Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Concanavalin A Complex with 4'-Nitrophenyl-Alpha-D- Glucopyranoside, PDB code: 1val:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:27.0 occ:1.00 OD2 A:ASP10 2.1 23.1 1.0 OE2 A:GLU8 2.3 35.0 1.0 OD1 A:ASP19 2.3 24.2 1.0 NE2 A:HIS24 2.3 26.7 1.0 O A:HOH242 2.4 42.1 1.0 O A:HOH243 2.4 32.0 1.0 CG A:ASP10 3.0 20.2 1.0 CG A:ASP19 3.1 24.0 1.0 CE1 A:HIS24 3.2 26.9 1.0 OD2 A:ASP19 3.3 21.7 1.0 CD2 A:HIS24 3.3 27.8 1.0 CD A:GLU8 3.4 33.7 1.0 CB A:ASP10 3.4 20.8 1.0 O A:HOH244 3.6 18.7 1.0 OE1 A:GLU8 3.8 33.3 1.0 CA A:CA239 3.9 29.4 1.0 OD1 A:ASP10 4.1 20.9 1.0 ND1 A:HIS24 4.3 25.7 1.0 CB A:ASP19 4.4 23.2 1.0 CG A:HIS24 4.4 27.2 1.0 CG A:GLU8 4.6 29.0 1.0 OG A:SER34 4.6 23.5 1.0 CA A:ASP19 4.8 32.1 1.0 CA A:ASP10 4.9 20.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:25.8 occ:1.00 OD2 B:ASP10 1.9 35.8 1.0 OD1 B:ASP19 2.2 41.7 1.0 OE2 B:GLU8 2.4 30.1 1.0 O B:HOH241 2.4 26.8 1.0 O B:HOH242 2.5 21.6 1.0 NE2 B:HIS24 2.8 35.7 1.0 CG B:ASP10 2.9 34.0 1.0 CG B:ASP19 3.0 39.0 1.0 OD2 B:ASP19 3.3 35.5 1.0 CE1 B:HIS24 3.3 31.1 1.0 CD B:GLU8 3.4 26.7 1.0 CB B:ASP10 3.4 31.3 1.0 CA B:CA239 3.5 22.3 1.0 OE1 B:GLU8 3.6 24.1 1.0 CD2 B:HIS24 4.0 32.9 1.0 OD1 B:ASP10 4.0 34.2 1.0 CB B:ASP19 4.2 36.5 1.0 O B:HOH244 4.3 38.2 1.0 ND1 B:HIS24 4.5 31.9 1.0 CA B:ASP19 4.6 38.4 1.0 OG B:SER34 4.7 25.6 1.0 CG B:GLU8 4.7 22.2 1.0 CG B:HIS24 4.9 32.4 1.0 CA B:ASP10 4.9 31.1 1.0 O B:VAL32 4.9 25.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:30.1 occ:1.00 O C:HOH242 2.1 10.6 1.0 NE2 C:HIS24 2.1 35.5 1.0 OE2 C:GLU8 2.3 31.1 1.0 OD2 C:ASP10 2.5 28.8 1.0 O C:HOH241 2.5 41.7 1.0 OD1 C:ASP19 2.6 36.8 1.0 CE1 C:HIS24 3.1 32.7 1.0 CG C:ASP19 3.1 36.2 1.0 CD2 C:HIS24 3.2 37.0 1.0 OD2 C:ASP19 3.2 33.8 1.0 CG C:ASP10 3.3 31.5 1.0 CD C:GLU8 3.4 28.4 1.0 CB C:ASP10 3.4 27.6 1.0 OE1 C:GLU8 3.9 26.9 1.0 OG C:SER34 4.2 26.6 1.0 ND1 C:HIS24 4.2 33.1 1.0 O C:HOH243 4.2 31.9 1.0 CG C:HIS24 4.3 37.0 1.0 CA C:CA239 4.4 32.5 1.0 OD1 C:ASP10 4.4 27.9 1.0 CB C:ASP19 4.5 36.9 1.0 CG C:GLU8 4.6 23.0 1.0 CD C:PRO20 4.8 43.6 1.0 CA C:ASP10 4.9 25.5 1.0 CA C:ASP19 4.9 42.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:32.8 occ:1.00 OD2 D:ASP10 2.0 35.5 1.0 OD1 D:ASP19 2.1 43.0 1.0 NE2 D:HIS24 2.2 33.5 1.0 OE2 D:GLU8 2.2 32.4 1.0 O D:HOH244 2.3 39.5 1.0 O D:HOH241 2.3 35.6 1.0 CG D:ASP10 2.9 34.7 1.0 CG D:ASP19 3.1 43.5 1.0 CE1 D:HIS24 3.2 31.4 1.0 CD2 D:HIS24 3.2 33.5 1.0 CD D:GLU8 3.2 31.0 1.0 CB D:ASP10 3.3 32.7 1.0 OD2 D:ASP19 3.5 39.0 1.0 OE1 D:GLU8 3.6 32.7 1.0 OD1 D:ASP10 4.0 33.5 1.0 OG D:SER34 4.2 33.6 1.0 CA D:CA239 4.3 36.0 1.0 CB D:ASP19 4.3 45.8 1.0 ND1 D:HIS24 4.3 31.9 1.0 CG D:HIS24 4.3 31.5 1.0 CG D:GLU8 4.5 27.0 1.0 CA D:ASP19 4.6 49.2 1.0 O D:HOH243 4.7 39.0 1.0 O D:VAL32 4.8 35.1 1.0 CA D:ASP10 4.8 29.8 1.0 CD D:PRO20 5.0 45.5 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