It happened on FM 1960 at Veterans Memorial just before 3 a.m. Friday.
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Investigators say the deputy was sitting at red light when the suspected drunk driver in a Grey Mercedes rear-ended his patrol car.
The crash then sent the deputy into the intersection, where a second vehicle hit the patrol car on its side.
Sheriff Ed Gonzalez warned of the dangers of driving while intoxicated on Twitter saying, "One incident involving impaired drivers puts everyone in the area at risk-including police and first responders."
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The deputy is expected to be okay.
The suspected drunk driver is in custody.