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Figure 3 | BMC Structural Biology

Figure 3

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

Figure 3

FEATURE predictions confirmed by experimentally solved structures. The structure of concanavalin A from canavalia ensiformis in its apo form (PDB ID: 1APN) is shown in blue. In the original apo structure, loop 15-23 (residues 15-23, sequence TDIGDPSYP) is unstructured. The structure of loop 15-23 was rebuilt using modeling methods. FEATURE predicts a calcium-binding site in 1APN in the presence of the structure of loop 15-23. Searching for homologs, we found that the calcium-binding form concanavalin A has been resolved experimentally (PDB ID: 1VAL). 1VAL binds to a calcium ion and a manganese ion. The close-up view (red for oxygen atoms) shows that the predicted site is similar with the calcium-binding site in 1VAL identified experimentally. The comparison also suggests that more than one metal ions binds to the predicted site. The RMSD between 1APN and 1VAL is 1.61 Å and that between the rebuilt loop in 1APN and the counterpart in 1VAL (pink) is 3.23 Å.

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