Stereo diagrams

X-ray crystallographic analyses alone could not sort out the reason for differences between the RSR, MM and other weak acting series. Figure 17.2a is a stereo diagram showing the overlap of four allosteric effectors that bind at the same deoxy-Hb site but differ in their allosteric potency. Only small differences in atomic positions are apparent when comparing the strong RSR molecules with the MM molecules. 

Stereo diagram of the NMR solution structure of the tick anticoagulant peptide. The crucial N-terminus Arg3 is indicated along with the pattern of cysteine bonds. 

Figurel.10. Stereo diagram of the acyl moiet of the spin-labeled tryptophanyl-acylenzyme reaction intermediate of a-chymotrypsin. Active site residues close to the acyl moiety are labeled (Makinen et al., 1998). Reproduced with permission.

It is difficult to summarize the observed interactions in horse liver alcohol dehydrogenase in a short space. The reader is advised to consult the original paper [51] which contains a vivid stereo diagram (one stereo diagram is equal to at least 103 words). However, for the present discussion it suffices to say that the situation in the enzyme substrate complex is not that of a simple three-point attachment. The observed stereochemical course is as follows ... 

Figure 26 Stereo diagrams illustrating (top) a compact conformation of N-acetyl-Ala19-NHCH3 after local minimization of the complete energy function to reach this particular local minimum, and (bottom) the global-minimum (right-handed a helix) structure attained by first optimizing the local electrostatic interactions and then carrying out a complete energy minimization.188...

Fig. 24.6. Stereo diagram showing the four fused water pentagons in the major groove of the A-DNA-type octanucleotide d(GCBrUABrUACC). Bromine atoms [or thymine methyl groups in the isomorphous d(GGTATACC)] are indicated by concentric circles. Note water molecules and phosphate oxygens surrounding the methyl groups (or bromine atoms) (see also Fig. 24.9a, [865])...

Fig. 24.8. Stereo diagram (side and top view) showing arrangement of spine of hydration in the minor groove of Z-DNA (see also Fig. 24.9 c, [876])...

Fig. 13. Stereo diagram of the fully open structure of human lactoferrin, determined crystallographically (109). The N-lobe is upper, the C-lobe, lower.

FIGURE 7. Stereo diagram of one subunit of flavocytochrome b. Only residues ln486 are shown, the remainder being involved in intermolecular interactions. The flavin-binding domain is at the top and the cytochrome domain is at the bottom. The flavin and heme groups are shown as skeletal models. 

FIGURE 8. stereo diagram of p-cresol methylhydroxylase. The flavoprotein subunit is on the left and the cytochrome subunit is on the right. The flavin-binding domain of the flavoprotein subunit is on the bottom and the catalytic domain is on the top. Skeletal models of the heme and FAD prosthetic groups are also shown. 

FIGURE 10. Stereo diagram of domain 1 of trimethylamine dehydrogenase. Residues ln371 are shown. Helices aj-ttg of the PgtXg TIM barrel are indicated. The iron sulfur cluster-binding loop consisting of an a-helix and a P-strand is located at the end of helix Og. 

FIGURE 11. stereo diagram of phthalate dioxygenase reductase. The FMN- and NADPH-binding domains are on the top and the 2Fe-2S binding domain is on the bottom. The FMN and 2Fe-2S prosthetic groups are shown as skeletal models. 

FIGURE 12. Stereo diagram of the complete fimiarate reductase complex. The FAD-binding subunit is at the top, the iron-sulfur subunit is in the center and die two membrane anchoring subunits that provide die binding sites for two molecules of menaquinone are at the bottom. In this molecule electron h ansfer occiffs from menaquinone at die bottom to FAD at die top during reduction of fumarate by menaquinone. Skeletal models of two molecules of menaquinone, a 3Fe-4S, a 4Fe-4S, a 2Fe-2S, an FAD molecule and one molecule of oxalate are included. 

FIGURE 11. Stereo diagram of the Qj site structure in chicken bc complex (structure IBCC), viewed parallel to the membrane with the matrix side on die top. The amphipathic helix a, transmembrane helices A, D, and E are shown in bold lines connecting a carbon atoms, while haem bn, ubiquinone (UQ) and selected residues are shown as diin wire models. The hydrogen bonds between ubiquinone and residues His202, Ser206 and Asp229 are drawn as dashed lines. 

Figure 3. Stereo diagram of GIF monomer. Two a-helices are labeled as al and a2. Six P-strands are labeled from pi to p6. Two P-strands from the other monomers (P3 and p6") are also shown.

Fig. 11. A stereodiagram of the Ca trace of apo- and holo-ALBP. The small stereo diagram at the bottom shows the Ca models of both the apo and the holo forms of crystalline ALBP. Every tenth residue is numbered, and because of the close similarity in the conformation of the two proteins much of the diagram appears as one solid line. At the top of the molecule (shown in the enlargement) Phe-57 appears twice. This is due to the fact that this side chain has two different conformations in the structures of the apo and holo forms. With Phe-57 swung to the left, the holo-form is viewed. When located in the rightmost position, Phe-57 is as appears in the apo form, seemingly closing the portal to the ligand-binding cavity.

Fig. 15. A stereo diagram of the Ca model of ALBP, the bound fatty acid, and the position of Tyr-19, including a Ca representation of the crystal structure of ALBP along with its bound fatty acid. Also shown is Tyr-19, the amino acid that is phosphorylated in vivo in both ALBP and P2. The amino acids are numbered according to the ALBP sequence.

Fig. 16. Differences in the binding cavity in vertebrate and insect iLBPs. The stereo-diagram illustrates the differences in the conformation of the fatty acids bound to crystalline vertebrate and insect iLBPs. The reader should also refer to Fig. 13. The differences in conformation of bound ligand are likely to be attributable to amino acids 22, 32, and 78 of ALBP and the corresponding side chains in crystalline MFB2. The diagram was produced from the coordinates after least-squares alignment as described in Fig. 5. Tbe atoms of MFB2 are represented with bold lines.

Fig. 6. Stereo diagram showing packing of molecules on a face of the face-centered cubic crystal of human rHF. For clarity, only 16 of the 24 subunits are shown. A lid of 8 subunits has been removed so that molecules are seen as hollow shells looking down a four-fold axis into their interiors. Subunits are drawn as a-carbon traces. Four intermo-lecular crystal contacts of the central molecule can be seen and a close-up of one of these is depicted in Fig. 7.

Fio 9. Stereo diagram of the three-fold channel region of human rHF viewed from outside the molecule. Only the narrow end of the channel, toward the cavity, is shown. In the center of the channel there is a large peak of electron density presumed to represent a Ca - ion (marked here with a star). It has six oxy ligands supplied by three glutamates and three waters (hydrogen bonded to aspartates) in octahedral geometry. 

Figure 6. Stereo diagram of the substrate binding domain using the substrate docking method.

---