Stereo drawings

X-Ray diffraction analysis of oriented polysaccharide fibers has had a long history. Marchessault and Sarko discussed this topic in Volume 22 of Advances, and a series of articles by Sundararajan and Marchessault in Volumes 33, 35, 36, and 40 surveyed ongoing developments. The comprehensive account presented here by Chandrasekaran (West Lafayette, Indiana) deals with some 50 polysaccharides, constituting a wide range of structural types, where accurate data and reliable interpretations are available. The regular helical structures of the polysaccharide chains, and associated cations and ordered water molecules, are presented in each instance as stereo drawings and discussed in relation to observed functional properties of the polymers. 

Fig. 16. Stereo drawing of the packing in the crystal structure of free host compound 4874) (H atoms are shown as sticks only)...

Fig. 27. Packing relations in the crystal structure of 47 benzene (1 1) 64>. Stereo drawing of complementary stick style and space filling representations of host and guest molecules, respectively (atomic radii of the corresponding guest atoms in the space filling style are set to about half of their common van der Waals values the H atoms of the host molecules are omitted)...

Fig. 33. Packing of the 22 DMF clathrate 48) (stereo drawing). The joined orienting effect of the host lattice and of the sensor groups is illustrated showing the fit of the guest molecules (with 3/4 of the van der Waals radii of the composing atoms, O atoms shaded) to the host matrix (stick style)...

Fig. 34. Stereo drawing of the packing in the 20 DMSO clathrate 851 (complementary space filling and stick style representations of host and guest molecules, respectively O atoms of the host are shaded). Space around guest molecules in the center of the drawing, related by the symmetry center operator, indicates the opportunity for disorder...

Fig. 2. Stereo drawing of all nonhydrogen atoms of basic pancreatic trypsin inhibitor. The main chain is shown with heavy lines and side chains with thin lines.

Fig. 13. Stereo drawing of one contour level in the electron density map at 2 A resolution for the residue 54-68 helix in staphylococcal nuclease. Carbonyl groups point up, in the C-terminal direction of the chain the asterisk denotes a solvent peak bound to a carbonyl oxygen in the last turn. Side chains on the left (including a phenylalanine and a methionine) are in the hydrophobic interior, while those on the right (including an ordered lysine) are exposed to solvent.

Fig. 15. Stereo drawing of a bent helix (glyceraldehyde-phosphate dehydrogenase residues 146-161) with an internal proline. The proline ring produces steric hindrance to the straight a-helical conformation as well as having no NH group available for a hydrogen bond. A proline is the commonest way of producing a bend within a single helix, as well as occurring very frequently at the comers between helices.

Fig. 32. Stereo drawings of particular examples of types II (a) and II (b) turns from the known protein structures, (a) Concanavalin A 43-46 (Gln-Asp-Gly-Lys) (b) car-boxypeptidase A 277-280 (Tyr-Gly-Phe-Leu).

Fig. 33. Stereo drawings of particular examples of types Via (a) and VIb (b) cis-proline turns, (a) Ribonuclease S 91-94 (Lys-Tyr-Pro-Asn) (b) Bence-Jones protein REI 6-9 (Gln-Ser-Pro-Ser).

Fig. 38. Stereo drawing of the polypeptide backbone of high-potential iron protein. Tight turns are shown with their central peptide as a dark line. The box in the center represents the iron-sulfur cluster.

Fig. 58. Stereo drawing of the rubredoxin backbone with the iron (filled circle) and its cysteine sulfur ligands and all the water molecules (open circles) identified during refinement of the structure at 1.2 A resolution. Adapted from Watenpaugh et al. (1979), Fig. 11, with permission.

Fig. 9. Stereo drawing of proposed bicarbonate binding site between the two /3 chains of caiman deoxyhemoglobin. The central sign marks the dyad symmetry axis. Bicarbonates and their binding residues are underlined. Capital letters mark helical and interhelical segments (61). Residues are marked in sequential, rather than struaural notation. The following list gives the structural numbers with the sequential ones in parentheses Ser NAl (1) Pro NA2 (2) Phe NAS (3) Ser A1 (4) Ala A2 (5) His AS (6) Lys EF6 (82) Glu HCl (144) Tyr HC2 (145) His HC3 (146) all /3.

Figure 16-3 Structure of the protein shell of ferritin (apoferritin). (A) Ribbon drawing of the 163-residue monomer. From Crichton.62 (B) Stereo drawing of a hexamer composed of three dimers. (C) A tetrad of four subunits drawn as a space-filling diagram and viewed down the four-fold axis from the exterior of the molecule. (D) A half molecule composed of 12 subunits inscribed within a truncated rhombic dodecahedron. B-D from Bourne et al.7i...

Figure 16-11 (A) Stereo drawing showing folding pattern for beef liver catalase and the positions of the NADPH (upper left) and heme (center). From Fita and Rossmann.198 (B) Diagram of proposed structure of an Fe(III)-OOH ferric peroxide complex of human catalase (see also Fig. 16-14).

FIGURE 1.14A Stereo drawing of the lactic acid molecule. 

Fig. 15. Stereo drawing of the most likely conformer of the cation as-Pt(NH3)2(d(GG-lV7,JV7))+ in solution as determined by high-resolution NMR techniques...

Fig. 9. Chain trace of one subunit of glutathione reductase. Stereo drawing from the work of Schulz and...

Fig. 15. Chain trace of E.coli dihydrofolate reductase. Bound inhibitor (meihoirexaie) is also shown, with nitrogen (black) and oxygen (shading) atoms indicated. Stereo drawing from the work of Kraut and colleagues [68]. 

Fig. 20. Chain trace of pig heart soluble malate dehydrogenase subunit. Stereo drawing from lhe work of... 

Fig. 25. Chain trace of one subunit of horse liver alcohol dehydrogenase. Stereo drawing from the work of Branden and colleagues [117], The catalytic zinc atom is central, the structural zinc atom is at the bottom right.

Fig. 28. The substrate binding pocket of horse liver alcohol dehydrogenase, as in Fig. 27, viewed here into the pocket towards the zinc (not itself shown). Stereo drawing from the work of Brandon and colleagues. 

Fig. 30. Horse liver alcohol dehydrogenase substrate binding pocket, unoccupied. Stereo drawing from the work of Branden and colleagues. 

Figure 18 Stereo drawings of the minimum-energy p sheets with five CH,CO— (L-Val)6-NHCH3 chains. A. Antiparallel structure. B. Parallel structure.15,1...

Fig. 20.11. Stereo drawing of d(CGCAAAAAAGCG). The amino N(6)-H groups of the central A-tract form three-center (bifurcated) hydrogen bonds with adenine N(6)-H acting as double donors due to the strong propeller twist of the A-T base pairs. Only bases are shown, sugar-phosphate backbone omitted for clarity [702]...

Fig. 4. Stereo drawing of the type-1 copper site in domain 3. The displayed bond distances are for subunit A.

Fig. 7. Stereo drawing of the region of the atomic model containing the type-1 copper center in domain 3 and the trinuclear copper center between domain 1 and domain 3.

Fig. 15. Stereo drawing of the binding site near the type-1 copper plus docked L-ascorbate. Atomic model plus Conolly dot surface, (a) Viewed perpendicular to the NDl His512-CUl bond, (b) Viewed parallel to the NDl His512-CUl bond.

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