Calcium in PDB 1azd: Concanavalin From Canavalia Brasiliensis

The structure of Concanavalin From Canavalia Brasiliensis, PDB code: 1azd was solved by J.Sanz-Aparicio, J.Hermoso, T.B.Grangeiro, J.J.Calvete, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.290, 71.650, 190.960, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 24

The structure of Concanavalin From Canavalia Brasiliensis also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin From Canavalia Brasiliensis (pdb code 1azd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Concanavalin From Canavalia Brasiliensis, PDB code: 1azd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca238 b:11.8 occ:1.00 OD1 A:ASN14 2.3 30.5 1.0 OD1 A:ASP10 2.5 20.1 1.0 O A:TYR12 2.5 23.1 1.0 OD2 A:ASP10 2.7 7.0 1.0 OD2 A:ASP19 2.8 29.1 1.0 CG A:ASP10 2.9 13.3 1.0 CG A:ASN14 3.5 25.0 1.0 C A:TYR12 3.7 23.5 1.0 CG A:ASP19 3.9 25.5 1.0 N A:ASN14 4.1 20.4 1.0 CB A:ASN14 4.2 22.7 1.0 OD1 A:ASP19 4.3 31.7 1.0 MN A:MN239 4.3 16.1 1.0 ND2 A:ASN14 4.4 20.6 1.0 CB A:ASP10 4.4 10.9 1.0 O A:ARG228 4.6 25.6 1.0 CB A:ARG228 4.6 27.6 1.0 O A:ASP208 4.6 9.2 1.0 CA A:TYR12 4.6 19.5 1.0 N A:TYR12 4.6 16.3 1.0 CA A:ARG228 4.7 26.4 1.0 OD1 A:ASP208 4.7 12.3 1.0 N A:PRO13 4.7 21.5 1.0 CA A:PRO13 4.7 20.5 1.0 CB A:TYR12 4.8 18.7 1.0 CA A:ASN14 4.8 21.7 1.0 C A:PRO13 4.9 19.8 1.0 CE1 A:HIS24 4.9 13.8 1.0

Calcium binding site 2 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca238 b:20.5 occ:1.00 OD1 B:ASN14 2.3 22.2 1.0 OD1 B:ASP10 2.5 24.8 1.0 O B:TYR12 2.6 19.4 1.0 OD2 B:ASP10 2.7 13.0 1.0 OD2 B:ASP19 2.8 22.0 1.0 CG B:ASP10 2.9 16.3 1.0 CG B:ASN14 3.4 17.2 1.0 C B:TYR12 3.8 18.3 1.0 CG B:ASP19 4.0 23.7 1.0 N B:ASN14 4.1 23.4 1.0 CB B:ASN14 4.2 19.0 1.0 OD1 B:ASP19 4.4 26.8 1.0 ND2 B:ASN14 4.4 12.4 1.0 MN B:MN239 4.5 12.1 1.0 CB B:ASP10 4.5 13.8 1.0 O B:ASP208 4.5 9.2 1.0 CB B:ARG228 4.5 20.1 1.0 O B:ARG228 4.5 11.3 1.0 OD1 B:ASP208 4.6 12.3 1.0 CA B:ARG228 4.6 17.8 1.0 CA B:TYR12 4.6 18.7 1.0 N B:TYR12 4.6 15.6 1.0 N B:PRO13 4.7 18.9 1.0 CB B:TYR12 4.8 23.1 1.0 CA B:PRO13 4.8 18.1 1.0 CA B:ASN14 4.8 23.3 1.0 C B:PRO13 4.9 22.1 1.0 CE1 B:HIS24 4.9 2.2 1.0

Calcium binding site 3 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca238 b:27.8 occ:1.00 OD1 C:ASN14 2.2 24.6 1.0 OD1 C:ASP10 2.5 24.8 1.0 O C:TYR12 2.6 16.2 1.0 OD2 C:ASP10 2.7 26.3 1.0 OD2 C:ASP19 2.8 28.2 1.0 CG C:ASP10 3.0 22.9 1.0 CG C:ASN14 3.4 20.9 1.0 C C:TYR12 3.8 17.5 1.0 CG C:ASP19 3.9 30.3 1.0 N C:ASN14 4.1 23.8 1.0 CB C:ASN14 4.2 21.6 1.0 OD1 C:ASP19 4.3 33.7 1.0 ND2 C:ASN14 4.4 22.0 1.0 OD1 C:ASP208 4.4 12.3 1.0 MN C:MN239 4.4 9.6 1.0 CB C:ASP10 4.5 15.5 1.0 O C:ARG228 4.5 20.7 1.0 CB C:ARG228 4.5 23.2 1.0 O C:ASP208 4.6 9.2 1.0 CA C:ARG228 4.6 21.1 1.0 CA C:TYR12 4.6 18.6 1.0 N C:TYR12 4.6 14.2 1.0 N C:PRO13 4.7 18.8 1.0 CA C:PRO13 4.8 18.6 1.0 CB C:TYR12 4.8 23.5 1.0 CA C:ASN14 4.8 24.0 1.0 C C:PRO13 4.9 20.2 1.0 CE1 C:HIS24 4.9 5.6 1.0

Calcium binding site 4 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca238 b:10.6 occ:1.00 OD1 D:ASN14 2.3 34.0 1.0 OD1 D:ASP10 2.5 23.9 1.0 O D:TYR12 2.5 25.6 1.0 OD2 D:ASP10 2.7 13.1 1.0 OD2 D:ASP19 2.8 29.0 1.0 CG D:ASP10 2.9 19.4 1.0 CG D:ASN14 3.5 31.4 1.0 C D:TYR12 3.7 23.9 1.0 CG D:ASP19 3.9 25.9 1.0 N D:ASN14 4.1 22.8 1.0 CB D:ASN14 4.2 27.2 1.0 OD1 D:ASP19 4.4 29.8 1.0 MN D:MN239 4.4 16.6 1.0 ND2 D:ASN14 4.4 33.8 1.0 CB D:ASP10 4.4 14.8 1.0 O D:ARG228 4.6 28.0 1.0 CB D:ARG228 4.6 28.0 1.0 CA D:TYR12 4.6 21.4 1.0 O D:ASP208 4.6 9.2 1.0 N D:TYR12 4.6 20.8 1.0 OD1 D:ASP208 4.6 12.3 1.0 CA D:ARG228 4.6 23.5 1.0 N D:PRO13 4.7 20.8 1.0 CA D:PRO13 4.7 17.9 1.0 CB D:TYR12 4.8 23.6 1.0 CA D:ASN14 4.8 27.2 1.0 C D:PRO13 4.9 18.5 1.0 CE1 D:HIS24 4.9 11.1 1.0

J.Sanz-Aparicio, J.Hermoso, T.B.Grangeiro, J.J.Calvete, B.S.Cavada. The Crystal Structure of Canavalia Brasiliensis Lectin Suggests A Correlation Between Its Quaternary Conformation and Its Distinct Biological Properties From Concanavalin A. Febs Lett. V. 405 114 1997.
ISSN: ISSN 0014-5793
PubMed: 9094437
DOI: 10.1016/S0014-5793(97)00137-3