Version of Bible kept in bird sanctuary (5)
I believe the answer is:
haven
'sanctuary' is the definition.
(I know that haven is a type of harbor)
'version of bible kept in bird' is the wordplay.
'version of bible' becomes 'AV' (abbreviation for Authorised Version).
'kept in' indicates putting letters inside.
'bird' becomes 'hen' (hen is a kind of bird).
'av' placed into 'hen' is 'HAVEN'.
(Other definitions for haven that I've seen before include "Sheltered port" , "Small port, refuge" , "Harbour, oasis" , "Refuge; harbour" , "Place of shelter" .)