Table 3 |
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Results of NMR ensembles scanned with FEATURE Ca2+ binding site model |
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Protein Name |
PDB ID |
Number of Models |
Number of Models Characterized as Calcium Binding |
|
|
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|
Lipoprotein receptor-related protein repeat 8 |
20 |
20 |
|
|
Lipoprotein receptor-related protein repeat 3 |
20 |
20 |
|
|
RALBP1-intercating protein |
18 |
18 |
|
|
Rous Sarcoma virus receptor |
20 |
20 |
|
|
Tyrosine-protein kinase SRC |
20 |
20 |
|
|
Calerythrin |
20 |
20 |
|
|
Human Notch1 |
16 |
16 |
|
|
Porcine pancreas phospholipase A2 |
18 |
1 |
|
|
Rational design of a calcium-binding adhesion protein |
20 |
3 |
|
|
Human beta parvalbumin |
20 |
20 |
|
|
Cytochrome c peroxidase * |
10 |
4 |
|
|
Matrilysin |
25 |
24 |
|
|
Calcium-binding protein p22 |
20 |
17 |
|
|
Sodium/calcium exchanger 1 domain 1 |
20 |
18 |
|
|
Sodium/calcium exchanger 1 domain 2 |
20 |
18 |
|
|
Rat megalin |
20 |
19 |
|
|
Relaxin receptor 1 |
24 |
22 |
|
|
Yeast frequenin |
15 |
15 |
|
|
|
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Scanning of the 18 NMR ensembles with the Ca2+ binding model revealed structural heterogeneity among the structures in the ensembles. In several, most of the models exhibited Ca2+ binding conformations, while in others, only a few. The first and the second columns contain names and PDB IDs of the examined proteins, respectively. The third and fourth columns show the total number of models and how many of those were identified by FEATURE as Ca2+ binding in the NMR ensemble, respectively. * – Results of this scan are shown in Figure 4. |
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Halperin et al. BMC Genomics 2008 9(Suppl 2):S2 doi:10.1186/1471-2164-9-S2-S2 |
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