Calcium in PDB 1joj: Concanavalin A-Hexapeptide Complex

The structure of Concanavalin A-Hexapeptide Complex, PDB code: 1joj was solved by D.Jain, K.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 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.685, 118.384, 253.593, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.1

The structure of Concanavalin A-Hexapeptide Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

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

Calcium binding site 1 out of 4 in the Concanavalin A-Hexapeptide 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-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:22.2 occ:1.00 O A:TYR12 2.5 14.6 1.0 O A:HOH328 2.5 17.4 1.0 OD2 A:ASP19 2.6 21.1 1.0 OD1 A:ASP10 2.8 16.6 1.0 OD2 A:ASP10 2.9 16.6 1.0 CG A:ASN14 3.2 26.2 1.0 CG A:ASP10 3.2 16.6 1.0 ND2 A:ASN14 3.4 26.2 1.0 OD1 A:ASN14 3.4 26.2 1.0 CG A:ASP19 3.5 21.1 1.0 C A:TYR12 3.7 14.6 1.0 N A:ASN14 3.8 22.9 1.0 CB A:ASN14 3.8 26.2 1.0 OD1 A:ASP19 3.9 21.1 1.0 CA A:ASN14 4.4 22.9 1.0 CA A:TYR12 4.5 14.6 1.0 CA A:PRO13 4.6 15.8 1.0 C A:PRO13 4.6 15.8 1.0 CB A:ASP19 4.6 21.1 1.0 CB A:TYR12 4.6 46.5 1.0 N A:PRO13 4.6 15.8 1.0 CB A:ARG228 4.6 27.1 1.0 N A:TYR12 4.6 14.6 1.0 OD2 A:ASP208 4.7 18.6 1.0 MN A:MN301 4.7 22.2 1.0 CA A:ARG228 4.7 18.4 1.0 CB A:ASP10 4.8 16.6 1.0 O A:ARG228 4.9 18.4 1.0 O A:ASP208 4.9 15.2 1.0

Calcium binding site 2 out of 4 in the Concanavalin A-Hexapeptide 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-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:22.2 occ:1.00 OD1 B:ASP10 2.4 18.5 1.0 OD1 B:ASN14 2.5 30.1 1.0 OD2 B:ASP19 2.5 28.4 1.0 O B:TYR12 2.5 21.8 1.0 OD2 B:ASP10 2.6 18.5 1.0 CG B:ASP10 2.8 18.5 1.0 CG B:ASN14 3.6 30.1 1.0 CG B:ASP19 3.6 28.4 1.0 C B:TYR12 3.7 21.8 1.0 OD1 B:ASP19 4.1 28.4 1.0 N B:ASN14 4.2 26.0 1.0 CB B:ASN14 4.2 30.1 1.0 CB B:ASP10 4.3 18.5 1.0 O B:ASP208 4.3 32.5 1.0 N B:TYR12 4.5 21.8 1.0 CA B:TYR12 4.5 21.8 1.0 MN B:MN303 4.6 22.2 1.0 OD2 B:ASP208 4.6 32.0 1.0 CA B:ARG228 4.7 24.9 1.0 ND2 B:ASN14 4.7 30.1 1.0 CB B:TYR12 4.7 29.6 1.0 N B:PRO13 4.7 22.1 1.0 O B:ARG228 4.7 24.9 1.0 CA B:ASN14 4.9 26.0 1.0 CB B:ARG228 4.9 51.9 1.0 CB B:ASP19 4.9 28.4 1.0 CA B:PRO13 4.9 22.1 1.0 C B:PRO13 5.0 22.1 1.0

Calcium binding site 3 out of 4 in the Concanavalin A-Hexapeptide 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-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca306 b:22.2 occ:1.00 OD2 C:ASP19 2.2 31.8 1.0 O C:HOH342 2.4 12.2 1.0 O C:TYR12 2.4 12.5 1.0 OD1 C:ASN14 2.5 14.2 1.0 OD1 C:ASP10 2.5 17.7 1.0 OD2 C:ASP10 2.6 17.7 1.0 CG C:ASP10 2.8 17.7 1.0 CG C:ASP19 3.4 31.8 1.0 CG C:ASN14 3.6 14.2 1.0 C C:TYR12 3.7 12.5 1.0 OD1 C:ASP19 3.9 31.8 1.0 N C:ASN14 4.0 12.2 1.0 CB C:ASN14 4.1 14.2 1.0 CB C:ASP10 4.3 17.7 1.0 MN C:MN305 4.4 22.2 1.0 CA C:TYR12 4.5 12.5 1.0 N C:TYR12 4.6 12.5 1.0 CB C:ASP19 4.6 31.8 1.0 O C:ASP208 4.6 15.4 1.0 N C:PRO13 4.6 12.5 1.0 ND2 C:ASN14 4.7 14.2 1.0 CA C:ASN14 4.7 12.2 1.0 CA C:PRO13 4.7 12.5 1.0 CE1 C:HIS24 4.8 20.3 1.0 CB C:TYR12 4.8 25.3 1.0 C C:PRO13 4.8 12.5 1.0 CA C:ARG228 4.9 16.1 1.0 O C:ARG228 4.9 16.1 1.0 OD2 C:ASP208 4.9 18.8 1.0 NE2 C:HIS24 4.9 20.3 1.0 CB C:ARG228 5.0 25.5 1.0

Calcium binding site 4 out of 4 in the Concanavalin A-Hexapeptide 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-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca308 b:22.2 occ:1.00 O D:TYR12 2.4 25.1 1.0 OD2 D:ASP19 2.6 31.7 1.0 O D:HOH321 2.7 12.2 1.0 OD1 D:ASP10 2.9 16.8 1.0 OD2 D:ASP10 3.0 16.8 1.0 CG D:ASN14 3.2 21.6 1.0 OD1 D:ASN14 3.2 21.6 1.0 CG D:ASP10 3.3 16.8 1.0 ND2 D:ASN14 3.4 21.6 1.0 CG D:ASP19 3.4 31.7 1.0 C D:TYR12 3.6 25.1 1.0 N D:ASN14 3.7 25.9 1.0 CB D:ASN14 3.7 21.6 1.0 OD1 D:ASP19 3.9 31.7 1.0 CA D:ASN14 4.3 25.9 1.0 C D:PRO13 4.5 20.1 1.0 CA D:PRO13 4.5 20.1 1.0 CA D:TYR12 4.5 25.1 1.0 CB D:ASP19 4.5 31.7 1.0 N D:PRO13 4.6 20.1 1.0 CB D:TYR12 4.6 43.4 1.0 CB D:ARG228 4.6 49.7 1.0 N D:TYR12 4.6 25.1 1.0 OD2 D:ASP208 4.7 22.8 1.0 MN D:MN307 4.7 22.2 1.0 CA D:ARG228 4.7 23.7 1.0 CB D:ASP10 4.8 16.8 1.0 O D:ARG228 4.9 23.7 1.0 O D:ASP208 5.0 16.1 1.0

D.Jain, K.J.Kaur, D.M.Salunke. Enhanced Binding of A Rationally Designed Peptide Ligand of Concanavalin A Arises From Improved Geometrical Complementarity. Biochemistry V. 40 12059 2001.
ISSN: ISSN 0006-2960
PubMed: 11580281
DOI: 10.1021/BI011254F