Calcium in PDB 1qgl: Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand

The structure of Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand, PDB code: 1qgl was solved by J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 2.66
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.100, 127.400, 118.900, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20

The structure of Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand (pdb code 1qgl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand, PDB code: 1qgl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca240 b:16.6 occ:1.00 O A:HOH247 2.1 4.2 1.0 OD1 A:ASN14 2.2 23.0 1.0 O A:TYR12 2.3 22.2 1.0 OD2 A:ASP19 2.3 18.0 1.0 O A:HOH242 2.3 11.4 1.0 OD2 A:ASP10 2.6 15.1 1.0 OD1 A:ASP10 2.6 17.4 1.0 CG A:ASP10 2.9 16.9 1.0 CG A:ASN14 3.3 21.5 1.0 CG A:ASP19 3.4 18.1 1.0 C A:TYR12 3.5 22.0 1.0 N A:ASN14 3.7 23.1 1.0 CB A:ASN14 3.9 21.7 1.0 OD1 A:ASP19 4.0 19.8 1.0 MN A:MN239 4.3 14.0 1.0 N A:PRO13 4.4 23.3 1.0 C A:PRO13 4.4 22.8 1.0 CA A:PRO13 4.4 22.8 1.0 CA A:TYR12 4.4 20.9 1.0 CB A:ASP10 4.4 17.0 1.0 CA A:ASN14 4.4 22.8 1.0 ND2 A:ASN14 4.5 20.3 1.0 N A:TYR12 4.5 20.8 1.0 OD1 A:ASP208 4.5 19.0 1.0 CB A:ASP19 4.6 18.4 1.0 CE1 A:HIS24 4.7 12.4 1.0 CB A:TYR12 4.7 21.8 1.0 O A:HOH244 4.7 9.3 1.0 CD1 A:TYR12 4.8 23.1 1.0 O A:ASP208 4.8 20.6 1.0 O A:ARG228 4.9 22.5 1.0 CA A:ARG228 4.9 22.8 1.0 CB A:ARG228 5.0 24.1 1.0

Calcium binding site 2 out of 2 in the Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Room Temperature Structure of Concanavalin A Complexed to Bivalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca240 b:25.4 occ:1.00 O B:HOH248 2.2 15.9 1.0 OD1 B:ASN14 2.2 30.1 1.0 O B:TYR12 2.3 31.1 1.0 OD2 B:ASP19 2.3 28.2 1.0 O B:HOH243 2.4 19.7 1.0 OD2 B:ASP10 2.5 24.5 1.0 OD1 B:ASP10 2.6 26.0 1.0 CG B:ASP10 2.8 24.8 1.0 CG B:ASN14 3.4 30.6 1.0 CG B:ASP19 3.5 29.2 1.0 C B:TYR12 3.5 30.0 1.0 N B:ASN14 3.8 31.7 1.0 CB B:ASN14 4.0 29.7 1.0 OD1 B:ASP19 4.0 31.8 1.0 MN B:MN239 4.2 25.8 1.0 CB B:ASP10 4.3 23.8 1.0 N B:PRO13 4.4 30.4 1.0 CA B:TYR12 4.4 29.1 1.0 C B:PRO13 4.4 30.6 1.0 CA B:PRO13 4.4 29.6 1.0 ND2 B:ASN14 4.5 29.8 1.0 OD1 B:ASP208 4.5 21.7 1.0 N B:TYR12 4.5 26.7 1.0 CA B:ASN14 4.5 31.6 1.0 O B:HOH245 4.6 18.1 1.0 CB B:ASP19 4.6 28.8 1.0 CE1 B:HIS24 4.6 22.0 1.0 CB B:TYR12 4.7 30.4 1.0 O B:ASP208 4.7 25.6 1.0 CD1 B:TYR12 4.8 34.2 1.0 CA B:ARG228 4.9 26.1 1.0 O B:ARG228 4.9 25.2 1.0

S.M.Dimick, S.C.Powell, S.A.Mcmahon, D.N.Moothoo, J.H.Naismith, E.J.Toone. On the Meaning of Affinity: Cluster Glycoside Effects and Concanavalin A J.Am.Chem.Soc. V. 121 10286 1999.
ISSN: ISSN 0002-7863