It is related to nina/una/ana (I have/you have/he or she has). In this case, instead of referring to a person having, it refers to a place having, so we use a locative (we had the three locatives: ku, pa and m). So, there are three forms: kuna/pana/mna (all translate as "the place has" or equivalently "there is/are"). The negative forms of these are hakuna/hapana/hamna.
In this case, the sentence is talking about a crack in a specific location, which is why they use "pana". If you were talking about say cracks inside a house, you might say "mna nyufa nyumbani".