Manganese in PDB 1ciw: Peanut Lectin Complexed with N-Acetyllactosamine

The structure of Peanut Lectin Complexed with N-Acetyllactosamine, PDB code: 1ciw 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	129.380, 126.922, 76.065, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.4

The structure of Peanut Lectin Complexed with N-Acetyllactosamine also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Peanut Lectin Complexed with N-Acetyllactosamine (pdb code 1ciw). 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 Complexed with N-Acetyllactosamine, PDB code: 1ciw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peanut Lectin Complexed with N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:40.5 occ:1.00 OD2 A:ASP123 1.9 14.0 1.0 O A:HOH509 2.0 17.4 1.0 OE2 A:GLU121 2.0 18.9 1.0 O A:HOH510 2.1 15.4 1.0 OD1 A:ASP132 2.3 25.8 1.0 NE2 A:HIS137 2.5 23.0 1.0 CG A:ASP123 2.8 8.4 1.0 CB A:ASP123 3.1 7.9 1.0 CD A:GLU121 3.1 17.3 1.0 CG A:ASP132 3.2 29.9 1.0 CE1 A:HIS137 3.4 21.8 1.0 CD2 A:HIS137 3.4 19.6 1.0 OD2 A:ASP132 3.5 27.4 1.0 OE1 A:GLU121 3.5 17.3 1.0 O A:HOH507 3.7 27.5 1.0 OD1 A:ASP123 3.9 12.5 1.0 CA A:CA237 3.9 17.6 1.0 CG A:GLU121 4.4 18.6 1.0 OG A:SER147 4.4 13.4 1.0 ND1 A:HIS137 4.5 21.4 1.0 O A:VAL145 4.5 18.5 1.0 CB A:ASP132 4.6 28.1 1.0 CG A:HIS137 4.6 16.4 1.0 CA A:ASP123 4.6 11.4 1.0 CD A:PRO133 4.9 34.4 1.0 CA A:ASP132 5.0 27.7 1.0

Manganese binding site 2 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peanut Lectin Complexed with N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:41.1 occ:1.00 O B:HOH533 1.8 46.9 1.0 OE2 B:GLU121 2.0 21.6 1.0 O B:HOH532 2.2 22.4 1.0 OD1 B:ASP132 2.2 24.6 1.0 OD2 B:ASP123 2.3 11.0 1.0 NE2 B:HIS137 2.6 15.8 1.0 CD B:GLU121 3.1 18.8 1.0 CG B:ASP132 3.3 21.3 1.0 CG B:ASP123 3.3 15.1 1.0 OE1 B:GLU121 3.4 22.4 1.0 CD2 B:HIS137 3.5 13.4 1.0 CE1 B:HIS137 3.6 11.4 1.0 CB B:ASP123 3.6 9.4 1.0 OD2 B:ASP132 3.7 22.2 1.0 OG B:SER147 3.8 16.3 1.0 O B:VAL145 4.1 16.3 1.0 O B:HOH407 4.1 21.2 1.0 O B:HOH530 4.3 27.8 1.0 CA B:CA237 4.4 11.9 1.0 CG B:GLU121 4.4 14.8 1.0 OD1 B:ASP123 4.4 15.6 1.0 CB B:ASP132 4.5 14.8 1.0 CG B:HIS137 4.6 12.6 1.0 ND1 B:HIS137 4.7 17.1 1.0 CD B:PRO133 4.7 19.5 1.0 CA B:ASP132 4.8 29.3 1.0

Manganese binding site 3 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Peanut Lectin Complexed with N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:44.7 occ:1.00 O C:HOH499 1.9 22.1 1.0 O C:HOH498 1.9 6.8 1.0 OD2 C:ASP123 2.0 30.3 1.0 OD1 C:ASP132 2.0 28.7 1.0 OE2 C:GLU121 2.3 17.2 1.0 NE2 C:HIS137 2.4 22.5 1.0 CG C:ASP123 3.0 24.0 1.0 CG C:ASP132 3.0 26.5 1.0 OD2 C:ASP132 3.3 17.7 1.0 CB C:ASP123 3.4 15.0 1.0 CE1 C:HIS137 3.4 22.4 1.0 CD2 C:HIS137 3.4 22.7 1.0 CD C:GLU121 3.4 15.9 1.0 O C:HOH496 3.7 12.7 1.0 OE1 C:GLU121 3.8 15.8 1.0 OD1 C:ASP123 4.0 27.6 1.0 CA C:CA237 4.0 21.2 1.0 CB C:ASP132 4.2 19.5 1.0 O C:HOH479 4.3 46.2 1.0 OG C:SER147 4.4 29.1 1.0 O C:VAL145 4.5 24.5 1.0 ND1 C:HIS137 4.5 25.3 1.0 CG C:HIS137 4.5 21.1 1.0 CD C:PRO133 4.6 34.1 1.0 CA C:ASP132 4.6 29.2 1.0 CG C:GLU121 4.7 13.9 1.0 CA C:ASP123 4.9 6.1 1.0

Manganese binding site 4 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Peanut Lectin Complexed with N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:36.5 occ:1.00 NE2 D:HIS137 2.1 12.8 1.0 OE2 D:GLU121 2.2 15.1 1.0 OD2 D:ASP123 2.2 23.5 1.0 OD1 D:ASP132 2.2 25.1 1.0 O D:HOH493 2.3 16.4 1.0 O D:HOH492 2.4 19.4 1.0 CG D:ASP123 3.0 19.2 1.0 CD2 D:HIS137 3.1 11.6 1.0 CE1 D:HIS137 3.1 13.3 1.0 CG D:ASP132 3.1 27.9 1.0 CB D:ASP123 3.2 14.8 1.0 CD D:GLU121 3.3 17.0 1.0 OD2 D:ASP132 3.5 23.9 1.0 OE1 D:GLU121 3.8 15.9 1.0 CA D:CA237 4.0 20.4 1.0 OD1 D:ASP123 4.1 19.2 1.0 ND1 D:HIS137 4.2 15.1 1.0 CG D:HIS137 4.2 11.5 1.0 OG D:SER147 4.2 15.4 1.0 O D:HOH490 4.3 21.0 1.0 CB D:ASP132 4.4 20.8 1.0 CD D:PRO133 4.5 31.2 1.0 CG D:GLU121 4.6 13.8 1.0 O D:VAL145 4.6 12.3 1.0 CA D:ASP132 4.7 27.8 1.0 CA D:ASP123 4.7 10.9 1.0 O D:HOH463 4.9 28.8 1.0

R.Ravishankar, K.Suguna, A.Surolia, M.Vijayan. Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N-Acetyllactosamine and A Comparative Study of Carbohydrate Binding in Gal/Galnac-Specific Legume Lectins. Acta Crystallogr.,Sect.D V. 55 1375 1999.
ISSN: ISSN 0907-4449
PubMed: 10417405
DOI: 10.1107/S0907444999006587