier as the atom to which they are bonded except if this would result in identical atom names. In this case an alphabetic character is used to avoid ambiguity. (iv)The ring-oxygen atom of the ribose is denoted O4 rather than O1. (v)The extra oxygen atom at the free 5& 39; phosphate terminus is designated OXT. This atom will be placed first in the coordinate set. For nucleotides which are simple derivatives (e.g., methyl or acetyl) of the parent nucleotide the modifying atoms or groups occur immediately after the atom to which they are bonded. In the case of an acetyl modifier, the three atoms are ordered carbonyl carbon, carbonyl oxygen, methyl car- bon. C.Non-Standard (HET) Groups Because of the repeated occurrence of certain cofactors, prosthetic groups, etc., the almost com- plete lack of uniformity in the nomenclature assigned by depositors, and in the absence of any authoritative precedent, the Data Bank has assigned a standard nomenclature and ordering of the atoms in some of these groups. These assignments appear on the subsequent pages, for the fol- lowing groups: page ATP ....................................................................................30 Coenzyme A ......................................................................31 Flavin mononucleotide (FMN) ..........................................32 Heme ..................................................................................33 Methotrexate ......................................................................34 NAD ...................................................................................35