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The lawyer took it for granted that his client was innocent.
Literal
Lawyer [topic-は] client [subject-が] not-guilty [nominalized-であること] [obj-を] natural [as-と] thought.
Two structures worth pulling apart. (1) ~であること is the nominalizer for a copular predicate ('the fact that X is Y') — の and こと both work as nominalizers, but こと is preferred here because the nominalized clause has a copular predicate. (2) ~を当然と思う is the frame 'to take X for granted,' with と marking the category into which one mentally places X.