Calcium in PDB 1jyi: Concanavalin A/12-Mer Peptide Complex

The structure of Concanavalin A/12-Mer Peptide Complex, PDB code: 1jyi was solved by D.Jain, K.J.Kaur, B.Sundaravadivel, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.545, 118.323, 252.591, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26.5

The structure of Concanavalin A/12-Mer Peptide Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A/12-Mer Peptide Complex (pdb code 1jyi). 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 A/12-Mer Peptide Complex, PDB code: 1jyi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:23.5 occ:1.00 O A:TYR12 2.3 14.0 1.0 OD1 A:ASP10 2.4 22.5 1.0 OD1 A:ASN14 2.4 27.4 1.0 OD2 A:ASP19 2.6 30.3 1.0 OD2 A:ASP10 2.6 22.5 1.0 CG A:ASP10 2.9 22.5 1.0 C A:TYR12 3.5 14.0 1.0 CG A:ASN14 3.6 27.4 1.0 CG A:ASP19 3.7 30.3 1.0 O A:ASP208 4.2 13.2 1.0 OD1 A:ASP19 4.2 30.3 1.0 N A:ASN14 4.2 30.1 1.0 CA A:TYR12 4.3 14.0 1.0 CB A:ASP10 4.4 22.5 1.0 N A:TYR12 4.4 14.0 1.0 OD2 A:ASP208 4.4 23.6 1.0 CB A:TYR12 4.5 29.1 1.0 N A:PRO13 4.5 26.9 1.0 ND2 A:ASN14 4.5 27.4 1.0 CB A:ASN14 4.6 27.4 1.0 CB A:ARG228 4.6 33.5 1.0 MN A:MN401 4.6 23.5 1.0 CA A:PRO13 4.7 26.9 1.0 O A:ARG228 4.7 22.0 1.0 CA A:ARG228 4.7 22.0 1.0 O A:HOH414 4.8 18.8 1.0 C A:PRO13 4.9 26.9 1.0 CD2 A:TYR12 4.9 29.1 1.0 CB A:ASP19 4.9 30.3 1.0

Calcium binding site 2 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:23.5 occ:1.00 OD1 B:ASP10 2.4 17.4 1.0 O B:TYR12 2.5 16.6 1.0 OD2 B:ASP10 2.6 17.4 1.0 OD1 B:ASN14 2.7 29.3 1.0 OD2 B:ASP19 2.7 28.6 1.0 CG B:ASP10 2.8 17.4 1.0 C B:TYR12 3.6 16.6 1.0 CG B:ASN14 3.8 29.3 1.0 CG B:ASP19 3.9 28.6 1.0 OD2 B:ASP208 4.0 26.1 1.0 O B:ASP208 4.2 28.8 1.0 N B:ASN14 4.3 41.6 1.0 N B:TYR12 4.3 16.6 1.0 CA B:TYR12 4.3 16.6 1.0 CB B:ASP10 4.3 17.4 1.0 CB B:TYR12 4.4 31.1 1.0 CB B:ASN14 4.4 29.3 1.0 OD1 B:ASP19 4.4 28.6 1.0 MN B:MN403 4.6 23.5 1.0 N B:PRO13 4.7 26.3 1.0 O B:ARG228 4.8 27.7 1.0 ND2 B:ASN14 4.9 29.3 1.0 CD2 B:TYR12 4.9 31.1 1.0 CB B:ARG228 4.9 41.2 1.0 CA B:PRO13 4.9 26.3 1.0 CA B:ARG228 4.9 27.7 1.0 CG B:ASP208 5.0 26.1 1.0 CA B:ASN14 5.0 41.6 1.0 CA B:ASP10 5.0 27.5 1.0

Calcium binding site 3 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca406 b:23.5 occ:1.00 OD1 C:ASN14 2.3 19.1 1.0 OD1 C:ASP10 2.5 22.0 1.0 O C:TYR12 2.6 9.4 1.0 OD2 C:ASP10 2.6 22.0 1.0 OD2 C:ASP19 2.6 27.8 1.0 CG C:ASP10 2.9 22.0 1.0 CG C:ASN14 3.5 19.1 1.0 C C:TYR12 3.7 9.4 1.0 CG C:ASP19 3.8 27.8 1.0 N C:ASN14 4.1 20.7 1.0 CB C:ASN14 4.2 19.1 1.0 O C:ASP208 4.3 17.1 1.0 CB C:ASP10 4.4 22.0 1.0 OD1 C:ASP19 4.4 27.8 1.0 N C:TYR12 4.5 9.4 1.0 CA C:TYR12 4.5 9.4 1.0 ND2 C:ASN14 4.5 19.1 1.0 CB C:TYR12 4.5 17.7 1.0 MN C:MN405 4.5 23.5 1.0 OD2 C:ASP208 4.6 20.7 1.0 CB C:ARG228 4.6 35.6 1.0 N C:PRO13 4.7 11.8 1.0 CA C:ARG228 4.8 7.3 1.0 O C:ARG228 4.8 7.3 1.0 CA C:ASN14 4.8 20.7 1.0 CB C:ASP19 4.9 27.8 1.0 CD2 C:TYR12 4.9 17.7 1.0 CA C:PRO13 4.9 11.8 1.0 O C:HOH416 5.0 26.1 1.0 C C:PRO13 5.0 11.8 1.0

Calcium binding site 4 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca408 b:23.5 occ:1.00 O D:TYR12 2.2 27.7 1.0 OD1 D:ASN14 2.4 31.3 1.0 OD1 D:ASP10 2.4 32.4 1.0 OD2 D:ASP10 2.8 32.4 1.0 CG D:ASP10 3.0 32.4 1.0 OD2 D:ASP19 3.2 38.4 1.0 C D:TYR12 3.4 27.7 1.0 CG D:ASN14 3.6 31.3 1.0 CG D:ASP19 4.2 38.4 1.0 CA D:TYR12 4.2 27.7 1.0 OD2 D:ASP208 4.2 28.1 1.0 O D:ASP208 4.3 15.5 1.0 N D:TYR12 4.3 27.7 1.0 N D:ASN14 4.3 33.5 1.0 CB D:TYR12 4.3 33.0 1.0 N D:PRO13 4.4 32.6 1.0 ND2 D:ASN14 4.4 31.3 1.0 CB D:ASP10 4.5 32.4 1.0 CA D:PRO13 4.6 32.6 1.0 OD1 D:ASP19 4.6 38.4 1.0 CB D:ASN14 4.6 31.3 1.0 O D:ARG228 4.7 27.8 1.0 MN D:MN407 4.7 23.5 1.0 CD2 D:TYR12 4.8 33.0 1.0 CA D:ARG228 4.8 27.8 1.0 C D:PRO13 4.8 32.6 1.0 O D:HOH419 4.9 15.5 1.0 CB D:ARG228 4.9 52.8 1.0

D.Jain, K.J.Kaur, B.Sundaravadivel, D.M.Salunke. Structural and Functional Consequences of Peptide-Carbohydrate Mimicry. Crystal Structure of A Carbohydrate-Mimicking Peptide Bound to Concanavalin A. J.Biol.Chem. V. 275 16098 2000.
ISSN: ISSN 0021-9258
PubMed: 10821862
DOI: 10.1074/JBC.275.21.16098