Calcium in PDB 1gic: Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside

The structure of Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside, PDB code: 1gic was solved by G.M.Bradbrook, T.Gleichmann, S.J.Harrop, J.R.Helliwell, J.Habash, A.J.Kalb(Gilboa), L.Tong, T.C.M.Wan, J.Yariv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.00
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	167.800, 167.800, 167.800, 90.00, 90.00, 90.00
R / Rfree (%)	17 / n/a

The structure of Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside (pdb code 1gic). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside, PDB code: 1gic:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca240 b:13.3 occ:1.00 O A:HOH300 2.2 11.1 1.0 O A:TYR12 2.3 12.4 1.0 OD2 A:ASP19 2.3 17.2 1.0 OD1 A:ASP10 2.3 12.1 1.0 O A:HOH299 2.5 13.9 1.0 OD1 A:ASN14 2.5 14.5 1.0 OD2 A:ASP10 2.6 11.3 1.0 CG A:ASP10 2.8 12.1 1.0 CG A:ASP19 3.5 16.8 1.0 C A:TYR12 3.5 12.2 1.0 CG A:ASN14 3.6 14.6 1.0 OD1 A:ASP19 3.9 16.4 1.0 N A:ASN14 4.1 16.1 1.0 CB A:ASN14 4.2 15.3 1.0 MN A:MN239 4.2 13.5 1.0 CB A:ASP10 4.3 11.5 1.0 CA A:TYR12 4.4 11.7 1.0 N A:TYR12 4.4 11.6 1.0 N A:PRO13 4.4 12.1 1.0 CA A:PRO13 4.5 13.5 1.0 O A:HOH301 4.5 11.8 1.0 CB A:TYR12 4.6 11.9 1.0 C A:PRO13 4.6 15.2 1.0 CE1 A:HIS24 4.7 11.0 1.0 CB A:ASP19 4.7 18.6 1.0 ND2 A:ASN14 4.7 14.2 1.0 O A:ASP208 4.7 11.4 1.0 CA A:ASN14 4.8 16.8 1.0 OD1 A:ASP208 4.8 16.8 1.0 NE2 A:HIS24 4.9 11.8 1.0 CB A:ARG228 4.9 16.7 1.0 O A:ARG228 4.9 16.5 1.0 CA A:ARG228 5.0 17.1 1.0

Calcium binding site 2 out of 2 in the Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca240 b:13.4 occ:1.00 O B:HOH314 2.1 7.1 1.0 OD1 B:ASP10 2.3 8.9 1.0 O B:TYR12 2.3 14.2 1.0 OD2 B:ASP19 2.4 12.9 1.0 O B:HOH315 2.4 11.3 1.0 OD2 B:ASP10 2.5 6.8 1.0 OD1 B:ASN14 2.5 15.2 1.0 CG B:ASP10 2.7 9.6 1.0 CG B:ASP19 3.5 15.3 1.0 C B:TYR12 3.6 12.6 1.0 CG B:ASN14 3.6 14.9 1.0 OD1 B:ASP19 3.9 15.6 1.0 N B:ASN14 4.1 14.8 1.0 MN B:MN239 4.2 14.2 1.0 CB B:ASN14 4.2 15.3 1.0 CB B:ASP10 4.2 9.6 1.0 CA B:TYR12 4.3 12.0 1.0 CB B:TYR12 4.4 12.7 1.0 N B:TYR12 4.4 12.7 1.0 N B:PRO13 4.5 13.7 1.0 O B:HOH316 4.5 11.0 1.0 O B:ASP208 4.5 12.9 1.0 CA B:PRO13 4.6 12.6 1.0 OD1 B:ASP208 4.6 11.8 1.0 ND2 B:ASN14 4.6 14.5 1.0 CB B:ASP19 4.7 17.5 1.0 C B:PRO13 4.8 15.0 1.0 CE1 B:HIS24 4.8 11.6 1.0 CB B:ARG228 4.8 10.8 1.0 CA B:ASN14 4.8 16.2 1.0 CD2 B:TYR12 4.8 15.0 1.0 CA B:ARG228 4.8 10.8 1.0 O B:ARG228 4.9 10.6 1.0

S.J.Harrop, J.R.Helliwell, T.C.Wan, A.J.Kalb, L.Tong, J.Yariv. Structure Solution of A Cubic Crystal of Concanavalin A Complexed with Methyl Alpha-D-Glucopyranoside. Acta Crystallogr.,Sect.D V. 52 143 1996.
ISSN: ISSN 0907-4449
PubMed: 15299735
DOI: 10.1107/S0907444995008742