Bones Charlie removed from southern African capital (5)
I believe the answer is:
sacra
'bones' is the definition.
(sacrum is a kind of bone)
'charlie removed from southern african capital' is the wordplay.
'charlie' becomes 'c' (phonetic alphabet: alpha, bravo, charlie etc.).
'removed from' is a deletion indicator.
'southern' becomes 's' (abbreviation).
'african capital' becomes 'Accra' (capital of Ghana).
's'+'accra'='saccra'
'saccra' with 'c' removed is 'SACRA'.
(Other definitions for sacra that I've seen before include "Bones that form the human pelvic arch" , "Triangular bones" .)