The best thing, generally, is to set up your not-for-profit as a completely separate entity from your other businesses, which means your LLC really shouldn't own the membership interest in your not-for-profit.
There really is no additional benefit to having a separate limited liability entity hold the membership interest to the not-for-profit, since the members will generally be insulated from liability of the corporation and the corporation insulated from the members' liability without any extra gimmicks in place.
And, depending on exactly how all your businesses would be related if the LLC owns the not for profit membership interest, it could make it more difficult to obtain and maintain tax exemption status under IRC 501(c).
If you, however, are adamant about having the not for profit interest held by your LLC, you should speak to a CPA to determine whether that would complicate the tax status of the not for profit or the LLC.
There is such a thing as a not-for-profit LLC, at least in theory, but I've never actually seen one and certainly would never recommend one. The IRS is familiar with the not for profit corporation, so why complicate things.
For donations to the not for profit to be tax deductible, the not for profit will have to be qualified as a 501(c)(3) charitable organization under the revenue code. You will need to speak with a CPA about obtaining this qualification and properly maintaining it.
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