Calcium in PDB 1bxh: Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside

The structure of Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside, PDB code: 1bxh was solved by D.N.Moothoo, B.Canaan, R.A.Field, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	119.700, 119.700, 68.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.8

The structure of Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside (pdb code 1bxh). 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 Complexed to Methyl ALPHA1-2 Mannobioside, PDB code: 1bxh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside


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 to Methyl ALPHA1-2 Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:15.6 occ:1.00 O A:TYR12 2.2 29.4 1.0 O A:HOH259 2.3 7.5 1.0 O A:HOH246 2.4 5.4 1.0 OD2 A:ASP19 2.4 30.2 1.0 OD1 A:ASP10 2.4 17.9 1.0 OD2 A:ASP10 2.5 17.0 1.0 OD1 A:ASN14 2.6 29.5 1.0 CG A:ASP10 2.8 19.1 1.0 C A:TYR12 3.4 29.0 1.0 CG A:ASP19 3.5 31.3 1.0 CG A:ASN14 3.6 29.9 1.0 N A:ASN14 3.9 32.7 1.0 OD1 A:ASP19 4.0 30.5 1.0 CB A:ASN14 4.1 30.3 1.0 CA A:TYR12 4.2 27.6 1.0 MN A:MN238 4.2 33.9 1.0 CB A:ASP10 4.3 18.3 1.0 N A:TYR12 4.3 26.7 1.0 CB A:TYR12 4.3 28.0 1.0 N A:PRO13 4.4 30.3 1.0 CA A:PRO13 4.5 30.5 1.0 C A:PRO13 4.6 31.0 1.0 CB A:ASP19 4.6 32.1 1.0 O A:ASP208 4.6 25.7 1.0 CE1 A:HIS24 4.6 21.0 1.0 CA A:ASN14 4.7 32.0 1.0 OD1 A:ASP208 4.7 28.0 1.0 O A:HOH244 4.7 2.0 1.0 ND2 A:ASN14 4.8 30.8 1.0 CD2 A:TYR12 4.8 29.4 1.0 CA A:ARG228 5.0 25.1 1.0 O A:ARG228 5.0 23.2 1.0

Calcium binding site 2 out of 4 in the Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside


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 to Methyl ALPHA1-2 Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:24.8 occ:1.00 O B:HOH244 2.2 19.6 1.0 OD2 B:ASP19 2.3 35.7 1.0 O B:TYR12 2.4 29.5 1.0 OD2 B:ASP10 2.5 22.4 1.0 OD1 B:ASN14 2.6 33.7 1.0 OD1 B:ASP10 2.7 22.8 1.0 O B:HOH242 2.7 25.2 1.0 CG B:ASP10 2.9 22.7 1.0 CG B:ASP19 3.4 35.9 1.0 CG B:ASN14 3.6 34.0 1.0 C B:TYR12 3.6 29.4 1.0 OD1 B:ASP19 3.9 37.6 1.0 MN B:MN238 4.0 34.6 1.0 N B:ASN14 4.0 32.1 1.0 CB B:ASN14 4.1 32.7 1.0 CB B:ASP10 4.4 20.8 1.0 CA B:TYR12 4.5 29.0 1.0 N B:PRO13 4.6 29.1 1.0 N B:TYR12 4.6 28.3 1.0 CB B:TYR12 4.6 30.5 1.0 CA B:PRO13 4.6 29.6 1.0 CB B:ASP19 4.6 35.8 1.0 O B:ASP208 4.7 22.7 1.0 CA B:ASN14 4.7 33.5 1.0 OD1 B:ASP208 4.7 26.3 1.0 O B:ARG228 4.7 22.0 1.0 ND2 B:ASN14 4.7 34.6 1.0 C B:PRO13 4.7 30.4 1.0 CA B:ARG228 4.7 23.8 1.0 CE1 B:HIS24 4.8 23.3 1.0 CB B:ARG228 4.9 24.9 1.0 CD2 B:TYR12 4.9 32.3 1.0

Calcium binding site 3 out of 4 in the Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:33.2 occ:1.00 O C:TYR12 2.0 33.2 1.0 OD2 C:ASP19 2.2 38.6 1.0 O C:HOH249 2.2 22.4 1.0 OD1 C:ASN14 2.5 38.5 1.0 OD1 C:ASP10 2.6 26.1 1.0 OD2 C:ASP10 2.6 28.6 1.0 O C:HOH246 2.8 18.5 1.0 CG C:ASP10 2.9 26.8 1.0 C C:TYR12 3.3 33.3 1.0 CG C:ASP19 3.3 39.5 1.0 CG C:ASN14 3.5 37.2 1.0 N C:ASN14 3.7 36.7 1.0 OD1 C:ASP19 3.9 41.0 1.0 CB C:ASN14 4.0 35.6 1.0 MN C:MN238 4.1 49.5 1.0 CA C:TYR12 4.2 33.0 1.0 N C:PRO13 4.2 34.0 1.0 CA C:PRO13 4.3 35.3 1.0 N C:TYR12 4.3 30.9 1.0 C C:PRO13 4.4 36.3 1.0 CB C:TYR12 4.4 35.2 1.0 CB C:ASP19 4.4 38.6 1.0 CB C:ASP10 4.4 24.8 1.0 CA C:ASN14 4.5 36.6 1.0 CE1 C:HIS24 4.5 28.3 1.0 ND2 C:ASN14 4.7 37.8 1.0 CD2 C:TYR12 4.8 41.0 1.0 O C:ASP208 4.8 27.4 1.0 OD1 C:ASP208 4.8 29.4 1.0 O C:HOH243 4.8 16.5 1.0

Calcium binding site 4 out of 4 in the Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin A Complexed to Methyl ALPHA1-2 Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca239 b:34.2 occ:1.00 O D:TYR12 2.3 36.4 1.0 O D:HOH256 2.4 23.4 1.0 OD2 D:ASP19 2.5 35.2 1.0 OD1 D:ASP10 2.6 26.3 1.0 OD2 D:ASP10 2.6 27.2 1.0 OD1 D:ASN14 2.6 38.5 1.0 CG D:ASP10 2.9 26.6 1.0 O D:HOH246 3.0 26.1 1.0 C D:TYR12 3.5 34.8 1.0 CG D:ASP19 3.6 39.2 1.0 CG D:ASN14 3.7 37.4 1.0 N D:ASN14 4.1 36.6 1.0 OD1 D:ASP19 4.2 40.6 1.0 CB D:ASN14 4.2 36.7 1.0 CA D:TYR12 4.3 33.9 1.0 CB D:TYR12 4.3 35.6 1.0 MN D:MN238 4.3 46.9 1.0 N D:TYR12 4.4 32.1 1.0 O D:HOH245 4.4 17.4 1.0 CB D:ASP10 4.4 25.7 1.0 O D:ASP208 4.4 28.0 1.0 OD1 D:ASP208 4.5 27.7 1.0 N D:PRO13 4.5 35.4 1.0 CA D:PRO13 4.7 35.7 1.0 C D:PRO13 4.7 36.5 1.0 CA D:ARG228 4.7 27.1 1.0 ND2 D:ASN14 4.7 38.6 1.0 O D:ARG228 4.8 27.4 1.0 CD2 D:TYR12 4.8 39.6 1.0 CA D:ASN14 4.8 37.1 1.0 CB D:ASP19 4.8 38.4 1.0 CE1 D:HIS24 4.9 25.3 1.0 CB D:ARG228 5.0 28.3 1.0

D.N.Moothoo, B.Canan, R.A.Field, J.H.Naismith. Man ALPHA1-2 Man Alpha-Ome-Concanavalin A Complex Reveals A Balance of Forces Involved in Carbohydrate Recognition. Glycobiology V. 9 539 1999.
ISSN: ISSN 0959-6658
PubMed: 10336986
DOI: 10.1093/GLYCOB/9.6.539