Dear Sir,
If your mother is regularly withdrawing amount from account and this deposits are made out of this amount only and from no other amount than you can surely deposit total value of Rs. 5 Lacs - Rs. 6 Lacs and no need to worry at all. There may be chances that you may receive an inquiry from Income Tax Department but said can be answer and no question of penalty can be there. Its genuine case of surplus fund on hand and no need to worry about any penalty applicability on it.