MetalPDB Glossary
CATH

Site classification based on mapping endogenous ligands belonging to a polypeptide chain onto the CATH database. CATH is a hierarchical classification of protein domain structures, which are grouped at four major levels: Class(C), Architecture(A), Topology(T) and Homologous superfamily (H). H identifiers are written as four numbers separated by periods (e.g., 3.10.200.10). The distinct H identifiers assigned to the ligands (i.e., the distinct protein domains to which the ligands belong) are used to designate sites (e.g., if the ligands of a site are all located in the same CATH domain whose identifier is 3.10.200.10, that site is classified as 3.10.200.10).

Coordination geometry

The geometrical arrangement of the atoms bound to a metal atom. It is described on the basis of the nearest idealized geometry as determined by the FindGeo program. Depending on the degree of matching with the nearest idealized geometry, the coordination geometry can be tagged as regular, distorted, or irregular.

Coordination number

The number of atoms to which a metal atom is bound.

Coordination sphere

The set of ligands for a metal atom.

EC number

Enzyme Commission (EC) numbers associated with all the polypeptide chains that bind at least one metal atom in the site. EC numbers are written as four numbers separated by periods (e.g., 4.2.1.1), and specify enzyme-catalyzed reactions following a hierarchical classification determined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB).

Endogenous ligand

A ligand which belongs to a polypeptide or a polynucleotide chain (i.e., an amino acid or a nucleotide residue).

Equistructural sites

Two sites are equistructural if (i) they are found in PDB chains with the same structure (this is assumed to be true when the two sites fall into the same Pfam domain or when the sequence identity between the two PDB chains is >= 50%), and (ii) after structural superposition of the PDB chains that contain them, they are superimposed (i.e., their geometric centers are at a distance < 3.5 A from each other). At variance with equivalent sites, equistructural sites can differ from each other for the nuclearity and/or for the chemical identity of the metal atoms. For example, equistructural sites can be found in two different PDB structures of the same macromolecule, in one of which the physiological metal has been substituted by another metal. All equistructural sites are grouped into clusters of equistructural sites. Note that if two sites are equivalent, then they are also equistructural, but the converse is not necessarily true.

Equivalent sites

Two sites are equivalent if (i) they are found in PDB chains with the same structure (this is assumed to be true when any the two sites fall into the same Pfam domain or when the sequence identity between the two PDB chains is >= 50%), and, after structural superposition of the PDB chains that contain them, they (ii) are superimposed (i.e., their geometric centers are at a distance < 3.5 A from each other) and (iii) have the same metal atoms in the same positions. Condition (iii) does not hold for equistructural sites. For condition (iii) to be fulfilled, equivalent sites must have the same nuclearity. Equivalent sites can be found in different PDB structures of the same macromolecule, or in different but structurally identical PDB chains of the same PDB structure. All equivalent sites are grouped into clusters of equivalent sites. Note that if two sites are equivalent, then they are also equistructural, but the converse is not necessarily true.

Exogenous ligand

A ligand which does not belong to a polypeptide or a polynucleotide chain (e.g., water, acetate, etc.). Exogenous ligands include organic cofactors such as heme and molybdopterin, as well as inorganic species such as sulfide in iron-sulfur clusters.

H-bond

A hydrogen bond formed by a ligand with any of its neighbours. Hydrogen bonds are attractive interactions formed by a hydrogen atom bound to an electronegative atom with another electronegative atom. When the ligand and the neighbour are both amino acid residues, hydrogen bonds are classified as main chain-main chain, main chain-side chain or side chain-side chain depending on whether the atoms involved in the interaction are from the backbone (amide and carbonyl groups) or from the side chain. Hydrogen bonds are identified by the HBPLUS program.

Ligand

A chemical species that binds at least one metal atom in the site by one or more of its atoms. Any non-hydrogen atom at a distance < 3.0 A from a metal atom is considered to be bound to that metal atom. Individual amino acid residues in polypeptide chains and individual nucleotide residues in polynucleotide chains are considered to be distinct ligands.

Location

Site classification based on whether the endogenous ligands all belong to a single PDB chain, or belong to at least two different PDB chains. The site is classified as within a chain in the former case, and as interface in the latter.

Neighbour

An amino acid or nucleotide residue in spaxial proximity of a ligand. Any amino acid or nucleotide residue having a non-hydrogen atom at a distance < 5.0 A from a ligand is considered to be a neighbour of that ligand.

Nuclearity

The number of metal atoms in the site. All sites are classified as mononuclear, dinuclear, trinuclear, etc. if they contain one, two, three, etc. metal atoms. Any two metal atoms which (i) are at a distance < 5.0 A from each other or (ii) have a ligand in common belong to the same site.

Organism name

Source organisms of all the polypeptide (not polynucleotide) chains that bind at least one metal atom in the site. Source: UniProt taxonomy.

PDB Chain

All the polypeptide and/or polynucleotide chains that bind at least one metal atom in the site. Identifier: [PDB ID]_[Chain ID] (e.g., 1ca2_A).

PFAM

Site classification based on mapping endogenous ligands belonging to a polypeptide chain onto the Pfam database. Pfam is a large collection of protein domain families, which are represented by multiple sequence alignments and hidden Markov models (HMMs). Domain family identifiers are written as PF followed by five digits (e.g., PF00194). The distinct domain family identifiers assigned to the ligands (i.e., the distinct protein domains to which the ligands belong) are used to designate sites (e.g., if the ligands of a site are all located in the same Pfam domain whose identifier is PF00194, that site is classified as PF00194).

Protein name

Recommended names of all the polypeptide (not polynucleotide) chains that bind at least one metal atom in the site. Source: UniProt.

Representative site

A site selected to represent a cluster of equivalent sites. The selection is done by choosing the PDB structure with the best X-ray resolution among those containing the sites in the cluster. NMR structures are generally discarded in favor of X-ray structures, unless all the sites in the cluster are found in NMR structures.

Salt bridge

A salt bridge formed by a ligand with any of its neighbours. Salt bridges are close-range electrostatic interactions formed by spatially proximal pairs of oppositely charged amino acid residues in protein structures.

SCOP

Site classification based on mapping endogenous ligands belonging to a polypeptide chain onto the SCOP database. SCOP is a hierarchical classification of protein domain structures, which are grouped at four major levels: Class, Fold, Superfamily and Family. Family identifiers are written as one letter and three numbers separated by periods (e.g., b.74.1.1). The distinct family identifiers assigned to the ligands (i.e., the distinct protein domains to which the ligands belong) are used to designate sites (e.g., if the ligands of a site are all located in the same SCOP domain whose identifier is b.74.1.1, that site is classified as b.74.1.1).

Site

Region of the structure of a biological macromolecule that consists of (i) one or more metal atoms, (ii) the ligands (endogenous and exogenous) of the metal atoms, and (iii) the neighbours of the ligands. Any two metal atoms which (i) are at a distance < 5.0 A from each other or (ii) have a ligand in common belong to the same site. Identifier: [PDB ID]_[Site number] (e.g., 1ca2_1).

UniProt

UniProt ID's of all the polypeptide (not polynucleotide) chains that bind at least one metal atom in the site. Source: UniProt.

vdW

A nonspecific interaction formed by a ligand with any of its neighbours. Any two non-hydrogen atoms from a ligand and one of its neighbours that are at a distance < 5.0 A are considered to be involved in a nonspecific interaction.