Calcium in PDB 2ea7: Crystal Structure of Adzuki Bean 7S Globulin-1

The structure of Crystal Structure of Adzuki Bean 7S Globulin-1, PDB code: 2ea7 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)	14.98 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.598, 48.550, 119.765, 90.00, 97.12, 90.00
R / Rfree (%)	19.3 / 22.8

The binding sites of Calcium atom in the Crystal Structure of Adzuki Bean 7S Globulin-1 (pdb code 2ea7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Adzuki Bean 7S Globulin-1, PDB code: 2ea7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Adzuki Bean 7S Globulin-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca450 b:42.8 occ:1.00 O A:PHE386 2.2 23.7 1.0 O C:HOH613 2.3 49.6 1.0 O A:GLU383 2.3 24.0 1.0 O A:ALA388 2.3 28.1 1.0 O A:HOH674 2.4 42.4 1.0 O A:PRO387 2.7 30.9 1.0 C A:PRO387 3.1 28.5 1.0 C A:ALA388 3.2 28.3 1.0 C A:PHE386 3.4 24.3 1.0 C A:GLU383 3.4 23.8 1.0 N A:ALA388 3.6 27.4 1.0 CA A:PRO387 3.8 28.1 1.0 CA A:ALA388 3.9 27.8 1.0 O C:HOH668 3.9 52.0 1.0 N A:PRO387 4.0 26.2 1.0 CA A:GLU383 4.1 23.2 1.0 N A:SER389 4.1 27.4 1.0 CG A:GLU383 4.2 32.4 1.0 CA A:SER389 4.4 27.4 1.0 N A:VAL384 4.5 23.7 1.0 O C:HOH666 4.5 58.2 1.0 CA A:PHE386 4.5 23.1 1.0 O C:SER198 4.6 58.9 1.0 N A:PHE386 4.6 21.5 1.0 CA A:VAL384 4.7 24.2 1.0 CB A:GLU383 4.8 27.1 1.0 O A:LEU382 4.8 21.3 1.0 C A:SER389 4.9 26.6 1.0 C A:VAL384 5.0 24.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Adzuki Bean 7S Globulin-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca452 b:54.4 occ:1.00 O B:ALA388 2.2 39.0 1.0 O B:PHE386 2.3 34.8 1.0 O B:GLU383 2.3 35.3 1.0 O A:HOH624 2.6 43.4 1.0 O B:PRO387 2.7 39.3 1.0 C B:ALA388 3.2 39.1 1.0 C B:PRO387 3.2 38.1 1.0 C B:PHE386 3.5 35.3 1.0 C B:GLU383 3.5 35.8 1.0 N B:ALA388 3.8 39.0 1.0 CA B:PRO387 3.9 37.7 1.0 N B:SER389 4.0 37.9 1.0 CA B:ALA388 4.0 39.0 1.0 N B:PRO387 4.1 36.7 1.0 CA B:SER389 4.1 37.4 1.0 OE1 A:GLU197 4.2 71.0 1.0 OE1 B:GLU383 4.3 46.2 1.0 CA B:GLU383 4.3 36.7 1.0 O A:SER198 4.4 65.9 1.0 N B:VAL384 4.5 35.2 1.0 CD B:GLU383 4.6 44.6 1.0 O B:LEU382 4.7 33.3 1.0 CA B:PHE386 4.7 33.8 1.0 CA B:VAL384 4.7 34.8 1.0 N B:PHE386 4.7 31.8 1.0 C B:SER389 4.8 38.1 1.0 CG B:GLU383 4.8 42.5 1.0 O B:HOH629 4.9 60.5 1.0 CG A:GLU197 5.0 70.6 1.0 CD A:GLU197 5.0 71.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Adzuki Bean 7S Globulin-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca453 b:65.5 occ:1.00 OD2 B:ASP128 2.2 38.1 1.0 O B:PRO126 2.4 30.7 1.0 ND2 B:ASN71 2.4 32.1 1.0 CG B:ASP128 3.2 36.8 1.0 CG B:ASN71 3.5 31.3 1.0 C B:PRO126 3.5 30.9 1.0 OD1 B:ASN71 3.8 35.7 1.0 OD1 B:ASP128 3.8 38.7 1.0 N B:ASP128 3.8 33.2 1.0 O B:HOH563 3.9 42.2 1.0 C B:ASP127 3.9 32.2 1.0 CG2 B:ILE212 4.0 57.3 1.0 CA B:ASP128 4.2 33.7 1.0 O B:ASP127 4.2 31.2 1.0 CB B:ASP128 4.2 35.5 1.0 OE1 B:GLN213 4.3 69.4 1.0 CB B:ILE212 4.3 57.9 1.0 N B:ASP127 4.4 30.8 1.0 CA B:ASP127 4.4 32.3 1.0 CA B:PRO126 4.4 30.4 1.0 CG1 B:ILE212 4.5 57.5 1.0 CG B:ARG209 4.5 47.9 1.0 O B:HOH700 4.6 37.6 1.0 CB B:ASN71 4.8 28.9 1.0 CB B:ARG209 4.8 47.7 1.0 CA B:ARG209 4.9 49.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Adzuki Bean 7S Globulin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Adzuki Bean 7S Globulin-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca451 b:47.5 occ:1.00 O C:GLU383 2.1 31.7 1.0 O C:PHE386 2.3 30.7 1.0 O C:ALA388 2.4 36.8 1.0 O C:HOH646 2.4 42.6 1.0 O C:HOH592 2.4 42.1 1.0 O C:PRO387 2.7 36.5 1.0 C C:PRO387 3.2 35.4 1.0 C C:GLU383 3.3 32.2 1.0 C C:ALA388 3.3 36.1 1.0 C C:PHE386 3.5 31.9 1.0 CA C:PRO387 3.8 33.8 1.0 N C:ALA388 3.8 36.1 1.0 O C:HOH745 3.8 73.5 1.0 CA C:GLU383 4.0 31.6 1.0 N C:PRO387 4.1 32.5 1.0 CA C:ALA388 4.1 36.5 1.0 N C:SER389 4.2 35.7 1.0 CA C:SER389 4.3 36.7 1.0 OE1 C:GLU383 4.3 42.7 1.0 N C:VAL384 4.4 30.8 1.0 CG C:GLU383 4.4 38.8 1.0 O B:SER198 4.5 56.2 1.0 O C:LEU382 4.6 26.9 1.0 CA C:VAL384 4.6 30.6 1.0 CD C:GLU383 4.6 40.2 1.0 CA C:PHE386 4.6 30.6 1.0 N C:PHE386 4.7 29.6 1.0 CB C:GLU383 4.9 36.2 1.0 C C:SER389 4.9 37.6 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