Molecular sites

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 188-189

Section 3.6.7.5.8. Molecular sites

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^a Merck Research Laboratories, Rahway, New Jersey, USA,^bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,^cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,^dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,^eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and ^fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.7.5.8. Molecular sites

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The data items in these categories are as follows:

(a) STRUCT_SITE [Scheme scheme174]

(b) STRUCT_SITE_KEYWORDS [Scheme scheme175]

(d) STRUCT_SITE_VIEW [Scheme scheme177]

The bullet ( $[\bullet]$ ) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ( $[\rightarrow]$ ) is a reference to a parent data item.

Substrate-binding sites, active sites, metal coordination sites and any other sites of interest may be described using data items in a collection of categories descending from STRUCT_SITE. These categories are intended to enable the author to generate views of molecular sites that could be used as figures in a report describing the structure or to enable a database to store standard views of common molecular sites (e.g. ATP-binding sites or the coordination of a calcium atom). The relationships between categories used to describe structural sites are shown in Fig. 3.6.7.16.

Figure 3.6.7.16 | top | pdf |

The family of categories used to describe molecular sites. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ( $[\bullet]$ ). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

An identifier for each site that an author wishes to describe is given using _struct_site.id and the site can be described using _struct_site.details.

Keywords can be given for each site using data items in the STRUCT_SITE_KEYWORD category. Because keywords can be given at many levels of the mmCIF description of a structure, it may be worth duplicating the most significant higher-level keywords at this level to ensure that the site is detected in all search strategies.

The structural elements that generate each molecular site can be specified using data items in the STRUCT_SITE_GEN category. `Structural elements' in this sense may be at any level of detail in the structure: single atoms, complete amino acids or nucleotides, or elements of secondary, tertiary or quaternary structure. Therefore the labels for each element may include, as required, the relevant *_alt, *_asym, *_atom, *_comp or *_seq parts of atom or residue identifiers. If the author has used an alternative labelling scheme, this can also be used. Noteworthy features of a structural element that forms part of the site can be described using the data item _struct_site_gen.details. Any crystallographic symmetry operations that are needed to form the site can be given using _struct_site_gen.symmetry.

Data items in the STRUCT_SITE_VIEW category allow the author to specify an orientation of the molecular site that gives a useful view of the components. The comments given in _struct_site_view.details could be used as a figure caption if the view is intended for use as a figure in a report.

Example 3.6.7.15 illustrates the use of these categories for describing a DNA binding site.

Example 3.6.7.15. A DNA binding site with an intercalated drug (NDB DDF040) described with data items in the STRUCT_SITE, STRUCT_SITE_KEYWORDS, STRUCT_SITE_GEN and STRUCT_SITE_VIEW categories.

[Scheme scheme178]

References

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 188-189