The atmosphere is made up from 77 percent nitrogen (N2), 22 percent oxygen (02) and all other gases are less than one percent of the atmosphere. The crust, part of the Geosphere is made up for almost 47 percent of Oxygen. Why can’t we breathe the crust?

Well, we can not breathe in solids. But I'm guessing that this question is more based on the type of oxygen that's in the crust.

There are oxygen ions in m=almost everything in the earths crust, yes, but we do not breathe in the same type of oxygen that is bound to their crystal structures.

There are plenty of oxygen atoms in the earth's crust, but there are very few oxygen molecules. The crust is primarily made up of silicate minerals…feldspars, pyroxenes, amphiboles, quartz, etc. There are also lots of oxide, carbonate, phosphate, and sulfate minerals. These all have large amounts of oxygen atoms tightly bound in their crystal structures. But this is not the free molecular oxygen that we breathe.

Because free oxygen molecules (O2) are very reactive, vanishingly little of it is found in the crust below the depths of shallow cool groundwater. Air, including its 20% oxygen, dissolves in rain as it falls from the sky. Some of this air-saturated water soaks into the earth and recharges the groundwater system, carrying the air with it. Nitrogen, argon, and other unreactive trace gases can be circulated quite deeply with this downflowing water…to 10km or more. However oxygen is very reactive, and so it reacts with the minerals in the rocks (or forms new minerals) before it gets transported very deep. You have probably seen evidence of this reaction in red or brown stained rocks exposed at the earth's surface that have been oxidized by downflowing surface waters.

In the geothermal industry, where wells produce deep, magmatically heated waters for power generation, we routinely see atmospheric nitrogen and argon in the produced fluids. This, along with the isotopic composition of the water, gives a clear indicator atmospheric origin of the water (most of it, at least). However there is absolutely no dissolved oxygen in those waters. It all reacted with the rock long ago.