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Results of the clustering analysis of the acceptor ubiquitin position in the initial modeling effort with the UBQ_E2_thioester protocol. This analysis produced 14 clusters. The Cα atoms for Ube2R1 Asp 143 and acceptor ubiquitin Arg 54 are depicted as red spheres. Cluster 3 permits the closest approach of Arg 54 and Asp 143, and models from that cluster were used for refinement. aUbiquitin, acceptor ubiquitin; dUbiquitin, donor ubiquitin.
