diff --git a/src/biotite/structure/atoms.py b/src/biotite/structure/atoms.py
index 2245e0cfa..0be02e172 100644
--- a/src/biotite/structure/atoms.py
+++ b/src/biotite/structure/atoms.py
@@ -233,7 +233,7 @@ def _del_element(self, index):
         else:
             raise TypeError(f"Index must be integer, not '{type(index).__name__}'")
 
-    def equal_annotations(self, item):
+    def equal_annotations(self, item, equal_nan=True):
         """
         Check, if this object shares equal annotation arrays with the
         given :class:`AtomArray` or :class:`AtomArrayStack`.
@@ -242,6 +242,8 @@ def equal_annotations(self, item):
         ----------
         item : AtomArray or AtomArrayStack
             The object to compare the annotation arrays with.
+        equal_nan: bool
+            Whether to count `nan` values as equal. Default: True.
 
         Returns
         -------
@@ -253,7 +255,18 @@ def equal_annotations(self, item):
         if not self.equal_annotation_categories(item):
             return False
         for name in self._annot:
-            if not np.array_equal(self._annot[name], item._annot[name]):
+            # ... allowing `nan` values causes type-casting, which is
+            #     only possible for floating-point arrays
+            allow_nan = (
+                equal_nan
+                if np.issubdtype(self._annot[name].dtype, np.floating)
+                else False
+            )
+            if not np.array_equal(
+                self._annot[name],
+                item._annot[name],
+                equal_nan=allow_nan,
+            ):
                 return False
         return True