Fear of pagan deity in charge (5)
I believe the answer is:
panic
'fear' is the definition.
(panic is a kind of fear)
'pagan deity in charge' is the wordplay.
'pagan deity' becomes 'pan' (spirit in classical myth).
'in charge' becomes 'ic' (abbreviation for 'in charge').
'pan'+'ic'='PANIC'
'of' acts as a link.
(Other definitions for panic that I've seen before include "Widespread fear" , "Extreme fear" , "Frantic fear" , "displaying great fear" , "Greek god" .)