Table V. A comparison of the active site of metal-bound endonuclease I (chain A) and the restriction endonuclease BglI.
| Endo I (domain AB) | BglI | Displacement (Å) | Water position in Endo I |
|---|---|---|---|
| Mn1 | Ca1 | 0.34 | – |
| Mn2 | Ca2 | 0.89 | – |
| Wat2 | Wat4a | 0.91 | II |
| Wat3 | Wat3 | 1.01 | III |
| Wat4 | Wat6 | 1.01 | IV |
| Wat5 | Wat5 | 1.22 | V |
| Wat6 | Wat7 | 1.69 | VI |
The 10 Cα and Cβ atoms of Pro54, Asp55, Glu65, Lys67 and Glu20 in endonuclease I wt + Mn were superimposed on the corresponding atoms in BgII (Pro115, Asp116, Asp142, Lys144 and Glu87) giving an r.m.s.d. of 0.48 Å. The matrix obtained from this superimposition was then used to transform the coordinates of BgII, and the displacement of equivalent atoms in the two proteins was then compared. Water positions are listed as in Table II.
aAttacking water molecule in the BgII structure.