International Tables for Crystallography (2012). Vol. F, ch. 23.5, pp. 800-820   | 1 | 2 |
doi: 10.1107/97809553602060000894

Chapter 23.5. Solvent structure

Contents

  • 23.5. Solvent structure  (pp. 800-820) | html | pdf | chapter contents |
    • 23.5.1. Introduction  (pp. 800-801) | html | pdf |
    • 23.5.2. Determination of water molecules  (pp. 801-802) | html | pdf |
    • 23.5.3. Structural features of protein–water interactions derived from database analysis  (pp. 802-808) | html | pdf |
      • 23.5.3.1. Water distribution around the individual amino-acid residues in protein structures  (pp. 802-805) | html | pdf |
      • 23.5.3.2. The effect of secondary structure on protein–water interactions  (pp. 805-806) | html | pdf |
      • 23.5.3.3. The effect of tertiary structure on protein–water interactions  (pp. 806-807) | html | pdf |
      • 23.5.3.4. Water mediation of protein–ligand interactions  (pp. 807-808) | html | pdf |
    • 23.5.4. Water structure in groups of well studied proteins  (pp. 808-814) | html | pdf |
      • 23.5.4.1. Crystal structures of homologous proteins  (pp. 808-809) | html | pdf |
        • 23.5.4.1.1. Serine proteases of the trypsin family  (p. 808) | html | pdf |
        • 23.5.4.1.2. Legume lectin family  (pp. 808-809) | html | pdf |
      • 23.5.4.2. Multiple crystal structures of the same protein  (pp. 809-814) | html | pdf |
        • 23.5.4.2.1. Elastase  (pp. 809-812) | html | pdf |
        • 23.5.4.2.2. T4 lysozyme  (pp. 812-813) | html | pdf |
        • 23.5.4.2.3. Ribonuclease T1  (p. 813) | html | pdf |
        • 23.5.4.2.4. Ribonuclease A  (pp. 813-814) | html | pdf |
        • 23.5.4.2.5. Protein kinase A  (p. 814) | html | pdf |
      • 23.5.4.3. Summary  (p. 814) | html | pdf |
    • 23.5.5. The classic models: small proteins with high-resolution crystal structures  (pp. 814-815) | html | pdf |
      • 23.5.5.1. Crambin  (pp. 814-815) | html | pdf |
      • 23.5.5.2. Bovine pancreatic trypsin inhibitor  (p. 815) | html | pdf |
      • 23.5.5.3. Summary  (p. 815) | html | pdf |
    • 23.5.6. Water molecules as mediators of complex formation  (pp. 815-817) | html | pdf |
      • 23.5.6.1. Antigen–antibody association  (pp. 815-816) | html | pdf |
      • 23.5.6.2. Protein–DNA recognition  (p. 816) | html | pdf |
      • 23.5.6.3. Cooperativity in dimeric haemoglobin  (pp. 816-817) | html | pdf |
      • 23.5.6.4. Summary  (p. 817) | html | pdf |
    • 23.5.7. Conclusions and future perspectives  (pp. 817-818) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 23.5.3.1. Distribution of water-molecule sites  (p. 803) | html | pdf |
      • Fig. 23.5.3.2. Distribution of atomic hydration values  (p. 804) | html | pdf |
      • Fig. 23.5.3.3. Diagram of edge (W1), end (W2) and middle (W3) categories of interactions of water molecules with main-chain atoms in antiparallel β-sheets  (p. 805) | html | pdf |
      • Fig. 23.5.3.4. Diagram of the hydrogen bonds in the α-helical structure in actinidin  (p. 806) | html | pdf |
      • Fig. 23.5.3.5. Schematic illustration of water molecules bound in different types of grooves between protein and ligand  (p. 807) | html | pdf |
      • Fig. 23.5.4.1. Stereoview of the set of 21 highly conserved buried waters in eukaryotic serine proteases  (p. 808) | html | pdf |
      • Fig. 23.5.4.2. View of the 33 conserved hydration sites in the lentil lectin crystal structures superimposed on the backbone of the lentil lectin dimer  (p. 809) | html | pdf |
      • Fig. 23.5.4.3. 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. 809) | html | pdf |
      • Fig. 23.5.4.4. Crystal structure of porcine pancreatic elastase represented as a ribbon diagram using MOLSCRIPT (Kraulis, 1991)  (p. 810) | html | pdf |
      • Fig. 23.5.4.5. Elastase structure represented as in Fig. 23.5.4.4. The crystallographic water molecules found in channels in 11 superimposed elastase structures solved in a variety of solvents are shown in yellow  (p. 811) | html | pdf |
      • Fig. 23.5.4.6. Elastase structure represented as in Fig. 23.5.4.4. The crystallographic water molecules involved in crystal contacts in 11 superimposed elastase structures solved in a variety of solvents are shown in green  (p. 811) | html | pdf |
      • Fig. 23.5.4.7. Elastase structure represented as in Fig. 23.5.4.4. The surface crystallographic water molecules found in 11 superimposed elastase structures solved in a variety of solvents are shown in blue  (p. 811) | html | pdf |
      • Fig. 23.5.4.8. Elastase structure represented as in Fig. 23.5.4.4. The 1661 water molecules found in 11 superimposed elastase structures of elastase are colour-coded as in Figs. 23.5.4.4–23.5.4.7  (p. 812) | html | pdf |
      • Fig. 23.5.4.9. Distribution of solvent-binding sites in 18 mutant T4 lysozymes from ten refined crystal structures  (p. 812) | html | pdf |
      • Fig. 23.5.4.10. Three-dimensional structure of RNase T1  (p. 813) | html | pdf |
      • Fig. 23.5.4.11. Overall structure of RNase A  (p. 813) | html | pdf |
      • Fig. 23.5.5.1. van der Waals surface diagram of the water pentagons A, C, D and E in crambin viewed in the negative a direction  (p. 815) | html | pdf |
      • Fig. 23.5.6.1. Scapharca HbI interface water molecules  (p. 817) | html | pdf |
    • Tables
      • Table 23.5.3.1. Specific hydrophilicity values for protein atoms  (p. 804) | html | pdf |
      • Table 23.5.4.1. Multiple-solvent crystal structures of elastase  (p. 810) | html | pdf |