Stereoscopic viewing

Figure Al.6.26. Stereoscopic view of ground- and excited-state potential energy surfaces for a model collinear ABC system with the masses of HHD. The ground-state surface has a minimum, corresponding to the stable ABC molecule. This minimum is separated by saddle points from two distmct exit chaimels, one leading to AB + C the other to A + BC. The object is to use optical excitation and stimulated emission between the two surfaces to steer the wavepacket selectively out of one of the exit chaimels (reprinted from [54]).

Fig. 13. Stereoscopic view of the packing arrangement of the four la molecules 37>. The thin lines indicate hydrogen bonds...

Figure 15 shows a stereoscopic view of the crystalline 1 1 complex where R7 = i-CsHn and R8 = (CH2)2Ph 9). The packing mode of the four molecules in the unit cell of this complex corresponds to the association scheme of tetramer 17 (Fig. 8). Of particular interest is that a pair of groups with similar geometrical shape, NMe2 and CHMe2 [part of C6H4NMe2 and (CH2)2CHMe2], are in close contact.

Fig. 12. Stereoscopic view and crystal packing of compound (82)B 57). (taken from Ref.57) with permission)...

Fig. 13. Stereoscopic view of methylphenyltrityltin bromide (S3)90,91, and of the crystal packing of compound (S3)91)...

Fig. 1. Stereoscopic view of the two reacting molecules of Ham the crystalline host-guest complex 12a...

Figure 6.8 Stereoscopic view of the dimeric building block of bacterioferritin (a) twofold axis horizontal (b) twofold axis approximately normal to the page. The protein is represented by a blue a-carbon trace, the haem by a stick model (pink) and the dinuclear metal site by dotted spheres (orange and yellow). From Frolow et ah, 1994. Reproduced by permission of Nature Publishing Group.

Fig. 8.5 Capsaicin accumulates in blisters/vesicles on surface of placenta, left panel) Total ion chromatogram of oil in habanero vesicle. The oil in the vesicle was collected directly with a Hamilton syringe, diluted with hexane, and analyzed on a varian GC-MS, DB-5 column. The capsaicin peak was identified based on match with NIST MS library, right upper panel) A stereoscope view of habanero placenta (5x magnification) and seeds are visible upper left panel). Arrows indicate blisters, right lower panel) A scanning electron micrograph of habanero placenta (40 X magnification). A color version of the image is on line...

Fig. 4. Stereoscopic views of the (top pair) A and (bottom pair) A isomers of Co(III) mimochrome I complex structure as determined by NMR spectroscopy. Reprinted with permission from Ref (118) copyright 1997 Wiley-VCH. 

Fig. 7. Stereoscopic view of the apo-maquette monomer, (a -SS-a ), solution structure. A superposition of the best solution structures derived from the NMR data is shown with the hydrophobic core facing the viewer. Reprinted with permission from Ref (20). Copyright 1999 American Chemical Society.

Figures 1,2, and 3 show stereoscopic views of their crystal packing. It is clearly seen that the exo-bicyclo [2.2.1] anhydride 1 has a hardly interlocked monolayer structure and so does the endo isomer 2 except for slight interpenetrations. These structural features facilitate molecular migrations upon chemical reaction, whereas the bicyclo[2.2.2] anhydride 3 exhibits strong interlocking, preventing molecular migrations.

Figure 2.4 Stereoscopic view of the unit cell of (Ph4P )2(Qo )(l ), [78. Iodide anions at the corners of the unit cell have been omitted for clarity.

Figure 2. Stereoscopic view of the four Mo2( 5-CsH5)2(CO)4-(m2-H)(m2-P(CH3)2) molecules in the triclinic unit cell of symmetry Cl...

Figure 8. A stereoscopic view of the packing in the inclusion compound of 1,1,6,6-tetraphenylhexa-2,4-dyne-1,6-diol, 2, with (a) chalcone and (b) 9-anthraldehyde. 9-Anthraldehyde gives cage-type and chalcone gives channel-type structures. [Reproduced with permission from F. Toda, Topics Curr. Chem. 140, 43 (1987).]...

Figure 2-13 (A) Stereoscopic view of the nucleotide binding domain of glyceraldehyde phosphate dehydrogenase. The enzyme is from Bacillus stearothermophilus but is homologous to the enzyme from animal sources. Residues are numbered 0-148. In this wire model all of the main chain C, O, and N atoms are shown but side chains have been omitted. The large central twisted P sheet, with strands roughly perpendicular to the page, is seen clearly hydrogen bonds are indicated by dashed lines. Helices are visible on both sides of the sheet. The coenzyme NAD+ is bound at the end of the P sheet toward the viewer. Note that the two phosphate groups in the center of the NAD+ are H-bonded to the N terminus of the helix beginning with RIO. From Skarzynski et al.llla (B) Structural formula for NAD+.

Figure 2-28 The eight-fold oc/(3 barrel structure of triose phosphate isomerase. From Richardson. (A) Stereoscopic view. (B) Ribbon drawing. Courtesy of Jane Richardson.117...

Figure 3-22 Stereoscopic view of a section of the structure of cutinase from the fungus Fusarium solani determined to a resolution of 0.10 nm. The three amino acid residues shown are serine 120 (top), histidine 188, and aspartate 175 (lower left). The structure is presented as a contour map with a "wire mesh" drawn at a "cutoff" level of density equal to 1 a above the average, where a is the root mean square density of the entire map. The side chains of these three residues constitute the "catalytic triad" in the active site of this enzyme (see Chapter 12). At this resolution more than one conformation of a group may often be seen. For example, the gamma oxygen (OG) of S120 is seen in two positions, the major one being toward His 188. When the map is drawn with a lower contour level the N-H proton on His 188 that is hydrogen bonded to Asp 175 can also be seen.410 Courtesy of Christian Cambillau.

In the fifth step of an X-ray structure determination the electron density map is calculated using the intensities and phase information. This map can be thought of as a true three-dimensional image of the molecule revealed by the X-ray microscope. It is usually displayed as a stereoscopic view on a computer graphics system (Fig. 3-22). It is also often prepared in the form of a series of transparencies mounted on plastic sheets. Each sheet represents a layer, perhaps 0.1 ran thick, with contour lines representing different levels of electron density. 

Figure 4-18 (A) Stereoscopic view of the interactions between the E. coli galactose chemoreceptor protein and a hound molecule of D-glucose. (B) Schematic drawing showing many of these interactions and the state of ionization deduced for the aspartate and arginine side chains. From Vyas et al.m...

Figure 4-21 Stereoscopic view of an N-linked oligosaccharide whose structure has been deduced by two-dimensional NMR spectroscopy and energy calculations. This is one of a range of allowed conformations. From Homans et al.257...

Figure 5-27 Stereoscopic view of a four-stranded intercalated DNA or I-DNA formed from d(C4). Two parallel duplexes with C CH+ pairs are intercalated into each other. From Chen et al.280...

Figure 5-32 (A) A three-dimensional computer graphics model proposed by Brimacombe et a/.3 11 for the single chain of E. coli 16S ribosomal RNA. The helices are depicted as cylinders, which are all connected. The small dark squares denote the positions of artificially formed RNA-protein crosslinks, marked with the appropriate protein number. For proteins exhibiting more than one crosslink site (e.g., SI7), the sites are denoted A or B, in each case A being the site nearer to the 5 terminus of the 16S RNA. (B) Stereoscopic view of tentative atomic model of 16S RNA in the 30S ribosomal subunit. The viewing direction is different from that in (A). From Mueller and Brimacombe.342 Courtesy of Richard Brimacombe.

Figure 5-38 (A) Sketch of a complex of a five-zinc finger protein bound to a high-affinity site in DNA. This protein is a human oncogene called GL1. Its gene is amplified in many tumors, but it is similar to many other transcription factors. The cylinders and ribbons highlight the a helices and P sheets. Cobalt ions, which replaced the Zn2+ in the crystals, are shown as spheres. (B) Stereoscopic view of the complex in a similar orientation.

C) Stereoscopic view emphasizing the contacts of side chains from fingers 5 and 6 with the DNA. The view is similar to that in (A) and (B) but the structure has been tilted back. Drawings courtesy of Nikola Pavletich.427... 

Figure 7-5 Stereoscopic view of the B5 pentamer of cholera toxin B. The pentamer, known as choleragenoid, has a central hole of 1.5 nm diameter into which a helix from the A subunit is inserted. As viewed here, the front surface of the pentamer has binding sites for the oligosaccharide chains of ganglioside CM, which serves as the toxin receptor. The back side binds the A subunit. See also Box 11-A. From Zhang et al,31...

Figure 7-15 (A) Schematic diagram of the icosahedral shell of a human rhinovirus showing the arrangement of the three subunits VP1, VP2, and VP3, each present as 60 copies. (B) Stereoscopic view of an image of the virus "decorated" by the binding of two immunoglobulinlike domains of the intercellular adhesion molecule ICAM-1, a natural receptor for the virus.

Figure 7-28 (A) Stereoscopic view of the (])X174 114 S mature virion viewed down a twofold axis after a cryoelec-tron microscopy reconstruction. From McKenna et al.225 (B) Morphogenesis of < )X174 (based on a report of Hayashi etal.231). Proteins A and C are required for DNA synthesis. Drawing from McKenna et al.225 Courtesy of Michael G. Rossmann.

Figure 8-21 Views of the tetrameric K+ channel from Streptococcus lividans. (A) Ribbon representation as an integral membrane protein. Aromatic amino acids on the membrane-facing surface are also shown. (B) Stereoscopic view. (C) Stereoscopic view perpendicular to that in (B) with a K+ ion in the center. From Doyle et al.366...

Figure 8-24 (A) MolScript ribbon drawing of the periplasmic histidine-binding protein HisJ, a component of an ABC transporter system of Salmonella. The bound L-histidine is shown as a ball-and-stick model. (B) Stereoscopic view of the histidinebinding site showing hydrogen-bonding interactions of protein side chains with the histidine. From Oh et al.i60 Courtesy of Giovanna Ferro-Luzzi Ames.

Figure 12-5 (A) Stereoscopic view of the structure of the catalytic site of phosphorylase b in the inhibited T-state with the inhibitor nojirimycin tetra-zole bound into the active site. Inorganic phosphate (P ) as well as the coenzyme pyridoxal 5 -phosphate (PLP) are also shown. (B) Details of interactions of the inhibitor, P , and PLP with the protein and with water molecules (small circles). This is a weak-binding state but the P has displaced the negatively charged side chain carboxylate of Asp 283 (visible at the lower right in A).

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