Structural elements, coloration

Figure 17.3 Anatomy of a redox enzyme representation of the X-ray crystallographic structure of Trametes versicolor laccase III (PDB file IKYA) [Bertrand et al., 2002]. The protein is represented in green lines and the Cu atoms are shown as gold spheres. Sugar moieties attached to the surface of the protein are shown in red. A molecule of 2,5-xyhdine that co-crystallized with the protein (shown in stick form in elemental colors) is thought to occupy the broad-specificity hydrophobic binding pocket where organic substrates ate oxidized by the enzyme. Electrons from substrate oxidation are passed to the mononuclear blue Cu center and then to the trinuclear Cu active site where O2 is reduced to H2O. (See color insert.)...

Hydrogen bonds are important structural elements of organic pigments in-tramolecularly, they enforce planarity in a molecule intermolecularly, they may even play a role in determining the basic color of a pigment. 

Fig. 10.15. Structure of the DegP hexamer. ball-and-stick model. The nomenclature of Ribbon presentation of the monomer, in which secondary structure elements, the termini of the individual domains are colored differently. the protein and regions that were not defined Residues of the catalytic triad are shown in a by electron density are indicated.

Fig. 10.16. Properties of the inner cavity. Half cut presentations of molecule A (left side view, center and right top views) with cut regions shown in dark gray. (Left) Surface representation of the internal tunnel illustrating its molecular-sieve character. Access is restricted to single secondary structure elements as shown by the modeled polyalanine helix, which is colored yellow. (Center) Top view on the...

Fig. 5. Three views of the NCP from Harp et al. [31]. (a) Ventral surface view, (b) Side view, (c) View down the molecular pseudo-dyad axis. The histones are represented by Ca ribbon models of the secondary structure elements, and the DNA model indicates the base pairing between complementary strands. The DNA is positioned asymmetrically by one-half base pair on the NCP. This results in a two sides arbitrarily referred to a dorsal and ventral (the surface shown here). The ventral surface of the NCP is best recognized by the extended N-terminal H3 tail protruding to the right. In these images, the pseudo-dyad axis is represented by vertical bars for both the ventral and side view. The pseudo-dyad axis passes through the center of the dyad view orthogonal to the plane of the page, (d) Color code for histone chains in the figures in this chapter. Note the change in hue denoting the two sides of the histone octamer.

The X-ray crystal structure of the benzhydroxamic acid complex of resting state HRP C has been solved to 2.0 A resolution 196). Important structural elements of the binding site are illustrated in Fig. 9 (see color insert). The donor molecule is located on the distal side of the heme plane and makes both hydrogen-bonded and hydrophobic interactions with the enzyme. Arg38, His42, Pro 139, and a distal water molecule located 2.6 A above heme iron contribute to an extensive hydrogen bond... 

Clinically used local anesthetics are either esters or amides. This structural element is unimportant for efficacy even drugs containing a methylene bridge, such as chlorpromazine (p. 236) or imipramine (p. 230), would exert a local anesthetic effect with appropriate application. Ester-type local anesthetics are subject to inactivation by tissue es-Ltillmann, Color Atlas of Pharmacology... 

HDAC7 in complex with TSA (PDB code 3C10) and (d) class lla human HDAC4 in complex with an hydroxamic acid inhibitor (PDB code 2vqm). The proteins are colored according to secondary structure elements, the catalytic Zn ions are shown as cyan spheres, the class lla-speciflc structural Zn ions as orange spheres and the structural l< ions as magenta spheres. 

Physical properties of solid materials which are greatly influenced by the presence of defects of lattice order in real single crystals are called structural-sensitive properties, and are distinguished from intrinsic properties, which are determined by the elements constituting the crystal, for example the chemical bonds, the structure, etc. Color, plasticity, glide, and semiconductor properties are structural-sensitive properties, whereas density, hardness, elasticity, and optical, thermal, and magnetic properties are the intrinsic properties. Structural-sensitive... 

With the introduction of the lattice structure and electroneutrality condition, one has to define two elementary SE units which do not refer to chemical species. These elementary units are l) the empty lattice site (vacancy) and 2) the elementary electrical charge. Both are definite (statistical) entities of their own in the lattice reference system and have to be taken into account in constructing the partition function of the crystal. Structure elements do not exist outside the crystal and thus do not have real chemical potentials. For example, vacancies do not possess a vapor pressure. Nevertheless, vacancies and other SE s of a crystal can, in principle, be seen , for example, as color centers through spectroscopic observations or otherwise. The electrical charges can be detected by electrical conductivity. 

To merge. kin files, select Append File tool of the File menu and open the hie to merge. To change default color, invoke Change Color tool of the Edit menu and click the structure element to open Color selection box from which the desired color can be assigned. Different structure views are created/added to the. kin hie by selecting Keep Current View tool of the Edit menu and entering View number and... 

Fig. 15 Ribbon diagrams of tubulin in complex with MT-stabilizing drugs as determined by EC or NMR. Left PTX/tubulin determined by EC (PDB entry 1JFF [83]). Center EpoA/tubulin determined by EC (PDB entry 1TVK [26]). Right EpoA/tubulin determined by solution NMR [76]. Drug molecules are represented as stick models (C red, O blue, N green, S yellow). Some secondary structure elements of tubulin are colored helix H7 (yellow), M loop (green), S9-S10 loop (blue). The side chain of His227 is depicted as cyan sticks...

Fig. 30 Taxoid site on (3-tubulin and predicted peloruside site on a-tubulin. a Surface representation (view from the inner side of the microtubule) of a tubulin dimer with FIX (red) bound to P-tubulin (green) and peloruside A (orange) bound to the predicted site in a-tubulin (blue), b View of the peloruside binding site. Hydrogen bonds are represented as yellow dashed lines, and the residues involved in these bonds are labeled. Some secondary structure elements are also labeled, c View of the taxol binding site. Some secondary structure elements are labeled. In panels b and c, H7 is colored in orange, and the N-terminal and intermediate domains are colored in green and blue, respectively. (Reprinted with permission from [17]. Copyright 2006 American Chemical Society)...

Fig. 3 Structural changes of tubulin subunits upon MT disassembly, a Structure of a 3 subunit of the T2R complex (pdb id 1SA0 [15]). The monomer is sub-divided in an N-terminal domain (blue) with bound GDP (ball-and-stick drawing, grey), the central helix H7 yellow), an intermediate domain green), and the C-terminal helices red), b Comparison of the 3 subunit conformation in the T2R complex (same color code as in a) and in a straight protofilament (nucleotide binding domain and C-terminal helix hairpin in cyan, H7 helix in salmon, intermediate domain in pink, pdb id 1JFF [70]) after superposition of the secondary structural elements of their N-terminal domain, c Schematic representation recapitulating the movements between straight and curved tubulin monomers (domains are color-coded as in a the nucleotide is depicted as a red sphere)...

Fig. 4 Left, location of the vinblastine and colchicine binding sites in tubulin (1Z2B structure), a- and (3-tubulin are represented as yellow and magenta ribbons, respectively vinblastine and DAMA-colchicine are represented as green and cyan spheres, respectively GTP and GDP are represented as pink sticks. Vinblastine binds at the interdimer interface, whereas colchicine binds at the intradimer interface. Right, zoom on the vinblastine binding site. Secondary structure elements contacting vinblastine are colored blue...

Several color reactions form the basis for both the detection and estimation of specific structural elements in lignin. For example, coniferyl alcohol-type units (8) ultimately may be transformed to the reddish purple chromophore (10) through the series of reactions outlined below (Lindgren and Mikawa 1957). 

F . 2.1 Stereo ribbon diagram of human CDK2 with bound ATP (IHCK.PDB). Structural elements are colored as follows, glycine-rich loop in dark blue, N-terminal beta sheet... 

Therefore, a substantial portion of the secondary structure elements can be readily identified in 3-D maps calculated to 6- to 8-A resolution by interactive visual inspection of the density volume, using 3-D volumerendering techniques (Fig. 9 see Color Insert). Examination of the density range distribution can also be used as a means to verify secondary structure elements identified on the basis of shaded surface representations. For example, the gray density displays of density sections extracted from a 3-D volume are often useful to verify the assignment based on information such as the relative densities of the identified a helices and (3... 

For more complex structures, it is possible to combine electron cryomicroscopy structures with sequence-based secondary structure predictions to interpret the observed secondary structure elements. In the outer shell protein P8 of rice dwarf virus (RDV), where nine helices were predicted in the domain formed by the N and C termini, it was possible to match the lengths of the helices identified in the 3-D density map to those predicted from a consensus secondary structure analyses (Fig. 13a see Color Insert). The connections between the helical densities can be seen in the lower domain of P8, allowing us to establish a rough backbone model for the lower domain of P8 (Zhou et at, 2001). 

Chapman and Liljas, Fig. 12. The shell-forming proteins of bluetongue virus and reovirus (a) bluetongue VPS protein (Grimes et al, 1998) (b) reovirus 11 protein (Reinisch et al., 2000). In the bluetongue VPS protein, three domains (apical, carapace, and dimerization domains) have been identified. The secondary structure elements have been colored to emphasize the general structural similarity between the two proteins. 

FIGURE 16.5 (See color insert following page 588.) Diagram showing the structural elements of a responsive sol/gel release system. 

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