diff --git a/src/alphafold3/structure/cpp/string_array_pybind.cc b/src/alphafold3/structure/cpp/string_array_pybind.cc
index 29fac72..a4fc4ec 100644
--- a/src/alphafold3/structure/cpp/string_array_pybind.cc
+++ b/src/alphafold3/structure/cpp/string_array_pybind.cc
@@ -174,6 +174,9 @@ py::array_t<bool> IsIn(
 py::array RemapMultipleArrays(
     const std::vector<py::array_t<PyObject*, py::array::c_style>>& arrays,
     const py::dict& mapping) {
+  if (arrays.empty()) {
+    return py::array_t<int64_t>(0);
+  }
   size_t array_size = arrays[0].size();
   for (const auto& array : arrays) {
     if (array.size() != array_size) {
@@ -184,10 +187,6 @@ py::array RemapMultipleArrays(
   // Create a result buffer.
   auto result = py::array_t<int64_t>(array_size);
   absl::Span<int64_t> result_buffer(result.mutable_data(), array_size);
-  PyObject* entry = PyTuple_New(arrays.size());
-  if (entry == nullptr) {
-    throw py::error_already_set();
-  }
   std::vector<absl::Span<PyObject* const>> array_spans;
   array_spans.reserve(arrays.size());
   for (const auto& array : arrays) {
@@ -197,34 +196,38 @@ py::array RemapMultipleArrays(
   // Iterate over arrays and look up elements in the `py_dict`.
   bool fail = false;
   for (size_t i = 0; i < array_size; ++i) {
+    PyObject* entry = PyTuple_New(arrays.size());
+    if (entry == nullptr) {
+      fail = true;
+      break;
+    }
     for (size_t j = 0; j < array_spans.size(); ++j) {
-      PyTuple_SET_ITEM(entry, j, array_spans[j][i]);
+      PyTuple_SET_ITEM(entry, j, Py_NewRef(array_spans[j][i]));
     }
     PyObject* result = PyDict_GetItem(mapping.ptr(), entry);
     if (result != nullptr) {
       int64_t result_value = PyLong_AsLongLong(result);
       if (result_value == -1 && PyErr_Occurred()) {
         fail = true;
+        Py_DECREF(entry);
         break;
       }
       if (result_value > std::numeric_limits<int64_t>::max() ||
           result_value < std::numeric_limits<int64_t>::lowest()) {
         PyErr_SetString(PyExc_OverflowError, "Result value too large.");
         fail = true;
+        Py_DECREF(entry);
         break;
       }
       result_buffer[i] = result_value;
     } else {
       PyErr_Format(PyExc_KeyError, "%R", entry);
       fail = true;
+      Py_DECREF(entry);
       break;
     }
+    Py_DECREF(entry);
   }
-
-  for (size_t j = 0; j < array_spans.size(); ++j) {
-    PyTuple_SET_ITEM(entry, j, nullptr);
-  }
-  Py_XDECREF(entry);
   if (fail) {
     throw py::error_already_set();
   }