Calcium in PDB 1gkb: Concanavalin A, New Crystal Form

The structure of Concanavalin A, New Crystal Form, PDB code: 1gkb was solved by K.Kantardjieff, B.Rupp, P.Hoechtl, B.Segelke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.63 / 1.56
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.700, 101.380, 111.970, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.6

The structure of Concanavalin A, New Crystal Form also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Manganese	(Mn)	2 atoms

The binding sites of Calcium atom in the Concanavalin A, New Crystal Form (pdb code 1gkb). 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, New Crystal Form, PDB code: 1gkb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Concanavalin A, New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A, New Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:20.3 occ:1.00 O A:HOH2318 2.3 23.0 1.0 OD1 A:ASN14 2.3 24.7 1.0 OD2 A:ASP19 2.4 24.6 1.0 O A:TYR12 2.4 24.1 1.0 OD1 A:ASP10 2.4 22.4 1.0 O A:HOH2343 2.5 20.9 1.0 OD2 A:ASP10 2.5 21.9 1.0 CG A:ASP10 2.9 21.4 1.0 CG A:ASN14 3.5 24.9 1.0 CG A:ASP19 3.5 25.1 1.0 C A:TYR12 3.6 24.4 1.0 N A:ASN14 3.9 26.1 1.0 OD1 A:ASP19 3.9 23.2 1.0 CB A:ASN14 4.1 24.9 1.0 MN A:MN801 4.2 22.8 1.0 CB A:ASP10 4.4 21.5 1.0 CA A:TYR12 4.4 24.2 1.0 N A:TYR12 4.5 23.1 1.0 N A:PRO13 4.5 25.9 1.0 CB A:TYR12 4.5 24.1 1.0 CA A:PRO13 4.6 26.2 1.0 CB A:ARG228 4.6 21.8 1.0 ND2 A:ASN14 4.6 24.8 1.0 C A:PRO13 4.6 27.4 1.0 O A:HOH2357 4.6 20.6 1.0 CE1 A:HIS24 4.6 23.6 1.0 CA A:ASN14 4.7 25.7 1.0 O A:ASP208 4.7 22.5 1.0 OD1 A:ASP208 4.7 21.6 1.0 O A:ARG228 4.8 24.3 1.0 CB A:ASP19 4.8 24.9 1.0 CD2 A:TYR12 4.8 25.7 1.0 CA A:ARG228 4.9 22.4 1.0 NE2 A:HIS24 4.9 22.5 1.0

Calcium binding site 2 out of 2 in the Concanavalin A, New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A, New Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:23.2 occ:1.00 O B:HOH2299 2.3 24.6 1.0 OD1 B:ASN14 2.4 27.1 1.0 O B:TYR12 2.4 24.8 1.0 OD2 B:ASP19 2.4 23.9 1.0 O B:HOH2319 2.4 23.1 1.0 OD1 B:ASP10 2.4 23.3 1.0 OD2 B:ASP10 2.6 23.6 1.0 CG B:ASP10 2.8 24.2 1.0 CG B:ASP19 3.5 26.7 1.0 CG B:ASN14 3.5 29.6 1.0 C B:TYR12 3.5 25.1 1.0 N B:ASN14 3.9 27.5 1.0 OD1 B:ASP19 4.0 24.8 1.0 CB B:ASN14 4.1 28.4 1.0 MN B:MN901 4.2 23.5 1.0 CA B:TYR12 4.3 24.9 1.0 CB B:ASP10 4.4 23.4 1.0 N B:TYR12 4.4 23.9 1.0 CB B:TYR12 4.5 24.8 1.0 N B:PRO13 4.6 25.7 1.0 O B:HOH2329 4.6 22.6 1.0 CE1 B:HIS24 4.6 24.3 1.0 O B:ASP208 4.6 21.8 1.0 OD1 B:ASP208 4.6 24.2 1.0 ND2 B:ASN14 4.6 30.3 1.0 CA B:PRO13 4.7 26.6 1.0 CA B:ASN14 4.7 28.0 1.0 CB B:ARG228 4.7 28.8 1.0 C B:PRO13 4.7 28.5 1.0 CB B:ASP19 4.8 26.1 1.0 O B:ARG228 4.8 26.7 1.0 CA B:ARG228 4.9 27.3 1.0 NE2 B:HIS24 4.9 24.1 1.0

K.Kantardjieff, P.Hochtl, B.Segelke, F.Tao, B.Rupp. Concanavalin A in A Dimeric Crystal Form: Revisiting Structural Accuracy and Molecular Flexibility Acta Crystallogr.,Sect.D V. 58 735 2002.
ISSN: ISSN 0907-4449
PubMed: 11976483
DOI: 10.1107/S0907444901019588