Calcium in PDB 2eaa: Crystal Structure of Adzuki Bean 7S Globulin-3

The structure of Crystal Structure of Adzuki Bean 7S Globulin-3, PDB code: 2eaa was solved by T.Fukuda, B.Mikami, S.Utsumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.873, 99.320, 216.868, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.7

The binding sites of Calcium atom in the Crystal Structure of Adzuki Bean 7S Globulin-3 (pdb code 2eaa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Adzuki Bean 7S Globulin-3, PDB code: 2eaa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Adzuki Bean 7S Globulin-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Adzuki Bean 7S Globulin-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:66.2 occ:1.00 O A:PHE385 2.3 38.4 1.0 O A:GLU382 2.3 37.8 1.0 O A:ALA387 2.4 40.1 1.0 O A:HOH1375 2.6 39.1 1.0 O A:PRO386 2.6 39.7 1.0 O C:HOH1354 2.7 54.5 1.0 C A:PRO386 3.2 39.0 1.0 C A:ALA387 3.3 39.3 1.0 C A:PHE385 3.5 39.0 1.0 C A:GLU382 3.5 38.6 1.0 CA A:PRO386 3.8 39.2 1.0 N A:ALA387 3.8 38.8 1.0 N A:PRO386 4.1 39.0 1.0 CA A:ALA387 4.1 38.5 1.0 N A:SER388 4.2 38.3 1.0 CA A:GLU382 4.2 39.0 1.0 CA A:SER388 4.3 39.4 1.0 O C:SER197 4.4 55.6 1.0 N A:VAL383 4.5 38.4 1.0 OE1 A:GLU382 4.5 53.0 1.0 CA A:VAL383 4.6 38.8 1.0 CA A:PHE385 4.6 37.9 1.0 O A:LEU381 4.7 36.1 1.0 N A:PHE385 4.7 38.5 1.0 CG A:GLU382 4.7 46.9 1.0 O A:HOH1428 4.8 58.8 1.0 CD A:GLU382 4.8 48.8 1.0 C A:SER388 5.0 38.6 1.0 C A:VAL383 5.0 37.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Adzuki Bean 7S Globulin-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Adzuki Bean 7S Globulin-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca905 b:78.3 occ:1.00 O B:PHE385 2.3 47.5 1.0 O B:PRO386 2.4 50.0 1.0 O A:HOH1400 2.5 47.8 1.0 O B:GLU382 2.5 48.7 1.0 O B:ALA387 2.5 54.5 1.0 C B:PRO386 2.9 49.8 1.0 C B:ALA387 3.2 53.6 1.0 C B:PHE385 3.4 47.7 1.0 N B:ALA387 3.6 50.4 1.0 CA B:PRO386 3.6 49.2 1.0 C B:GLU382 3.7 48.4 1.0 CA B:ALA387 3.9 52.2 1.0 N B:PRO386 3.9 48.1 1.0 OE2 B:GLU382 4.0 59.4 1.0 N B:SER388 4.1 54.6 1.0 CA B:SER388 4.4 55.9 1.0 O A:SER197 4.4 66.9 1.0 CA B:GLU382 4.5 48.5 1.0 CA B:PHE385 4.6 46.6 1.0 OE2 A:GLU196 4.7 83.5 1.0 N B:VAL383 4.7 47.7 1.0 CD B:GLU382 4.7 58.0 1.0 CA B:VAL383 4.8 46.8 1.0 N B:PHE385 4.8 46.2 1.0 OE1 A:GLU196 4.9 84.7 1.0 CG B:GLU382 4.9 54.9 1.0 O B:LEU381 4.9 45.6 1.0 CD A:GLU196 5.0 83.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Adzuki Bean 7S Globulin-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Adzuki Bean 7S Globulin-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca904 b:79.5 occ:1.00 O C:GLU382 2.3 36.0 1.0 O C:ALA387 2.4 43.7 1.0 O C:PHE385 2.5 42.4 1.0 O C:PRO386 2.6 43.7 1.0 C C:PRO386 3.2 43.5 1.0 C C:ALA387 3.3 43.7 1.0 C C:GLU382 3.5 36.4 1.0 C C:PHE385 3.6 40.6 1.0 OE1 C:GLU382 3.8 47.8 1.0 N C:ALA387 3.8 43.8 1.0 CA C:PRO386 3.9 43.1 1.0 N C:SER388 4.1 42.6 1.0 CA C:ALA387 4.1 43.3 1.0 N C:PRO386 4.2 42.5 1.0 CA C:SER388 4.2 43.0 1.0 CA C:GLU382 4.3 37.1 1.0 N C:VAL383 4.5 35.7 1.0 O B:SER197 4.6 64.6 1.0 CD C:GLU382 4.6 47.3 1.0 CG C:GLU382 4.7 44.6 1.0 CA C:VAL383 4.7 34.6 1.0 CA C:PHE385 4.8 39.6 1.0 O C:LEU381 4.8 38.0 1.0 C C:SER388 4.8 41.8 1.0 N C:PHE385 4.8 38.7 1.0

T.Fukuda, N.Maruyama, M.R.Salleh, B.Mikami, S.Utsumi. Characterization and Crystallography of Recombinant 7S Globulins of Adzuki Bean and Structure-Function Relationships with 7S Globulins of Various Crops. J.Agric.Food Chem. V. 56 4145 2008.
ISSN: ISSN 0021-8561
PubMed: 18461964
DOI: 10.1021/JF072667B