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I wanted to put some protection on my PI's pins and chose the zener voltage protection one, as described here. I used TZX3V3A zener diodes and 330 ohms resistors. Like this :

Schematics

Then I tried to connect an external IC with I2C but it failed. However, when I remove the zener diodes it works perfectly.

I also tested my diodes separately with higher voltage and they seem to do their job nicely.

Any ideas why it won't work ? Or some more things I could try ?

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The Zener diode will not provide the protection you think, for many reasons.

The real reason it doesn't work is the 330Ω resistor. This will form a voltage divider (330/(1800 + 300) or 1/7 and mean the absolute minimum the I2C circuit could pull the Pi is 3.3/7 or ~ 0.5v plus the drop across the driver.

The I2C interface uses a number of open collector/drain devices with pull-up to the supply (the Pi has on-board 1.8k pull-up), so there should be no need for "protection" as there should be no active pull-up involved. If you want to be sure check that the external circuits have no pull-up to 5V (or indeed any other supply). If you want to be extra secure use a Schottky diode to clamp the I2C pins to 3.3v

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Zeners have some current leaking, even if voltage is below their rating. Since I2C uses pull-ups resistors (1.8K) and no direct 3.3V, this leakage will lower the voltage. I think this is what is happening in your case. Try measuring the voltage at the GPIO pin, using a multimeter.

Try removing the 330 resistor. Alternatively use a 3.6V zener instead.

I also found this question that is similar.

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