Or HaChaim on Exodus 3:5/אור החיים על שמות ג׳:ה׳

1 אל תקרב הלום, של נעליך, "Do not come closer; remove your shoes, etc." G'd gave two instructions. 1) not to come closer. 2) to remove his shoes because even the site on which Moses was standing at that moment was already holy ground. Why did G'd not instruct Moses to remove his shoes before he had accidentally stepped on holy ground wearing shoes? At that time G'd could have warned Moses not to step on holy ground (even without shoes).

2We observe throughout the Torah that G'd's principal concern is with the negative commandments, since failure to observe them is injurious to the soul of the person who violates them. This is what Solomon referred to in Kohelet 12,7 when he spoke about the importance of the spirit G'd has given man returning to G'd after man dies. Shabbat 152 understand the word נתנה as if it it were written אשר נתנה לך, "which has been given to you," meaning that just as a pure soul was given to man so a pure soul has to be returned to G'd. On the other hand, positive commandments are designed to enable man to achieve the "good" G'd has made available to man. As a rule, failure to observe the positive commandments does not result in penalties with the exception of certain basic commandments such as Passover and circumcision [without which a Jew cannot demonstrate his Jewish identity, Ed.].

3In this instance G'd commanded Moses both something negative, i.e. "do not come closer!" as well as something positive, i.e. "remove your shoes!" Our sages in Eyruvin 96 state that wherever the Torah uses the expression פן or אל such as here, what follows is a negative commandment. The words "remove your shoes," are a positive commandment, however. If Moses were to cross the invisible dividing line by approaching closer to the burning bush (as he had intended to) he would be violating a negative commandment. Were he to fail to remove his shoes, however, this would imply a lack of respect for G'd but it would not constitute transgression of a negative commandment because the commandment had been phrased positively, though it implied that no shoes were to be worn there. The Torah always speaks about שמירה, i.e. care not to violate a negative commandment, before demanding עשיה, performance of a related positive commandment (compare Deuteronomy 4,6; 15,5, Genesis 26,5 et al). This is why the sequence in which G'd commanded Moses at this point is no departure from the Torah's norm.

4We still have to answer what G'd had in mind when He did not call out to Moses before the latter had a chance to stand on holy ground clad in shoes. Perhaps Moses did not qualify for an address by G'd unless He had been told not to come still closer. Perhaps the site on which Moses stood at that time became sanctified only by reason of G'd having revealed Himself to Moses there. Perhaps the reason G'd wanted to speak with Moses at that site was in order to have an excuse to sanctify that spot. Perhaps this was the reason for the extra word הוא in the expression אדמת קודש הוא. That word was not really necessary.