by 
davoomac
ANSWERS: 2
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The stock answer is that magical energies were not known on Krypton, so their bodies were ill-prepared to withstand that very alien form of radiation. This is why the insane Captain Marvel was able to beat the supersnot out of Superman in Kingdom Come by calling down the magic lightning of Shazam on him.
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There has been some speculations on just How Magic is able to harm him. Some believe that his body produces an aura/energy field that grants him to a great extent his Invulnerability, and that Maical energies can by pass that field and affect him directly. Others believe that Magic can affect nearly all beings if high enough levels, but that Superman has his extreme naturability durability/healing factor to assist him dealing with its effects. Finally, there appears to be adifference in just what is the nature of the Magic and its affects upon him, for if he is being either punched by someone Magically empowered, or else faces a "magical" energy blast on his body, he takes both well, but is affected much more so by spells to change him say into a frog... Some say that he has a "special" weakness to magic, more so than other beings, and though true in the PC days, it appears that his vulnerability today means that he can be affected and hurt by magic, not Invulnerable to it, but no less/more than any other non magically empowered Super being.
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