Table 3

Results of NMR ensembles scanned with FEATURE Ca2+ binding site model

Protein Name

PDB ID

Number of Models

Number of Models Characterized as Calcium Binding


Lipoprotein receptor-related protein repeat 8

1CR8

20

20

Lipoprotein receptor-related protein repeat 3

1D2L

20

20

RALBP1-intercating protein

1IQ3

18

18

Rous Sarcoma virus receptor

1JRF

20

20

Tyrosine-protein kinase SRC

1KSW

20

20

Calerythrin

1NYA

20

20

Human Notch1

1PB5

16

16

Porcine pancreas phospholipase A2

1SFW

18

1

Rational design of a calcium-binding adhesion protein

1T6W

20

3

Human beta parvalbumin

1TTX

20

20

Cytochrome c peroxidase *

2B10

10

4

Matrilysin

2DDY

25

24

Calcium-binding protein p22

2E+30

20

17

Sodium/calcium exchanger 1 domain 1

2FWS

20

18

Sodium/calcium exchanger 1 domain 2

2FWU

20

18

Rat megalin

2I1P

20

19

Relaxin receptor 1

2JM4

24

22

Yeast frequenin

2JU0

15

15


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.

Halperin et al. BMC Genomics 2008 9(Suppl 2):S2   doi:10.1186/1471-2164-9-S2-S2

Open Data