Figure 17.

(A, B, C). Surface rendering of the pore of entry to the Na⁺ binding site of human thrombin in the structure 1SG8 (Pineda et al. 2004a) (A), compared with the same region in murine thrombin (B) and the thrombin chimera (C). Residues lining the pore are color coded according to their physical properties (red=positively charged, blue=negatively charged, orange=hydrophobic, white=all others). In the human enzyme, the pore is defined by residue D222 in the 220-loop and the sequence PDEGKR from P186 to R187 in the 186-loop (Table 2) (A). In murine thrombin (B), residue 222 is Lys and the corresponding sequence in the 186-loop is VNDTKR (Table 2). The side chain of K222 completely occludes the pore. The side chain of N186a is glycosylated (NAG). Occlusion of the pore is also seen in the thrombin chimera (C), in which the human enzyme carries all residues around the pore as in murine thrombin. There is no glycosylation of N196a in the chimera. (D, E, F). Architecture of the pore of entry to the Na⁺ binding site in the same orientation as shown in the surface rendering (panels A, B, C), with relevant residues rendered in CPK model (C in yellow) and the 2Fo-Fc electron density maps contoured at the 0.7 σ level for the structures presented in this study (panels E, F). The human enzyme (D) shows the pore wide open, whereas K222 in murine thrombin (E) occludes the pore and positions the Nζ atom within H-bonding distance from K185, D186b and K186d. The backbone O atom of residue 186b is flipped relative to the position assumed in the fast form of the human enzyme. Also shown is the indole side chain of W20, which is Ser in human thrombin, as a structural signature of the murine enzyme. K222 in the thrombin chimera (F) is positioned as in the murine thrombin structure.