Table 1

Differentially protonated residues in catB and pKa values

Average values during 40ns MD


Residue

predicted crystal

pH 5,5

pH 8


C29

2,14

3.7 ± 1.5

7.3 +1.6


E36

5,9

5.4 ± 0.5

3.4 ± 1.2


H97

6,9

7.1 ± 0.2

7.3 ± 0.4


H110

6,6

6.6 ± 0.8

8.1 ± 0.7


E171

7,7

7.4 ± 0.2

6.5 ± 0.4


H190

7,2

7.1 ± 0.2

7.4 ± 0.7


H199

7,8

8.1 ± 2

4.5 ± 1.7


pKa values predicted by PROPKA and the state of ionizable groups under different pH conditions are indicated. The protonation state of C29 at pH 8 were obtained taking into account deprotonation of H199 as previously proposed for papain. The protonation states of the catalytic residues (C29 and H199) are highlighted.

Costa et al. BMC Genomics 2010 11(Suppl 5):S5   doi:10.1186/1471-2164-11-S5-S5

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