In the area of protein structural motifs, niches are three or four amino acid residue features in which main-chain CO groups are bridged by positively charged or δ+ groups. The δ+ groups include groups with two hydrogen bond donor atoms such as NH2 groups and water molecules. In typical proteins, 7% of amino acid residues belong to niches bound to a δ+ group, while another 7% have the conformation but no single cationic bridging group is detected.
Niches are of two kinds, distinguished as niche3 (3 residues, i to i+2) and niche4 (4 residues, i to i+3). In a niche3 motif the δ+-binding carbonyl group is from residues i and i+2 while in a niche4 motif it is from residues i and i+3.
A niche3 has the α conformation for residue i+1 and the β conformation for residue i+2; a niche4 has the α conformation for residues i+1 and i+2 and the β conformation for residue i+3.
A niche occurs commonly at the C-terminus of α-helices especially of 310 helices.
Metal ions that occur bound to niches in proteins are Na+, K+, Ca++ and Mg++. Proteins with regulatory cations often employ niches for metal binding (thrombin, Na+; annexin, Ca++; pyruvate dehydrogenase, K+).
A major cation transporter in cells is calcium ATPase. In the Ca++-bound crystal structures the two calcium ions side-by-side within the transmembrane domain are thought to be at the halfway stage of being transported. As well as being bound by various side chain carbonyl groups, one of these calcium ions is bound by a niche3/niche4 (both in the one motif) at residues 304–307 at the C-terminus of an α-helix.
Another small tripeptide motif that binds cations or δ+ groups via main-chain CO groups is called the catgrip.