User:Karl E. Zahn/Sandbox RB69 1/palm-domain
From Proteopedia
The two-metal ion mechanism employed during the DNA pol catalytic cycle relies on coordination of divalent cations by conserved motifs in the palm domain[1][2]. The palm domain of RB69 DNA pol (residues 383-468, 573-729) contains such (DTD) that are particularly conserved in family B DNA pols. Interestingly, the residue T622 in this sequence must obtain a high energy conformation in order to correctly orient the Asp residues. This property is evident in Ramachandran plots of RB69 DNA pol where T622 is an obvious out-layer.
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A common strategy for crystallizing DNA polymerases in complex with both DNA and an incoming nucleoside triphosphate utilizes a dideoxy-terminated primer strand in the DNA molecule. Since the 3'-OH is absent, the reaction can not proceed following binding and alignment of the substrates. However, since the 3'-OH is required to complete contacts to the coordination sphere of metal ion A, complexes with chain terminated primers often illustrate perturbation or absence of this ion[3]
