bring more money
5,000?yen is about 150 nis. It does not strike me as a good idea to travel abroad with so little money. Suppose you want to buy something to eat, or that all ATMs stop working. Better be safe than sorry, and bring a little more cash with you.
My advice is to take along some Euros or Dollars and exchang them in the airport. International money is also good for buying coffee or whatever during connection stops.
As for withdrawing from ATMs, as mentioned above, all 7-Eleven ATMs can withdraw money with international credit cards (just choose 'credit' when asked). ATMs in other konbinis will probably not work for that purpose. Some post offices have ATMs that are compatible with international withdrawal, but you should ask at the reception to make sure.
Finding a 7-Eleven store should be quite easy, even if you just walk around randomly. There's one every 100 meter, it seems.
