Manganese in PDB 1cq9: Peanut Lectin-Triclinic Form

The structure of Peanut Lectin-Triclinic Form, PDB code: 1cq9 was solved by R.Ravishankar, K.Suguna, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.640, 71.790, 86.420, 65.35, 77.66, 72.31
R / Rfree (%)	21.7 / 27.8

The structure of Peanut Lectin-Triclinic Form also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Peanut Lectin-Triclinic Form (pdb code 1cq9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Peanut Lectin-Triclinic Form, PDB code: 1cq9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:32.1 occ:1.00 OE2 A:GLU121 2.2 10.3 1.0 OD1 A:ASP132 2.3 29.6 1.0 OD1 A:ASP123 2.5 8.6 1.0 NE2 A:HIS137 2.6 19.4 1.0 CD A:GLU121 3.2 9.3 1.0 CG A:ASP132 3.3 29.1 1.0 OE1 A:GLU121 3.4 11.4 1.0 CG A:ASP123 3.5 7.2 1.0 CD2 A:HIS137 3.6 13.8 1.0 CE1 A:HIS137 3.6 16.1 1.0 OD2 A:ASP132 3.8 24.3 1.0 CB A:ASP123 3.8 5.1 1.0 OG A:SER147 4.0 2.3 1.0 O A:VAL145 4.1 20.4 1.0 CA A:CA237 4.4 2.0 1.0 CB A:ASP132 4.5 27.3 1.0 CG A:GLU121 4.5 5.4 1.0 OD2 A:ASP123 4.6 5.9 1.0 CD A:PRO133 4.6 35.8 1.0 ND1 A:HIS137 4.7 17.2 1.0 CG A:HIS137 4.8 19.2 1.0 CA A:ASP132 4.8 20.8 1.0

Manganese binding site 2 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn240 b:35.0 occ:1.00 OD1 B:ASP132 2.1 32.0 1.0 OE2 B:GLU121 2.5 13.0 1.0 NE2 B:HIS137 2.6 2.0 1.0 OD1 B:ASP123 3.0 35.5 1.0 CG B:ASP132 3.2 31.6 1.0 CD2 B:HIS137 3.4 2.0 1.0 CD B:GLU121 3.4 12.8 1.0 OG B:SER147 3.5 2.0 1.0 CE1 B:HIS137 3.6 2.0 1.0 OE1 B:GLU121 3.6 10.3 1.0 OD2 B:ASP132 3.8 29.0 1.0 O B:VAL145 3.9 2.0 1.0 CG B:ASP123 3.9 36.1 1.0 CB B:ASP123 4.1 36.4 1.0 CB B:ASP132 4.4 29.2 1.0 CD B:PRO133 4.5 36.3 1.0 CA B:ASP132 4.5 5.3 1.0 CA B:CA239 4.6 2.0 1.0 CG B:HIS137 4.6 2.0 1.0 CB B:SER147 4.7 2.0 1.0 ND1 B:HIS137 4.7 2.0 1.0 CG B:GLU121 4.8 7.4 1.0 CG2 B:THR150 4.8 20.3 1.0

Manganese binding site 3 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn242 b:39.8 occ:1.00 OE2 C:GLU121 2.3 18.6 1.0 OD1 C:ASP132 2.4 30.4 1.0 OD1 C:ASP123 2.7 28.3 1.0 NE2 C:HIS137 3.1 31.3 1.0 CD C:GLU121 3.1 18.6 1.0 OE1 C:GLU121 3.2 16.4 1.0 CG C:ASP132 3.4 34.0 1.0 O C:VAL145 3.6 22.3 1.0 OG C:SER147 3.7 27.3 1.0 CG C:ASP123 3.7 24.0 1.0 OD2 C:ASP132 3.8 29.9 1.0 CD2 C:HIS137 3.9 26.3 1.0 CE1 C:HIS137 4.1 27.7 1.0 CB C:ASP123 4.2 21.1 1.0 CG C:GLU121 4.6 16.3 1.0 CB C:ASP132 4.7 31.4 1.0 CA C:CA241 4.7 2.1 1.0 CD C:PRO133 4.7 29.2 1.0 OD2 C:ASP123 4.8 26.5 1.0 C C:VAL145 4.8 20.9 1.0 CA C:ASP132 4.9 23.2 1.0 CB C:SER147 4.9 24.9 1.0

Manganese binding site 4 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn244 b:10.8 occ:1.00 OD1 D:ASP132 2.0 10.2 1.0 OE2 D:GLU121 2.4 2.0 1.0 OD1 D:ASP123 2.5 2.0 1.0 NE2 D:HIS137 2.5 9.0 1.0 CG D:ASP132 3.1 13.3 1.0 CD D:GLU121 3.4 2.0 1.0 CD2 D:HIS137 3.4 6.1 1.0 CE1 D:HIS137 3.5 4.2 1.0 CG D:ASP123 3.6 2.0 1.0 OE1 D:GLU121 3.7 2.0 1.0 OD2 D:ASP132 3.7 14.8 1.0 O D:VAL145 3.8 39.2 1.0 CB D:ASP123 3.9 2.0 1.0 OG D:SER147 4.2 18.9 1.0 CB D:ASP132 4.3 13.6 1.0 CA D:CA243 4.4 2.0 1.0 CD D:PRO133 4.5 29.4 1.0 CA D:ASP132 4.6 10.2 1.0 ND1 D:HIS137 4.6 7.4 1.0 CG D:HIS137 4.6 6.8 1.0 OD2 D:ASP123 4.7 2.0 1.0 CG D:GLU121 4.8 2.0 1.0

R.Ravishankar, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan. Crystal Structures of the Peanut Lectin-Lactose Complex at Acidic pH: Retention of Unusual Quaternary Structure, Empty and Carbohydrate Bound Combining Sites, Molecular Mimicry and Crystal Packing Directed By Interactions at the Combining Site. Proteins V. 43 260 2001.
ISSN: ISSN 0887-3585
PubMed: 11288176
DOI: 10.1002/PROT.1037