Figure 3

Examples of identified structural motifs. Nine different structural motifs with their ligands are shown. Only the residues comprising the motif and their ligands are shown in the picture. All the atoms are coloured by type. Carbon atoms of the ligands are in white and carbon atoms of the protein are in light purple. (A) Zinc binding motif (id 112) involving six folds all using three cysteine residues to bind a ZN atom. (B) Ribose binding element (id 11) using a T-[AS]-G motif to interact with the O4 of ribose in two nucleotide-like ligands. (C) Ribose binding motif (id 472) using a phenylalanine and two threonine residues to interact with ribose in two different nucleotides. The two ribose fragments are coplanar but lay in opposite orientations. (D) Mannose binding motif (id 378) comprising two collinear residues G-[DE] and a third aspartic acid residue in position +4 in a fold and -134 in the other. (E) A Flavin binding motif (id 426). Residues A-P-X-[AS] interact mainly with the central ring of the two flavin mononucleotides. The two molecules are coplanar but have different orientations. (F) A motif interacting with pyrimidine ring derivatives (id 429); residues A-X(n)-[SA]-[IV] interact in one case with the flavin and in the other with a flavin precursor. (G) Nucleobase binding motif (id 634). Four different folds share the three residue motif [AS]-[DEN]-[IV] that makes hydrogen bond contacts with the pyrimidine ring of four different purines. (H) Phosphate binding motif (id 31) present in six different folds possessing the G-[STA]-[IVL] pattern. The interacting fragment is a phosphate group coming from a variety of ligands. (I) Phosphate binding motif (id 398): two aspartic acids and a leucine or isoleucine residues interact with the oxygen atoms of different phosphate groups in three different folds. In a fourth fold a slightly different motif interacts with an oxygen atom of a β-D-xylopyranose molecule.