Calcium in PDB 1jyc: Concanavalin A/15-Mer Peptide Complex

The structure of Concanavalin A/15-Mer Peptide Complex, PDB code: 1jyc was solved by D.Jain, K.J.Kaur, 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 (°)	103.113, 118.547, 254.994, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24

The structure of Concanavalin A/15-Mer Peptide Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A/15-Mer Peptide Complex (pdb code 1jyc). 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/15-Mer Peptide Complex, PDB code: 1jyc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.6 occ:1.00 O A:TYR12 2.3 35.7 1.0 OD1 A:ASN14 2.4 39.5 1.0 OD1 A:ASP10 2.5 20.4 1.0 OD2 A:ASP19 2.7 16.3 1.0 OD2 A:ASP10 2.9 20.4 1.0 CG A:ASP10 3.1 20.4 1.0 O A:HOH461 3.1 79.4 1.0 C A:TYR12 3.3 35.7 1.0 CG A:ASN14 3.4 39.5 1.0 CB A:TYR12 3.7 39.6 1.0 CG A:ASP19 3.8 16.3 1.0 CA A:TYR12 3.9 35.7 1.0 OD2 A:ASP208 4.1 14.4 1.0 N A:ASN14 4.2 26.1 1.0 CB A:ASN14 4.2 39.5 1.0 O A:ASP208 4.2 16.5 1.0 N A:TYR12 4.2 35.7 1.0 ND2 A:ASN14 4.3 39.5 1.0 N A:PRO13 4.4 29.4 1.0 OD1 A:ASP19 4.4 16.3 1.0 CB A:ASP10 4.6 20.4 1.0 CA A:ARG228 4.6 17.1 1.0 O A:ARG228 4.7 17.1 1.0 MN A:MN401 4.8 28.7 1.0 CG A:TYR12 4.8 39.6 1.0 CB A:ARG228 4.8 35.2 1.0 CD2 A:TYR12 4.8 39.6 1.0 CA A:PRO13 4.8 29.4 1.0 CA A:ASN14 4.9 26.1 1.0 C A:PRO13 4.9 29.4 1.0 O A:HOH440 4.9 29.0 1.0 CB A:ASP19 5.0 16.3 1.0

Calcium binding site 2 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:24.9 occ:1.00 OD1 B:ASN14 2.3 40.1 1.0 OD2 B:ASP19 2.3 37.0 1.0 O B:TYR12 2.3 29.3 1.0 OD1 B:ASP10 2.4 27.2 1.0 OD2 B:ASP10 2.7 27.2 1.0 CG B:ASP10 2.9 27.2 1.0 CG B:ASP19 3.5 37.0 1.0 CG B:ASN14 3.5 40.1 1.0 C B:TYR12 3.5 29.3 1.0 OD1 B:ASP19 4.0 37.0 1.0 N B:ASN14 4.0 51.9 1.0 CB B:ASN14 4.3 40.1 1.0 CA B:TYR12 4.3 29.3 1.0 N B:TYR12 4.4 29.3 1.0 CB B:ASP10 4.4 27.2 1.0 ND2 B:ASN14 4.4 40.1 1.0 N B:PRO13 4.5 18.6 1.0 CB B:TYR12 4.6 28.2 1.0 MN B:MN403 4.6 27.0 1.0 CA B:PRO13 4.6 18.6 1.0 OD2 B:ASP208 4.6 36.3 1.0 CB B:ASP19 4.6 37.0 1.0 O B:ASP208 4.6 27.5 1.0 CE1 B:HIS24 4.7 23.8 1.0 C B:PRO13 4.8 18.6 1.0 CA B:ASN14 4.8 51.9 1.0 CA B:ARG228 4.9 22.3 1.0 O B:ARG228 5.0 22.3 1.0

Calcium binding site 3 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca406 b:10.8 occ:1.00 OD1 C:ASN14 2.3 27.7 1.0 OD2 C:ASP19 2.4 28.0 1.0 O C:TYR12 2.4 15.0 1.0 OD1 C:ASP10 2.5 21.9 1.0 OD2 C:ASP10 2.8 21.9 1.0 CG C:ASP10 3.0 21.9 1.0 CG C:ASN14 3.5 27.7 1.0 CG C:ASP19 3.6 28.0 1.0 C C:TYR12 3.6 15.0 1.0 OD1 C:ASP19 4.1 28.0 1.0 N C:ASN14 4.2 22.2 1.0 CB C:ASN14 4.3 27.7 1.0 ND2 C:ASN14 4.4 27.7 1.0 CA C:TYR12 4.4 15.0 1.0 N C:TYR12 4.4 15.0 1.0 OD2 C:ASP208 4.4 23.8 1.0 CB C:ASP10 4.4 21.9 1.0 O C:ASP208 4.5 17.6 1.0 CB C:TYR12 4.6 18.3 1.0 N C:PRO13 4.6 15.3 1.0 MN C:MN405 4.7 28.7 1.0 CB C:ASP19 4.8 28.0 1.0 CA C:PRO13 4.8 15.3 1.0 CA C:ARG228 4.8 12.6 1.0 CE1 C:HIS24 4.8 39.9 1.0 O C:ARG228 4.9 12.6 1.0 CA C:ASN14 4.9 22.2 1.0 C C:PRO13 4.9 15.3 1.0 CB C:ARG228 4.9 61.1 1.0

Calcium binding site 4 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca408 b:27.1 occ:1.00 O D:TYR12 2.4 40.9 1.0 OD1 D:ASN14 2.4 54.2 1.0 OD1 D:ASP10 2.5 38.5 1.0 OD2 D:ASP19 2.6 30.9 1.0 OD2 D:ASP10 2.8 38.5 1.0 CG D:ASP10 3.0 38.5 1.0 C D:TYR12 3.4 40.9 1.0 CG D:ASN14 3.5 54.2 1.0 CB D:TYR12 3.7 40.4 1.0 CG D:ASP19 3.8 30.9 1.0 CA D:TYR12 4.0 40.9 1.0 N D:ASN14 4.2 35.6 1.0 CB D:ASN14 4.2 54.2 1.0 OD2 D:ASP208 4.2 30.7 1.0 N D:TYR12 4.2 40.9 1.0 O D:ASP208 4.3 28.2 1.0 OD1 D:ASP19 4.3 30.9 1.0 ND2 D:ASN14 4.4 54.2 1.0 N D:PRO13 4.4 30.8 1.0 CB D:ASP10 4.5 38.5 1.0 MN D:MN407 4.6 27.0 1.0 CA D:ARG228 4.7 30.5 1.0 O D:ARG228 4.7 30.5 1.0 CG D:TYR12 4.8 40.4 1.0 CB D:ARG228 4.8 55.0 1.0 CA D:PRO13 4.8 30.8 1.0 CD2 D:TYR12 4.8 40.4 1.0 O D:HOH436 4.9 21.2 1.0 CA D:ASN14 4.9 35.6 1.0 C D:PRO13 4.9 30.8 1.0 CB D:ASP19 4.9 30.9 1.0

D.Jain, K.J.Kaur, D.M.Salunke. Plasticity in Protein-Peptide Recognition: Crystal Structures of Two Different Peptides Bound to Concanavalin A Biophys.J. V. 80 2912 2001.
ISSN: ISSN 0006-3495
PubMed: 11371463