I suppose that in the domain.conf.php on the database section you couold put you certificate
[database]
type=mysqli
host=XXX.XXX.XXX.XXX
port=3306
username=DB_USER
password="DB_PASSWORD"
name=DATABASE_NAME
persistent=
mysql4_compatibility=1
protocol=tcp
compress= [ASUME 1 or 0]
ssl= [ASUME 1 or 0]
capath=PATH/FOR/YOUR/CERTIFICATE.CER
ca=PATH/FOR/CA/CERTIFICATE.CER