Manganese in PDB 1jyi: Concanavalin A/12-Mer Peptide Complex

The structure of Concanavalin A/12-Mer Peptide Complex, PDB code: 1jyi was solved by D.Jain, K.J.Kaur, B.Sundaravadivel, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.545, 118.323, 252.591, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26.5

The structure of Concanavalin A/12-Mer Peptide Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Concanavalin A/12-Mer Peptide Complex (pdb code 1jyi). 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/12-Mer Peptide Complex, PDB code: 1jyi:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:23.5 occ:1.00 OD1 A:ASP19 2.3 30.3 1.0 NE2 A:HIS24 2.3 10.2 1.0 O A:HOH414 2.4 18.8 1.0 OD2 A:ASP10 2.4 22.5 1.0 O A:HOH411 2.4 17.1 1.0 OE2 A:GLU8 2.4 17.9 1.0 CG A:ASP19 3.2 30.3 1.0 CG A:ASP10 3.2 22.5 1.0 CD2 A:HIS24 3.2 10.2 1.0 CE1 A:HIS24 3.4 10.2 1.0 CD A:GLU8 3.4 17.9 1.0 OD2 A:ASP19 3.5 30.3 1.0 CB A:ASP10 3.5 22.5 1.0 OE1 A:GLU8 3.7 17.9 1.0 OG A:SER34 4.0 18.3 1.0 OD1 A:ASP10 4.2 22.5 1.0 CB A:ASP19 4.4 30.3 1.0 CG A:HIS24 4.4 10.2 1.0 ND1 A:HIS24 4.4 10.2 1.0 CA A:ASP19 4.6 30.0 1.0 CA A:CA402 4.6 23.5 1.0 CD A:PRO20 4.7 28.0 1.0 O A:VAL32 4.7 11.6 1.0 CG A:GLU8 4.8 17.9 1.0 CA A:ASP10 5.0 16.7 1.0

Manganese binding site 2 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:23.5 occ:1.00 OD1 B:ASP19 2.3 28.6 1.0 O B:HOH417 2.4 39.1 1.0 O B:HOH415 2.4 32.4 1.0 OE2 B:GLU8 2.4 20.1 1.0 OD2 B:ASP10 2.5 17.4 1.0 NE2 B:HIS24 2.6 24.3 1.0 CG B:ASP19 3.3 28.6 1.0 CG B:ASP10 3.3 17.4 1.0 CE1 B:HIS24 3.5 24.3 1.0 CD B:GLU8 3.5 20.1 1.0 OD2 B:ASP19 3.6 28.6 1.0 CD2 B:HIS24 3.6 24.3 1.0 CB B:ASP10 3.7 17.4 1.0 OE1 B:GLU8 3.9 20.1 1.0 OG B:SER34 4.0 31.5 1.0 OD1 B:ASP10 4.3 17.4 1.0 CB B:ASP19 4.6 28.6 1.0 O B:VAL32 4.6 23.9 1.0 ND1 B:HIS24 4.6 24.3 1.0 CA B:CA404 4.6 23.5 1.0 CG B:HIS24 4.7 24.3 1.0 CG B:GLU8 4.8 20.1 1.0 CA B:ASP19 4.8 37.4 1.0 CD B:PRO20 4.9 26.0 1.0

Manganese binding site 3 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn405 b:23.5 occ:1.00 OD1 C:ASP19 2.2 27.8 1.0 O C:HOH416 2.3 26.1 1.0 OE2 C:GLU8 2.3 23.2 1.0 O C:HOH419 2.4 18.7 1.0 OD2 C:ASP10 2.4 22.0 1.0 NE2 C:HIS24 2.5 16.3 1.0 CG C:ASP19 3.1 27.8 1.0 CD2 C:HIS24 3.2 16.3 1.0 CD C:GLU8 3.3 23.2 1.0 CG C:ASP10 3.4 22.0 1.0 OD2 C:ASP19 3.4 27.8 1.0 CE1 C:HIS24 3.6 16.3 1.0 CB C:ASP10 3.6 22.0 1.0 OE1 C:GLU8 3.7 23.2 1.0 OG C:SER34 4.1 9.4 1.0 CB C:ASP19 4.3 27.8 1.0 CG C:HIS24 4.5 16.3 1.0 OD1 C:ASP10 4.5 22.0 1.0 CA C:CA406 4.5 23.5 1.0 ND1 C:HIS24 4.6 16.3 1.0 CA C:ASP19 4.6 41.1 1.0 CG C:GLU8 4.6 23.2 1.0 O C:VAL32 4.8 23.8 1.0

Manganese binding site 4 out of 4 in the Concanavalin A/12-Mer Peptide Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Concanavalin A/12-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn407 b:23.5 occ:1.00 NE2 D:HIS24 2.4 23.2 1.0 O D:HOH419 2.4 15.5 1.0 OD2 D:ASP10 2.5 32.4 1.0 OE2 D:GLU8 2.5 24.4 1.0 OD1 D:ASP19 2.7 38.4 1.0 O D:HOH411 2.7 36.4 1.0 CE1 D:HIS24 3.1 23.2 1.0 CG D:ASP19 3.2 38.4 1.0 OD2 D:ASP19 3.2 38.4 1.0 CG D:ASP10 3.3 32.4 1.0 CD2 D:HIS24 3.4 23.2 1.0 CD D:GLU8 3.5 24.4 1.0 CB D:ASP10 3.7 32.4 1.0 OE1 D:GLU8 3.8 24.4 1.0 OG D:SER34 3.9 31.4 1.0 ND1 D:HIS24 4.3 23.2 1.0 OD1 D:ASP10 4.3 32.4 1.0 CG D:HIS24 4.4 23.2 1.0 CB D:ASP19 4.5 38.4 1.0 O D:VAL32 4.7 19.3 1.0 CA D:CA408 4.7 23.5 1.0 CD D:PRO20 4.8 28.5 1.0 CG D:GLU8 4.8 24.4 1.0 CA D:ASP19 4.8 33.5 1.0

D.Jain, K.J.Kaur, B.Sundaravadivel, D.M.Salunke. Structural and Functional Consequences of Peptide-Carbohydrate Mimicry. Crystal Structure of A Carbohydrate-Mimicking Peptide Bound to Concanavalin A. J.Biol.Chem. V. 275 16098 2000.
ISSN: ISSN 0021-9258
PubMed: 10821862
DOI: 10.1074/JBC.275.21.16098