1

その巨大{きょだい}な学園{がくえん}は都会{とかい}のど真{ま}ん中{なか}の一等地{いっとうち}聳{そび}えたっていた

I can understand the meaning of this sentence but I can't comprehend what「に」is meaning in it.

3

The immediate question

This に is the locative に indicating where something is happening.

どこ​[に]{●}​立【た】ちますか。
Where [LOC] stand [question mark].
→ Where [do you] stand?
ここ​[に]{●}​立【た】ちます。
Here [LOC] stand.
→ [I] stand here.

In your sample sentence, the に tells us where the action is taking place -- specifically, where その巨大【きょだい】な学園【がくえん】 ("that giant school") is 聳【そび】え立【た】っている ("standing really tall → towering").

Deeper analysis

I suspect you're having trouble breaking down the grammar of the sentence. Let's do that now.

その巨大{きょだい}な学園{がくえん}は都会{とかい}のど真{ま}ん中{なか}の一等地{いっとうち}聳{そび}えたっていた

1) What are we talking about here? Look for the topic particle は:

その巨大{きょだい}な学園{がくえん}​[は]{●}

So we're talking about a 学園{がくえん}. The words before the 学園{がくえん} modify that noun and tell us more about it: the 学園{がくえん} is, more specifically, その ("that") 巨大【きょだい】 ("giant") 学園{がくえん} ("school").

2) What are we saying about the 学園{がくえん}? What is it doing? What is the main verb of our sentence? In Japanese, that's generally at the end:

聳【そび】えたっていた

This is a verb phrase with three verbs: 聳【そび】える ("to be really tall"), 立【た】つ ("to stand"), and いた, the past tense of いる ("to be"), used to form progressive constructions.

Putting these back together, we get "being really tall" + "standing" + "was" → "was standing really tall" → "was towering".

3) Where is the action happening? We can usually tell by looking for the locative particle に:

都会{とかい}のど真{ま}ん中{なか}の一等地{いっとうち}[に]{●}

So the action is happening in the location marked by the に: in this case, in an 一等地【いっとうち】, literally a "first-class [piece of] land", i.e. a "prime location". The words before the 一等地【いっとうち】 tell us more about it, so we know that it is 都会{とかい}のど真{ま}ん中{なか}の, or "right in the middle of the city".


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