Structure, three-dimensional torsional angles

II has a two-dimensional structure with an asymmetric unit of 16.75 non-hydrogen atoms (Figure 5a). The Pb2+ cations are in three crystallographically distinct positions with Pb(l) and Pb(3) landing with 0.5 occupancies in 4fand 4h special positions, respectively, and Pb(2) with a full occupancy. One CHDC anion, one-quarter of the oxalate anion (with C at 4h), one hydroxyl anion (with the O at 4/), one independent oxo dianion (at 4/), and one-quarter of a lattice water molecule (at 2a) are also in the asymmetric unit. Three of the four anions are shown in Figure lc—e. The CHDC anion in the anti, e,e conformation with a torsional angle of 176.74(2)° has (2223) connectivity and binds to six Pb2+ cations [three Pb(2) and three Pb(3)]. The oxalate anion has (2222) connectivity and binds to six Pb2+ cations [two Pb-... 

One could completely describe the three-dimensional structure of a protein by placing it in a Cartesian coordinate system and listing (x, y, z) coordinates for each atom in the protein. Indeed, this is how experimentally determined protein structures are stored in the Protein Data Bank at the Brookhaven National Laboratory in the United States of America. However, the structure of a protein can be more succinctly described by listing the angles of rotation (torsion angles) of each of the bonds in the protein (see Fig. 4-4). For example, the backbone conformation of an amino acid residue can be specified by listing the torsion angles (rotation around the N—Ca bond), (rotation around the Ca—C bond), and ca (rotation around the N—C bond). 

The zero position for is defined with the —N—H group trans to the Ca—C bond, and for l> with the Ca—N bond trans to the —C=0 bond (Fig. 4-4). The peptide-bond torsion angle (ca) is generally 180° (see Example 4.10). A full description of the three-dimensional structure of a protein also requires a knowledge of the side-chain x torsion angles. 

What is the best way to describe the overall shape of a molecule Typically, in a journal article describing a crystal structure, there are lists of bond distances, interbond angles, and torsion angles, which describe the three-dimensional structure. Of these parameters, the torsion angles are the most used in a description of the overall shape of a molecule. " In this Chapter we will describe some basic principles that have resulted from measurements of torsion angles. We aim to show how X-ray crystallographic results provide clear illustrations of molecular shapes. 

The three-dimensional steric disposition of the flexible acetylcholine molecule and those of its congeners can be defined on the basis of torsion angle t. Summations and definitions of nomenclature incident to use of torsion angles are found in refs. 257 and 258. Structure (220) defines relevant torsion angles in the acetylcholine molecule. 

Three-Dimensional Quantitative Structure-Activity Relationship Approaches An early study by Seidel et al. showed that a certain 3D feature, such as a torsion angle, can be used to help explain calcium channel activity of a series of DHPs [123], For a set of rigid analogues of nifedipine, their calcium channel affinities (log A)) were correlated with the deviation from 90° of the torsion angle between the two rings (Aa) ... 

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