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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 Ã… 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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