Three-dimensional structures, drawing

Label all the bond angles in yonr three-dimensional structure. Draw a bond-line formnla for the compound. 

Fischer projection A method of representing three-dimensional structures in two-dimensional drawings in which the chiral atom(s) lies in the plane of the paper. The two enantiomeric forms of glyceraldehyde are represented as... 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

A synthesis of the important biosynthetic intermediate mevalonic acid starts with the enzymatic hydrolysis of the diester A by pig liver esterase. The pro-R group is selectively hydrolyzed. Draw a three-dimensional structure of the product. 

FIGURE 6.7 The three-dimensional structures of two proteins that contain substantial amounts of rx-helix in their structures. The helices are represented by the regularly coiled sections of the ribbon drawings. Myohemery-thrin is the oxygen-carrying protein in certain invertebrates, including Sipunculids, a phylum of marine worm. (Jane Richardson)... 

Drawing the Three-Dimensional Structure of a Chiral Molecule... 

C09-0103. How many different structural isomers are there for octahedral molecules with the general formula A Xz Draw three-dimensional structures of each. 

The three dimensional structure was obtained by means of single crystal X-ray diffraction. CuKa radiation, a graphite monochromator, and a photomultiplier tube were used to collect 1825 total reflections on an automated diffractometer. Of these, 1162 were used for the analysis. Figure 2 shows a computer generated drawing of halcinonide. The position of the chlorine atom was not clear from the Patterson map, but the direct method program "MULTAN" gave its position. 

Schematic drawing of the three-dimensional structure of D. gigas [NiFe] hydrogenase and close up on the active site... 

Solubility of the Components of DNA Draw the following structures and rate their relative solubilities in water (most soluble to least soluble) deoxyribose, guanine, phosphate. How are these solubilities consistent with the three-dimensional structure of double-stranded DNA ... 

In step b branch migration takes place, separating the nonhomologous base pairs TA and CG and causing mismatched pairs which will be subject to repair. (B) Proposed three-dimensional structure (after drawing by Bennett and West).292... 

The three-dimensional structure of cholera toxin.6 Side view of the p subunit pentamer as a ribbon drawing. Bound noncovalently to it are five molecules of the ganglioside Gm1 (compare with the structure in Fig. 7-5). The diacyl glycerol parts of the gangliosides are buried in the membrane that lies below the toxin molecule. Courtesy ofW.G.J. Hoi. 

Figure 11-14 Ribbon drawing of the three-dimensional structure of adapter protein Grb2. The two SH3 domains at the N and C termini are labeled, as is the central SH2 domain. Produced with programs MolScript and Raster3D. From Maignan et al.i76 Courtesy of Amaud Ducruix.

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the 50S subunit of ribosomes of Halocirculci marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban et al.17 Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et al.33a (C) Simplified drawing of the secondary structure of E. coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al.78 Similar diagrams for Haloarcula marismortui17 and for the mouse79 reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a 50S subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

Draw three-dimensional structures of PCI3 and PCI5, and then explain why one of the molecules has a dipole moment and one does not. 

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