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Immersive virtual reality helps students visualize three-dimensional (3D) structures while moving around in a virtual environment and collaborating with their peers. In this study, we investigated the impact of students' movement and collaboration in deepening their understanding of science concepts. Ten pairs of first-year university students experienced learning activities on enzyme-substrate reactions in immersive virtual reality. Students' conversations and movements inside the virtual space were recorded and analyzed. The results showed more exploration of the virtual environments, such as walking inside the enzyme and pulling the substrate, relates to more discovery of concepts and richer scientific discussions. By engaging students in collaboration and embodied learning, immersive virtual reality offers a unique opportunity to learn and explore the 3D molecular world.