International Tables for Crystallography (2006). Vol. F, ch. 23.4, pp. 623-647   | 1 | 2 |
doi: 10.1107/97809553602060000717

Chapter 23.4. Solvent structure

Contents

  • 23.4. Solvent structure  (pp. 623-647) | html | pdf | chapter contents |
    • 23.4.1. Introduction  (pp. 623-624) | html | pdf |
    • 23.4.2. Determination of water molecules  (pp. 624-625) | html | pdf |
    • 23.4.3. Structural features of protein–water interactions derived from database analysis  (pp. 625-630) | html | pdf |
      • 23.4.3.1. Water distribution around the individual amino-acid residues in protein structures  (pp. 625-627) | html | pdf |
      • 23.4.3.2. The effect of secondary structure on protein–water interactions  (pp. 627-629) | html | pdf |
      • 23.4.3.3. The effect of tertiary structure on protein–water interactions  (p. 629) | html | pdf |
      • 23.4.3.4. Water mediation of protein–ligand interactions  (pp. 629-630) | html | pdf |
    • 23.4.4. Water structure in groups of well studied proteins  (pp. 630-637) | html | pdf |
      • 23.4.4.1. Crystal structures of homologous proteins  (pp. 630-631) | html | pdf |
        • 23.4.4.1.1. Serine proteases of the trypsin family  (pp. 630-631) | html | pdf |
        • 23.4.4.1.2. Legume lectin family  (p. 631) | html | pdf |
      • 23.4.4.2. Multiple crystal structures of the same protein  (pp. 631-636) | html | pdf |
        • 23.4.4.2.1. Elastase  (pp. 632-634) | html | pdf |
        • 23.4.4.2.2. T4 lysozyme  (pp. 634-635) | html | pdf |
        • 23.4.4.2.3. Ribonuclease T1  (p. 635) | html | pdf |
        • 23.4.4.2.4. Ribonuclease A  (pp. 635-636) | html | pdf |
        • 23.4.4.2.5. Protein kinase A  (p. 636) | html | pdf |
      • 23.4.4.3. Summary  (pp. 636-637) | html | pdf |
    • 23.4.5. The classic models: small proteins with high-resolution crystal structures  (pp. 637-638) | html | pdf |
      • 23.4.5.1. Crambin  (p. 637) | html | pdf |
      • 23.4.5.2. Bovine pancreatic trypsin inhibitor  (p. 637) | html | pdf |
      • 23.4.5.3. Summary  (pp. 637-638) | html | pdf |
    • 23.4.6. Water molecules as mediators of complex formation  (pp. 638-640) | html | pdf |
      • 23.4.6.1. Antigen–antibody association  (p. 638) | html | pdf |
      • 23.4.6.2. Protein–DNA recognition  (pp. 638-639) | html | pdf |
      • 23.4.6.3. Cooperativity in dimeric haemoglobin  (pp. 639-640) | html | pdf |
      • 23.4.6.4. Summary  (p. 640) | html | pdf |
    • 23.4.7. Conclusions and future perspectives  (p. 640) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 23.4.3.1. Distribution of water-molecule sites  (p. 626) | html | pdf |
      • Fig. 23.4.3.2. Distribution of atomic hydration values  (p. 627) | html | pdf |
      • Fig. 23.4.3.3. Diagram of edge (W1), end (W2) and middle (W3) categories of interactions of water molecules with main-chain atoms in antiparallel β-sheets  (p. 628) | html | pdf |
      • Fig. 23.4.3.4. Diagram of the hydrogen bonds in the α-helical structure in actinidin  (p. 628) | html | pdf |
      • Fig. 23.4.3.5. Schematic illustration of water molecules bound in different types of grooves between protein and ligand  (p. 630) | html | pdf |
      • Fig. 23.4.4.1. Stereoview of the set of 21 highly conserved buried waters in eukaryotic serine proteases  (p. 631) | html | pdf |
      • Fig. 23.4.4.2. View of the 33 conserved hydration sites in the lentil lectin crystal structures superimposed on the backbone of the lentil lectin dimer  (p. 631) | html | pdf |
      • Fig. 23.4.4.3. A [2F_{o} - F_{c}] electron-density map contoured at the 1.2σ level shows a distinct ellipsoidal density for acetonitrile 707 and a spherical density for a nearby water molecule  (p. 632) | html | pdf |
      • Fig. 23.4.4.4. Crystal structure of porcine pancreatic elastase represented as a ribbon diagram using MOLSCRIPT (Kraulis, 1991)  (p. 633) | html | pdf |
      • Fig. 23.4.4.5. Elastase structure represented as in Fig. 23.4.4.4. The crystallographic water molecules found in channels in 11 superimposed elastase structures solved in a variety of solvents are shown in yellow  (p. 633) | html | pdf |
      • Fig. 23.4.4.6. Elastase structure represented as in Fig. 23.4.4.4. The crystallographic water molecules involved in crystal contacts in 11 superimposed elastase structures solved in a variety of solvents are shown in green  (p. 634) | html | pdf |
      • Fig. 23.4.4.7. Elastase structure represented as in Fig. 23.4.4.4. The surface crystallographic water molecules found in 11 superimposed elastase structures solved in a variety of solvents are shown in blue  (p. 634) | html | pdf |
      • Fig. 23.4.4.8. Elastase structure represented as in Fig. 23.4.4.4. The 1661 water molecules found in 11 superimposed elastase structures of elastase are colour-coded as in Figs. 23.4.4.4 –23.4.4.7  (p. 634) | html | pdf |
      • Fig. 23.4.4.9. Distribution of solvent-binding sites in 18 mutant T4 lysozymes from ten refined crystal structures  (p. 635) | html | pdf |
      • Fig. 23.4.4.10. Three-dimensional structure of RNase T1  (p. 636) | html | pdf |
      • Fig. 23.4.4.11. Overall structure of RNase A  (p. 636) | html | pdf |
      • Fig. 23.4.5.1. van der Waals surface diagram of the water pentagons A, C, D and E in crambin viewed in the negative a direction  (p. 637) | html | pdf |
      • Fig. 23.4.6.1. Scapharca HbI interface water molecules  (p. 639) | html | pdf |
    • Tables
      • Table 23.4.3.1. Specific hydrophilicity values for protein atoms  (p. 627) | html | pdf |
      • Table 23.4.4.1. Multiple-solvent crystal structures of elastase  (p. 632) | html | pdf |