Sandbox Reserved 428: Difference between revisions

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<scene name='Sandbox_Reserved_428/Binds_to_dna/1'>DNA Binding</scene>

The ~~interactions~~ that ~~hold this protein together are aided~~ by the ~~interaction~~ of Mg2+ atoms. ~~They hold together~~ the active site of the ~~dimers~~. ~~This is a charge-charge interaction~~, ~~since~~ the ~~Magnesium has~~ a 2+ ~~charge~~. The ~~oxygen atoms also have a partial negative charge which~~ interactions with ~~this positive charge~~.

DNA recognition sites on the EcoRV molecule, called R-loops, bind to the major grooves of the double stranded DNA. The EcoRV molecule binds to this double stranded DNA by hydrogen bonding. This bond 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 of the 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.

These six ionic interactions all have about the same binding distance except for one bond between the oxygen from the Asp74 residue and the Mg2+ ion that is significantly longer. The five similar bond lengths are all about 2.08 Å, but the bond between Mg2+ and the Asp74 oxygen spans a distance of 2.9 Å. This is noted because the Asp90 and scissile phosphodiester molecules that bind to this Mg2+ ion change their bonding interactions with hydrogen to accommodate the addition of the Mg2+ ion. The Asp74 residue maintains its hydrogen bond interactions on its side chain with the main chain of the Ile91 residue and the water molecule, which is why it keeps a greater distance between itself and the Mg2+ ion.

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Sandbox Reserved 428: Difference between revisions

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@@ Line 27: / Line 27: @@
 <scene name='Sandbox_Reserved_428/Binds_to_dna/1'>DNA Binding</scene>
-The interactions that hold this protein together are aided by the interaction of Mg2+ atoms.  They hold together the active site of the dimers.  This is a charge-charge interaction, since the Magnesium has a 2+ charge.  The oxygen atoms also have a partial negative charge which interactions with this positive charge.
+DNA recognition sites on the EcoRV molecule, called R-loops, bind to the major grooves of the double stranded DNA.  The EcoRV molecule binds to this double stranded DNA by hydrogen bonding.   This bond 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 of the 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.
+These six ionic interactions all have about the same binding distance except for one bond between the oxygen from the Asp74 residue and the Mg2+ ion that is significantly longer.  The five similar bond lengths are all about 2.08 Å, but the bond between Mg2+ and the Asp74 oxygen spans a distance of 2.9 Å.  This is noted because the Asp90 and scissile phosphodiester molecules that bind to this Mg2+ ion change their bonding interactions with hydrogen to accommodate the addition of the Mg2+ ion.  The Asp74 residue maintains its hydrogen bond interactions on its side chain with the main chain of the Ile91 residue and the water molecule, which is why it keeps a greater distance between itself and the Mg2+ ion.
 ===Additional Features===