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Figure 2 | BMC Structural Biology

Figure 2

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

Figure 2

FEATURE predictions confirmed by experimentally solved structures. The structure of obelin from obelia longissima in its apo form (PDB ID: 1SL9) is shown in blue. In the original structure, loop 122-128 (residues 122-128, sequence: FDKDGSG) is unstructured. The structure of this region was built using modeling methods. FEATURE predicts a calcium-binding site in 1SL9 in the presence of the structure rebuilt for loop 122-128. The predicted site adopts an EF-hand motif. Searching for homologs, we found that the calcium-binding form obelin has been resolved experimentally (PDB ID: 1SL7). The predicted binding site in 1SL9 is similar with one of the three calcium-binding sites observed in 1SL7. Both sites are in close association with oxygen atoms (red in close-up view) from residues 125D, 129T and 134E. The RMSD between 1SL9 and 1SL7 is 3.01 Å and that between the rebuilt loop in 1SL9 and the counterpart in 1SL7 (pink) is 2.27 Å.

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