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Entry M0165    3.1.31.1    micrococcal nuclease

Next Step

Step 01

Glu43 deprotonates the calcium activated water molecule, which then attacks the DNA phosphate bond in a nucleophilic substitution. The 3' DNA hydroxyl protonates from Arg87.

Rate Determining Step

GIF of Reaction Step M0165.stg01


Comment: Reaction proceeds through a pentavalent transition state.



Mechanisms

Proton Transfer
Bimolecular Nucleophilic Substitution

Mechanism Components

Overall Reactant Used
Bond Formation
Bond Cleavage
Overall Product Formed
Hydrolysis

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Glu43 Side Chain reactant Hydrogen Bond Acceptor
Proton Acceptor
Arg35 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Arg87 Side Chain reactant Hydrogen Bond Donor
Proton Donor
Electrostatic Stabiliser

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
calcium CA 1 x spectator Substrate Binding
Activator
Increase Electrophilicity
Electrostatic Stabiliser

Reactive Centre

Bonds Formed Bonds Cleaved Bonds Changed in Order Atom Types Involved
O-H
O-H
P-O
N-H
O-H
P-O
None
H
N
O
P

View similar reactions in MACiE.


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