I was going to say one was the Unitarian Church led by Starr King on what's modern day Union Square but I'm a couple of blocks off.

Per Ron Henggeler who has identified hundreds of buildings in the 1878 diorama, one is Trinity Episcopal Church (at Post and Powell) and the other is the original Temple Emanu-El. Both were destroyed in the April 1906 earthquake and fire and relocated elsewhere. With a few exceptions - including the top area in the far right panel saved by the legendary golden fire hydrant - more or less everything to the right of the fourth panel ended up as charred rubble.

Interestingly enough, the third panel from the left (which along with the fourth is closest to where Muybridge took the panorama) contains the site of modern day Grace Cathedral, where the lot underneath was involved a land feud for the ages prior to the death of one of the litigants.