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Entry M0321    3.1.13.5    ribonuclease D

Next Step

Step 01

The hydroxide ion, coordinated to one of the active site Zn cations attacks at the pentavalent 5' phosphorous centre.

GIF of Reaction Step M0321.stg01


Comment: Several conserved acidic residues coordinate to the Zn atoms within the active site, although Tyr151 and Asp155, positioned in exo-site 3, have been implicated in stabilising and directing the nucleophile [1,4].



Mechanisms

Bimolecular Nucleophilic Substitution

Mechanism Components

Bond Cleavage
Bond Formation
Overall Reactant Used
Overall Product Formed
Metal De-coordination
Intermediate Formation

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Asp155A Side Chain spectator Metal Ligand
Attractive Charge Charge Interaction
Electrostatic Stabiliser
Tyr151A Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
zinc ZN 1001 A spectator Substrate Binding
Activator
Increase Nucleophilicity
Electrostatic Stabiliser
zinc ZN 1002 A spectator Substrate Binding
Activator
Electrostatic Stabiliser
Increase Electrophilicity

Reactive Centre

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

View similar reactions in MACiE.


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