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Figure 6 | BMC Structural Biology

Figure 6

From: Prediction of calcium-binding sites by combining loop-modeling with machine learning

Figure 6

Novel FEATURE predictions. Structure of bacillus anthraz toxin protective antigen (PDB ID: 1ACC) and the predicted site. Loop 275-288 (residues 275-288, sequence: EDQSTQNTDSETRT) in 1ACC is unstructured. FEATURE predicts a calcium-binding site in 1ACC in the presence of the rebuilt structure for loop 275-288. The close-up view shows the close association between the predicted site and three residues 275E, 276D and 278S. The predicted site is part of domain 2 of 1ACC, which forms a beta-barrel with modified Greek-key topology, including a large flexible loop between strands. Calcium is predicted to bind in a cup-shaped depression formed by the loops of the beta-barrel structure. This beta-structure shares high structural homologies with the C2 calcium-binding domain, which often coordinates 2-3 calcium ions through its loops. Experimental evidence in the original work suggests that loop 275-288 is involved in membrane insertion. This corresponds to the fact that the C2 domain of many proteins plays important roles in calcium-dependent membrane binding. In summary, both structural and functional evidences show that calcium binding to the loops of the beta-structure is very likely. In addition, a calcium-binding site is observed in 1ACC, but it is 61.38 Å apart from our predicted novel site. The close up view (red for oxygen atoms) shows the close associations between the predicted sites and loop 275-288.

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