Sandbox Reserved 428: Difference between revisions
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<scene name='Sandbox_Reserved_428/Binds_to_dna/1'>DNA Binding</scene> | <scene name='Sandbox_Reserved_428/Binds_to_dna/1'>DNA Binding</scene> | ||
DNA recognition sites on the EcoRV molecule, called R-loops, bind to the major grooves of the double stranded DNA. | DNA recognition sites on the EcoRV molecule, called R-loops, bind to the major grooves of the double stranded DNA at its recognition sequence GATATC by hydrogen bonding. This enzyme is a type II restriction endonuclease, which means this enzyme cleaves the DNA recognition sequence at the center (between the T and A base pairs). These hydrogen bonds makes the DNA form a kinked conformation that is later stabilized by the addition of the Mg2+ ion. The Mg2+ ion is a catalyst that causes the DNA to shift in a way that increases the rate necessary for DNA cleavage. | ||
The Mg2+ binding site is formed when ionic interactions cause the slightly acidic Asp90 residue and the slightly negatively charged scissile phosphodiester group to approach each other. This allows the Mg2+ ion to bind to this enzyme, also with ionic interactions between the positively charged Mg2+ and the partially negative charged oxygen atoms from multiple molecules. These molecules that bind to the Mg2+ ion are the carboxylate oxygen atoms from the Asp74 and Asp90 residues, the nonesterified oxygen from the scissile phosphodiester group, and three additional oxygen atoms from three water molecules. These six ionic bonds form an octahedral shape in the active site of this enzyme. | The Mg2+ binding site is formed when ionic interactions cause the slightly acidic Asp90 residue and the slightly negatively charged scissile phosphodiester group to approach each other. This allows the Mg2+ ion to bind to this enzyme, also with ionic interactions between the positively charged Mg2+ and the partially negative charged oxygen atoms from multiple molecules. These molecules that bind to the Mg2+ ion are the carboxylate oxygen atoms from the Asp74 and Asp90 residues, the nonesterified oxygen from the scissile phosphodiester group, and three additional oxygen atoms from three water molecules. These six ionic bonds form an octahedral shape in the active site of this enzyme. | ||
