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I think you may be confused here. You can buy as many different funds as you want to inside a single IRA account. There is only a single IRA maintenance fee for a single IRA, no matter how many funds you own inside it.
Sorry RK. ddeitch is right. The IRA custodial fee is $10 per EACH FUND whose balance is below $5000 (except for your primary money market fund).

Now I'm confused! Perhaps this helps

Vanguard charges investors a $10 maintenance fee per year on each index fund with less than $10,000 of assets. There is an additional $10 IRA custodial fee for each fund with less than $5,000 unless total assets are more than $50,000. So one's total fees will amount to either $10 or $20 per fund per year depending on the size of one's investments.
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