Atoms citation sequence

If two or more kinds of a terms occur in the same name, their order of citation is by descending group number of the Periodic Table and increasing atomic number in the group as illustrated by the sequence in Table I. 

Figure 4.10. PDB file (partial) for 3D structure of hen s egg-white lysozyme (ILYZ.pdb). The abbreviated file shows partial atomic coordinates for residues 34-36. Informational lines such as AUTHOR (contributing authors of the 3D structure), REVDAT, JRNL (primary bibliographic citation), REMARK (other references, corrections, refinements, resolution and missing residues in the structure), SEQRES (amino acid sequence), FTNOTE (list of possible hydrogen bonds), HELIX (initial and final residues of a-helices), SHEET (initial and final residues of / -sheets), TURN (initial and final residues of turns, types of turns), and SSBOND (disulfide linkages) are deleted here for brevity. Atomic coordinates for amino acid residues are listed sequentially on ATOM lines. The following HETATM lines list atomic coordinates of water and/or ligand molecules.

Chain hydrides with a backbone of alternating atoms of two elements A and E, neither of which is carbon, i.e. of sequences (AE) A, where element A occurs later in the sequence of Table VI, can be named by successive citation of the following name parts ... 

Determination of the head atom, and subunit citation order, is as follows O is senior to S, and S is senior to N therefore, one of the two oxygen atoms must be the head atom. The SRU must therefore be either row A, atoms 1 to 12, or row B, atoms 1 to 12. The row A sequence places the N atom in position 6, whereas the row B sequence places it in position 5 the latter is therefore correct, and the final SRU is -(-0-C-0-C-NH-C-C-S-C-NH-C-C-) -... 

For a sequence of more than four asymmetric carbon atoms, two or more prefixes are used. The sequence of asymmetric carbon atoms is divided so that there is a four-carbon prefix for the carbon atoms closest to the principal function, and so that the other prefixes contain the maximal possible number of asymmetric carbon atoms. In the actual name, the order of citation of the prefixes is to start with the grouping furthest removed from the principal function. The most common examples of compounds requiring this type of compound prefixes are the sugars and glycitols with seven or more carbon atoms, two examples of which are given in the accompanying formulas. 

The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. Annotations in the structure entries include amino acid or nucleotide sequences (with notes of any conflicts between the structure in the PDB and sequence databases), source organism from which the biological material was derived, references to papers, secondary structure, complexes with small molecules included within the structure, etc. Third party annotations include images and movies of structures, pointers to other databases which contain information on the structural class or family of the particular structure pointers to particular specialized databases (maintained by others) such as the kinase , esther , or obsolete entries databases, and those that provide additional experimental information such as NMR and other solution data, abstracts of articles, etc. 

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