Hum... it's conceivable his powers offer some resistance to transmutation, but I think he has no on panel showings of this. His reaction time is supposed to be 0.013 second. How fast is she? I can see him winning if he attacks first with an EMP or iron rip, otherwise it's gonna be complicated, she can probably affect him inside the shields.
He's made a solid comb out of the air before and IRCC the caption says it envolved subatomic transmutation, but it strained him. He has altered metal in the 'molecular' (metal doesn't have molecules) and subatomic level before, it's a lot easier for him do metal. He also altered organic molecules and manipulated the metabolism of others in the molecular level through direct (manipulation of ions and neutral atoms) and indirect ways (UV irradiation with extremely fine control).
Most of these should be in his respect forum. There is also a fanmade site dedicated to him that has all of these, but it's been ages since I saw it, I'll try to find it.
He does not, however, have molecular control of his own body, not like apocalipse or thanos do anyway. But he can channel his powers trhough his own body to increase his strengh, durability, stamina and speed, presumabily he can do to himself any of the metabolism manipulation he does to others. But it's far from claiming atomic control over himself.
Since his powers deal with electromagnetic force that makes atoms and molecules what they are it's conceivable they provide some passive defense against it, but feats are ellusive. In fact protheus did manage to turn some, but not all of the iron in his blood into lead. One could think that proves he doesn't a have resistance to it and the only reason proteus did not do it all the way or turn him into glass was PIS, or that he has a partial resistance to it and that's why he survived. Of course protheus is a reality warper not just a mater manipulator, so it's not exactly the same scenario.
His reaction time is something like 0.013 seconds and an EMP could propbably shut her down immediatly, iron rip and tearing her apart should work too. How durable and fast is she?
Speed is debatable. She was fast enough to duck in and out of a rift in space-time to save Crystal.
Durability is solid. She can survive reentry into the atmosphere, she brushed off hurricane force winds, she took Vision's phased/solidified fist to the head, she's been shown pretty much immune to heat damage, and she's been completely atomized by Blastaar and then reassembled herself.
She definitely has more control over her own body AND Magneto's body than he does. He's toast.
Even if he were to start to iron rip her or something before hand, which I doubt would be the case with her actually being superhuman, she could just revert the process and turn him to salt.
Has Sersi ever transmuted someone through a force field because from what I understand her powers we stopped by IW's. I know Mag's and Sue have different types of force fields so it's entirely possible that his won't work against Sersi like that, but it is something to take into consideration.
I don't doubt that she has much better overall matter manipulation including of living systems. But when it comes to a metal and they are both struggling for control over the iron in her blood, he would probably win. Then again, if she can attack him simultaneously, things would likely get complicated for him.
Since she can reassemble, would tearing her apart put her down long enough for a victory? How long does it take?