Calcium in PDB 1val: Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside

The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside, PDB code: 1val was solved by P.N.Kanellopoulos, P.A.Tucker, S.J.Hamodrakas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.660, 155.670, 71.420, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 27.4

The structure of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside (pdb code 1val). 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 Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside, PDB code: 1val:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-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 Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:29.4 occ:1.00 OD1 A:ASN14 2.1 31.3 1.0 O A:HOH241 2.2 28.1 1.0 OD2 A:ASP19 2.2 21.7 1.0 OD2 A:ASP10 2.3 23.1 1.0 O A:HOH244 2.4 18.7 1.0 OD1 A:ASP10 2.5 20.9 1.0 O A:TYR12 2.6 21.1 1.0 CG A:ASP10 2.7 20.2 1.0 CG A:ASN14 3.2 27.9 1.0 CG A:ASP19 3.4 24.0 1.0 C A:TYR12 3.8 24.5 1.0 MN A:MN238 3.9 27.0 1.0 OD1 A:ASP19 3.9 24.2 1.0 CB A:ASN14 4.0 26.9 1.0 N A:ASN14 4.0 21.3 1.0 CB A:ASP10 4.2 20.8 1.0 ND2 A:ASN14 4.3 26.3 1.0 CB A:ASP19 4.6 23.2 1.0 O A:HOH242 4.6 42.1 1.0 CA A:ASN14 4.7 25.7 1.0 N A:PRO13 4.7 21.2 1.0 CA A:TYR12 4.7 26.1 1.0 CA A:PRO13 4.7 21.9 1.0 N A:TYR12 4.7 27.0 1.0 C A:PRO13 4.8 19.8 1.0 O A:ARG228 4.8 29.2 1.0 CE1 A:HIS24 4.8 26.9 1.0 CA A:ARG228 4.8 29.2 1.0 OD2 A:ASP208 4.8 31.9 1.0 CB A:ARG228 4.9 30.6 1.0 O A:ASP208 4.9 22.1 1.0 CD1 A:ILE17 5.0 40.9 1.0

Calcium binding site 2 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-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 Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:22.3 occ:1.00 OD2 B:ASP19 2.1 35.5 1.0 OD2 B:ASP10 2.2 35.8 1.0 O B:HOH244 2.2 38.2 1.0 OD1 B:ASN14 2.4 33.8 1.0 O B:HOH243 2.4 24.0 1.0 OD1 B:ASP10 2.5 34.2 1.0 CG B:ASP10 2.6 34.0 1.0 O B:TYR12 2.7 22.3 1.0 CG B:ASP19 3.2 39.0 1.0 O B:HOH242 3.2 21.6 1.0 CG B:ASN14 3.5 29.6 1.0 MN B:MN238 3.5 25.8 1.0 OD1 B:ASP19 3.6 41.7 1.0 C B:TYR12 3.9 24.8 1.0 N B:ASN14 4.0 35.0 1.0 CB B:ASN14 4.1 32.0 1.0 CB B:ASP10 4.2 31.3 1.0 CB B:ASP19 4.4 36.5 1.0 ND2 B:ASN14 4.5 23.6 1.0 CA B:PRO13 4.6 31.2 1.0 O B:ASP208 4.6 24.0 1.0 C B:PRO13 4.7 34.8 1.0 N B:PRO13 4.7 28.2 1.0 CA B:ASN14 4.7 35.5 1.0 CE1 B:HIS24 4.8 31.1 1.0 CA B:TYR12 4.8 22.9 1.0 O B:ARG228 4.8 26.4 1.0 N B:TYR12 4.8 26.8 1.0 OD2 B:ASP208 4.9 26.6 1.0

Calcium binding site 3 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:32.5 occ:1.00 O C:HOH244 2.2 28.8 1.0 O C:TYR12 2.2 23.9 1.0 O C:HOH243 2.2 31.9 1.0 OD2 C:ASP10 2.3 28.8 1.0 OD2 C:ASP19 2.7 33.8 1.0 OD1 C:ASP10 2.8 27.9 1.0 CG C:ASP10 2.9 31.5 1.0 OD1 C:ASN14 3.3 44.8 1.0 C C:TYR12 3.5 26.3 1.0 CG C:ASP19 3.9 36.2 1.0 N C:ASN14 3.9 37.0 1.0 CG C:ASN14 4.0 44.0 1.0 CB C:ASN14 4.2 36.8 1.0 MN C:MN238 4.4 30.1 1.0 N C:PRO13 4.4 27.1 1.0 CA C:TYR12 4.4 29.1 1.0 CB C:ASP10 4.4 27.6 1.0 O C:HOH242 4.4 10.6 1.0 CA C:PRO13 4.5 31.7 1.0 N C:TYR12 4.5 33.8 1.0 OD1 C:ASP19 4.6 36.8 1.0 CB C:TYR12 4.6 32.5 1.0 C C:PRO13 4.6 36.0 1.0 O C:ARG228 4.6 39.0 1.0 CA C:ASN14 4.7 34.0 1.0 CA C:ARG228 4.7 38.1 1.0 O C:ASP208 4.8 29.4 1.0 CB C:ARG228 4.9 43.8 1.0 CB C:ASP19 4.9 36.9 1.0 OD1 C:ASP208 5.0 38.0 1.0

Calcium binding site 4 out of 4 in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca239 b:36.0 occ:1.00 OD2 D:ASP19 1.9 39.0 1.0 O D:TYR12 2.1 35.6 1.0 O D:HOH243 2.3 39.0 1.0 OD1 D:ASN14 2.4 44.8 1.0 OD1 D:ASP10 2.4 33.5 1.0 O D:HOH242 2.5 16.5 1.0 OD2 D:ASP10 2.8 35.5 1.0 CG D:ASP10 3.0 34.7 1.0 CG D:ASP19 3.1 43.5 1.0 C D:TYR12 3.3 38.3 1.0 CG D:ASN14 3.4 41.1 1.0 N D:ASN14 3.7 41.4 1.0 OD1 D:ASP19 3.8 43.0 1.0 CB D:ASN14 3.9 40.9 1.0 CA D:TYR12 4.1 37.3 1.0 CB D:ASP19 4.2 45.8 1.0 N D:PRO13 4.3 40.4 1.0 MN D:MN238 4.3 32.8 1.0 CB D:TYR12 4.3 38.1 1.0 N D:TYR12 4.3 36.8 1.0 CA D:ASN14 4.4 42.8 1.0 CB D:ASP10 4.5 32.7 1.0 CA D:PRO13 4.5 39.0 1.0 ND2 D:ASN14 4.5 42.7 1.0 C D:PRO13 4.5 40.1 1.0 O D:HOH244 4.6 39.5 1.0 O D:ASP208 4.7 32.9 1.0 CE1 D:HIS24 4.8 31.4 1.0 CD1 D:TYR12 4.9 42.1 1.0 CA D:ARG228 4.9 36.7 1.0 CB D:ARG228 5.0 38.3 1.0 O D:ARG228 5.0 35.8 1.0

P.N.Kanellopoulos, K.Pavlou, A.Perrakis, B.Agianian, C.E.Vorgias, C.Mavrommatis, M.Soufi, P.A.Tucker, S.J.Hamodrakas. The Crystal Structure of the Complexes of Concanavalin A with 4'-Nitrophenyl-Alpha-D-Mannopyranoside and 4'-Nitrophenyl-Alpha-D-Glucopyranoside. J.Struct.Biol. V. 116 345 1996.
ISSN: ISSN 1047-8477
PubMed: 8812993
DOI: 10.1006/JSBI.1996.0052