I've read in Geshe Kelsang Gyatso in "Great Treasury of Merit", that the three (principal) places, also called the 'three doors', are the body (crown chakra), speech (throat chakra), and mind (heart chakra).
Same like what Pabongka Rinpoche said, the three Vajras are a white OM (at the crown), a red AH (at the throat), and a blue HUM (at the heart). These are known as the 'three vajras' because they are the nature of the vajra body, the vajra speech, and the vajra mind of all the Buddhas.
A Buddha's body, speech, and mind are called 'vajras' because they are immortal and indestructible, completely beyond birth, ageing and death.