Stereo views

Fig. 3.—Parallel packing arrangement of the 2-fold helices of cellulose I (1). (a) Stereo view of two unit cells approximately normal to the ac-plane. The two comer chains (open bonds) in the back, separated by a, form a hydrogen-bonded sheet. The center chain is drawn in filled bonds. All hydrogen bonds are drawn in dashed lines in this and the remaining diagrams, (b) Projection of the unit cell along the c-axis, with a down and b across the page. No hydrogen bonds are present between the comer and center chains.

Fig. 8.—Packing arrangement of four symmetry-related 2-fold helices of mannan II (6). (a) Stereo view of two unit cells approximately normal to flic frc-plane. The two chains in the back (open bonds) and the two in the front (filled bonds) are linked successively by 6-0H-- 0-6 bonds. The front and back chains, both at left and right, are further connected by 0-2 -1V -0-2 bridges, (h) Projection of the unit cell along the c-axis the a-axis is down the page. This highlights the two sets of interchain hydrogen bonds between antiparallel chains, distinguished by filled and open bonds. The crossed circles are water molecules at special positions.

Fig. 9. — Antiparallel packing arrangement of the 3-fold helices of (1— 4)-(3-D-xylan (7). (a) Stereo view of two unit cells roughly normal to the helix axis and along the short diagonal of the ab-plane. The two helices, distinguished by filled and open bonds, are connected via water (crossed circles) bridges. Cellulose type 3-0H-0-5 hydrogen bonds stabilize each helix, (b) A view of the unit cell projected along the r-axis highlights that the closeness of the water molecules to the helix axis enables them to link adjacent helices.

Fig. 12.—Packing arrangement of shallow, 6-fold, V-amylose (10) helices, (a) Stereo view of two unit cells approximately normal to the fee-plane. The helix at the center (filled bonds) is antiparallel to the two helices at the comers in the back (open bonds). Intrachain hydrogen bonds (3-OH - - 0-2 and 6-OH 0-3) are shown in thin lines.

Fig. 21.—Structure of the 6-fold anhydrous curdlan III (19) helix, (a) Stereo view of a full turn of the parallel triple helix. The three strands are distinguished by thin bonds, open bonds, and filled bonds, respectively. In addition to intrachain hydrogen bonds, the triplex shows a triad of 2-OH - 0-2 interchain hydrogen bonds around the helix axis (vertical line) at intervals of 2.94 A. (b) A c-axis projection of the unit cell contents illustrates how the 6-0H - 0-4 hydrogen bonds between triple helices stabilize the crystalline lattice.

Fig. 23.—(a) Stereo view of about two turns of the 2-fold helix of potassium galactoglucan (22). Each carboxylate group is bound to a potassium ion (crossed circle). The helix is stabilized by hydrogen bonds from the acetate and pyruvate groups to the main chain via water molecules (open circles). 

Fig. 24.—(a) Stereo view of slightly over a turn of the 3-fold double helix of i-carrageenan (23). The two chains are distinguished by open and filled bonds for clarity. The vertical line is the helix axis. Six interchain hydrogen bonds per turn among the galactose residues stabilize the double helix. The sulfate groups lined up near the periphery are crucial for intermolecular interactions. 

Fig. 28.—Antiparallel packing arrangement of 4-fold helices of sodium hyaluronate (26). (a) Stereo view of a unit cell approximately normal to the hc-plane. The two comer chains in the front (filled bonds) are linked directly by hydrogen bonds. The chain at the center (open bonds) interacts with die comer chains via sodium ions (crosses circles) and hydrogen bonds.

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

Fig. 33.—A stereo view of the 2-fold helix of keratan 6-sulfate (39) stabilized by intrachain hydrogen-bonds. The sulfate groups are located on the periphery of the sinuous chain.

Fig. 38.—Stereo view of three turns of the 2-fold galactomannan (45) helix containing galactose side-chains on alternate mannose residues. In this conformation, the side chains are turned up toward the non-reducing end, and the backbone is stabilized by intrachain hydrogen bonds. The helix axis is represented by the vertical line.

Fig. 39.—fa) Stereo view of two turns of the left-handed. 2-fold helix of E. coli capsular polysaccharide (46) stabilized by hydrogen bonds involving both main and side chains. The vertical line represents the helix axis. 

Fig. 2. Stereo view of the active site off), gigas hydrogenase (reprinted with permission from (65) copyright 1997, American Chemical Society). LI and L2 are diatomic ligands that form hydrogen bonds with the protein- they are supposed to be the two CN s molecules. The third ligand L3 sits in a hydrophobic pocket and is assumed to be the CO. The designates the putative oxo bridging ligand.

FIGURE 2.6 The procarcinogen benzo[a]pyrene oriented in the CYPlAl active site (stereo view) via n- n stacking between aromatic rings on the substrate and those of the complementary amino acid side chains, such that 7,8-epoxidation can occur. The substrate is shown with pale lines in the upper structures. The position of metabolism is indicated by an arrow in the lower structure (after Lewis 1996). 

Fig. 2.12 The j8-peptide 3,4-helical structure. (A) Stereo-view along the helix axis of the left-handed 3,4-helix formed by, 8 -peptide 66 in solution as determined by NMR in CD3OH (adapted from [103, 154]). Side-chains have been omitted for clarity. (B) Top view.

Fig. 2.30 Comparison of antiparallel hairpin structures in / -peptides 120-122. (A) / -Pep-tides 120, 121 with a 12-membered R/S dini-pecotic (Nip or/ -HPro) turn segment (gray color). Summary of backbone-backbone and side-chain-side-chain NOEs collected in CD2CI2 and X-ray crystal structure of 121 (stereo-view) [154, 193], The intramolecular H-bond N" 0 distances are shown. The angles (N-H -O) are 170.8° (inner H-bond) and 1 72.3 ° (outer H-bond). (B) jS-Peptide 122 with...

Fig. 2.36 The y-peptide 2.614-helical fold. (A) Stereo-view along the helix axis of the (P)-2.6i4-helical structure adopted by y -hexapep-tide 141 in pyridine. This low energy confor-mer was obtained by simulated annealing calculations under NMR restraints. Side-chains have been partially omitted for clarity.

Fig. 2.47 The (P)-2.5-helical structure of N.N -linked oligoureas as determined by NMR meaurements in pyridine-c/5. (A) Stereo-view along the helix axis of a low energy conformer of nonamer 178 generated by restrained molecular dynamics calculations. (Adapted from [274]). The helix is characterized by (i) a rigid +)-SYnclinal arrangement around the C(a)-...

Figure 30 Lateral stereo views of adamantane derivative thiacalix[4]arene top) presented in Fig. 29. A CHCI3 molecule has been entrapped inside the inclusion compound. The bottom view left bottom) and top view right bottom) are also shown. H atoms have been removed from the inclusion compound for more clarity [128].

The structures of CaC2 and NaN3 (stereo views). Heavy outlines body-centered tetragonal unit cell of CaC2. Dashed line at NaN3 direction of the elongation of the NaCl cell... 

Fig. 23. Stereo view of the 1 1 20 cyclohexene clathrate viewed down the channel axis (the inclusion compound of 20 with cyclohexane is isomorphous)26)...

Figure 5.5 Stereo view of the Fe3+ binding site of (a) hFBP (b) human lactoferrin, N-lobe and (c) human transferrin (N-lobe). From Bruns, 1997. Reproduced by permission of Nature Publishing Group. 

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