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PcrA helicase substrate complex
PcrA.DNA.ADPNP  Detail of duplex DNA binding site.

duplex

The protein has been rotated by about 90o so that you are now viewing the complex looking straight at the duplex DNA binding site. The single stranded DNA is running into the protein and away from the screen. The five base pairs nearest the ss/dsDNA junction are distorted and already partially unwound. Note that in this region the protein is negatively charged (red). Further away from the junction the protein surface is positively charged and creates a good binding surface for B-form DNA. 

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