Opening of organ permitted (6)
I believe the answer is:
eyelet
'opening' is the definition.
(hole for putting a shoelace through)
'organ permitted' is the wordplay.
'organ' becomes 'eye' (eye is a kind of organ).
'permitted' becomes 'let' (to let something happen is to permit it).
'eye'+'let'='EYELET'
'of' is the link.
(Other definitions for eyelet that I've seen before include "Small hole for lace, etc" , "Small hole through which lace passes" , "A lace is passed through it" , "Hole in shoe through which lace passes" , "Small hole for lacing" .)