Manganese in PDB 1jyc: Concanavalin A/15-Mer Peptide Complex

The structure of Concanavalin A/15-Mer Peptide Complex, PDB code: 1jyc was solved by D.Jain, K.J.Kaur, 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 (°)	103.113, 118.547, 254.994, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24

The structure of Concanavalin A/15-Mer Peptide Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Concanavalin A/15-Mer Peptide Complex (pdb code 1jyc). 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/15-Mer Peptide Complex, PDB code: 1jyc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:28.7 occ:1.00 OD2 A:ASP10 2.3 20.4 1.0 OD1 A:ASP19 2.3 16.3 1.0 OE2 A:GLU8 2.3 28.6 1.0 NE2 A:HIS24 2.5 23.4 1.0 O A:HOH440 2.6 29.0 1.0 O A:HOH453 2.6 13.8 1.0 CG A:ASP19 3.1 16.3 1.0 CG A:ASP10 3.3 20.4 1.0 CD A:GLU8 3.3 28.6 1.0 CD2 A:HIS24 3.4 23.4 1.0 CE1 A:HIS24 3.5 23.4 1.0 OD2 A:ASP19 3.5 16.3 1.0 OE1 A:GLU8 3.6 28.6 1.0 CB A:ASP10 3.7 20.4 1.0 OG A:SER34 3.9 17.8 1.0 O A:HOH461 4.1 79.4 1.0 O A:HOH422 4.2 59.8 1.0 CB A:ASP19 4.3 16.3 1.0 OD1 A:ASP10 4.4 20.4 1.0 CA A:ASP19 4.6 49.7 1.0 ND1 A:HIS24 4.6 23.4 1.0 CG A:HIS24 4.6 23.4 1.0 O A:VAL32 4.6 23.8 1.0 CG A:GLU8 4.7 28.6 1.0 CA A:CA402 4.8 17.6 1.0

Manganese binding site 2 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:27.0 occ:1.00 OD1 B:ASP19 2.3 37.0 1.0 OD2 B:ASP10 2.3 27.2 1.0 OE2 B:GLU8 2.3 31.9 1.0 NE2 B:HIS24 2.4 23.8 1.0 CD B:GLU8 3.1 31.9 1.0 OE1 B:GLU8 3.3 31.9 1.0 CG B:ASP19 3.3 37.0 1.0 CG B:ASP10 3.4 27.2 1.0 CE1 B:HIS24 3.4 23.8 1.0 CD2 B:HIS24 3.4 23.8 1.0 OG B:SER34 3.7 32.3 1.0 CB B:ASP10 3.8 27.2 1.0 OD2 B:ASP19 3.8 37.0 1.0 OD1 B:ASP10 4.5 27.2 1.0 O B:VAL32 4.5 27.6 1.0 ND1 B:HIS24 4.5 23.8 1.0 CB B:ASP19 4.5 37.0 1.0 CG B:HIS24 4.5 23.8 1.0 CG B:GLU8 4.5 31.9 1.0 CA B:CA404 4.6 24.9 1.0 CA B:ASP19 4.7 38.8 1.0

Manganese binding site 3 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn405 b:28.7 occ:1.00 OD1 C:ASP19 2.2 28.0 1.0 OE2 C:GLU8 2.3 41.3 1.0 OD2 C:ASP10 2.3 21.9 1.0 NE2 C:HIS24 2.4 39.9 1.0 CD C:GLU8 3.1 41.3 1.0 O C:HOH418 3.2 56.1 1.0 OE1 C:GLU8 3.3 41.3 1.0 CG C:ASP19 3.3 28.0 1.0 CD2 C:HIS24 3.3 39.9 1.0 CE1 C:HIS24 3.3 39.9 1.0 CG C:ASP10 3.4 21.9 1.0 OG C:SER34 3.7 15.4 1.0 CB C:ASP10 3.8 21.9 1.0 OD2 C:ASP19 3.8 28.0 1.0 ND1 C:HIS24 4.5 39.9 1.0 CG C:HIS24 4.5 39.9 1.0 CB C:ASP19 4.5 28.0 1.0 CG C:GLU8 4.5 41.3 1.0 OD1 C:ASP10 4.5 21.9 1.0 O C:VAL32 4.6 11.6 1.0 CA C:ASP19 4.6 18.7 1.0 CA C:CA406 4.7 10.8 1.0

Manganese binding site 4 out of 4 in the Concanavalin A/15-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/15-Mer Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn407 b:27.0 occ:1.00 OD2 D:ASP10 2.2 38.5 1.0 OD1 D:ASP19 2.3 30.9 1.0 OE2 D:GLU8 2.4 34.7 1.0 O D:HOH436 2.4 21.2 1.0 NE2 D:HIS24 2.4 32.2 1.0 O D:HOH435 2.7 43.1 1.0 CG D:ASP19 3.1 30.9 1.0 CG D:ASP10 3.2 38.5 1.0 CE1 D:HIS24 3.3 32.2 1.0 CD2 D:HIS24 3.4 32.2 1.0 OD2 D:ASP19 3.4 30.9 1.0 CD D:GLU8 3.4 34.7 1.0 CB D:ASP10 3.6 38.5 1.0 OE1 D:GLU8 3.7 34.7 1.0 OG D:SER34 4.0 11.9 1.0 CB D:ASP19 4.3 30.9 1.0 OD1 D:ASP10 4.3 38.5 1.0 ND1 D:HIS24 4.5 32.2 1.0 CG D:HIS24 4.5 32.2 1.0 CA D:ASP19 4.5 41.6 1.0 CA D:CA408 4.6 27.1 1.0 CG D:GLU8 4.7 34.7 1.0 O D:VAL32 4.7 16.2 1.0 CD D:PRO20 5.0 54.8 1.0

D.Jain, K.J.Kaur, D.M.Salunke. Plasticity in Protein-Peptide Recognition: Crystal Structures of Two Different Peptides Bound to Concanavalin A Biophys.J. V. 80 2912 2001.
ISSN: ISSN 0006-3495
PubMed: 11371463