Manganese in PDB 2zmn: Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc, PDB code: 2zmn was solved by K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	158.061, 91.758, 73.570, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.7

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc (pdb code 2zmn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc, PDB code: 2zmn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:37.6 occ:1.00 OD1 A:ASP131 2.2 33.6 1.0 O A:HOH603 2.2 31.6 1.0 OE2 A:GLU122 2.3 19.1 1.0 O A:HOH604 2.3 11.2 1.0 NE2 A:HIS136 2.3 19.4 1.0 OD2 A:ASP124 2.3 27.0 1.0 CG A:ASP131 3.1 33.0 1.0 CE1 A:HIS136 3.1 20.0 1.0 CG A:ASP124 3.3 27.3 1.0 CD A:GLU122 3.3 19.1 1.0 CD2 A:HIS136 3.4 19.9 1.0 OD2 A:ASP131 3.5 34.0 1.0 CB A:ASP124 3.6 25.9 1.0 OE1 A:GLU122 3.7 19.8 1.0 OG A:SER146 4.2 24.2 1.0 CB A:ASP131 4.2 30.8 1.0 ND1 A:HIS136 4.3 21.3 1.0 OD1 A:ASP124 4.4 26.3 1.0 CA A:CA303 4.5 18.9 1.0 CG A:HIS136 4.5 20.6 1.0 O A:VAL144 4.5 24.0 1.0 CG A:GLU122 4.6 18.2 1.0 CD A:PRO132 4.7 26.7 1.0 O A:HOH605 4.8 18.4 1.0 NE1 A:TRP130 4.8 31.9 1.0 CA A:ASP131 4.8 29.0 1.0 O A:HOH607 4.8 26.8 1.0 CD1 A:TRP130 4.9 32.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:26.2 occ:1.00 OE2 B:GLU122 2.2 19.1 1.0 OD1 B:ASP131 2.2 29.0 1.0 OD2 B:ASP124 2.4 25.4 1.0 O B:HOH623 2.4 8.7 1.0 NE2 B:HIS136 2.6 16.5 1.0 O B:HOH622 2.7 35.1 1.0 CG B:ASP131 3.1 29.5 1.0 CD B:GLU122 3.2 17.9 1.0 CG B:ASP124 3.4 26.4 1.0 CE1 B:HIS136 3.4 15.8 1.0 OE1 B:GLU122 3.5 17.5 1.0 OD2 B:ASP131 3.5 32.8 1.0 CD2 B:HIS136 3.6 17.2 1.0 CB B:ASP124 3.7 25.4 1.0 OG B:SER146 4.0 21.4 1.0 O B:HOH624 4.2 19.6 1.0 O B:VAL144 4.3 22.5 1.0 CB B:ASP131 4.3 28.8 1.0 CA B:CA303 4.4 20.5 1.0 OD1 B:ASP124 4.5 27.9 1.0 CG B:GLU122 4.5 17.9 1.0 ND1 B:HIS136 4.6 17.6 1.0 NE1 B:TRP130 4.6 28.9 1.0 CG B:HIS136 4.7 17.1 1.0 CD1 B:TRP130 4.8 29.1 1.0 CA B:ASP131 4.9 27.7 1.0 CD B:PRO132 4.9 25.1 1.0 CZ B:PHE107 4.9 16.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn300 b:47.7 occ:1.00 OD1 C:ASP131 2.2 34.3 1.0 O C:HOH604 2.2 17.2 1.0 OE2 C:GLU122 2.2 23.6 1.0 NE2 C:HIS136 2.3 20.2 1.0 OD2 C:ASP124 2.5 27.0 1.0 CE1 C:HIS136 3.2 20.9 1.0 CG C:ASP131 3.2 34.1 1.0 CD C:GLU122 3.3 21.3 1.0 CD2 C:HIS136 3.4 20.5 1.0 CG C:ASP124 3.5 26.8 1.0 OE1 C:GLU122 3.7 21.1 1.0 CB C:ASP124 3.7 25.6 1.0 OD2 C:ASP131 3.8 36.4 1.0 OG C:SER146 3.9 25.0 1.0 CB C:ASP131 4.3 32.1 1.0 O C:HOH605 4.3 29.3 1.0 ND1 C:HIS136 4.4 21.3 1.0 O C:VAL144 4.4 25.2 1.0 CG C:HIS136 4.5 20.8 1.0 CG C:GLU122 4.6 20.6 1.0 OD1 C:ASP124 4.6 26.8 1.0 CA C:CA303 4.6 28.8 1.0 CD C:PRO132 4.7 27.9 1.0 CA C:ASP131 4.8 31.3 1.0 NE1 C:TRP130 4.8 34.2 1.0 CD1 C:TRP130 4.9 33.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha- 1,6 Glc within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn300 b:42.9 occ:1.00 OD1 D:ASP131 2.2 33.0 1.0 O D:HOH604 2.3 21.1 1.0 NE2 D:HIS136 2.3 20.4 1.0 OE2 D:GLU122 2.4 20.6 1.0 OD2 D:ASP124 2.9 25.6 1.0 CE1 D:HIS136 3.2 20.3 1.0 CG D:ASP131 3.3 32.3 1.0 CD D:GLU122 3.4 19.6 1.0 CD2 D:HIS136 3.4 21.2 1.0 O D:HOH605 3.6 29.3 1.0 OG D:SER146 3.7 22.0 1.0 OE1 D:GLU122 3.8 19.0 1.0 CG D:ASP124 3.8 26.7 1.0 OD2 D:ASP131 3.9 34.9 1.0 CB D:ASP124 4.0 25.7 1.0 CB D:ASP131 4.3 30.3 1.0 O D:VAL144 4.3 21.0 1.0 ND1 D:HIS136 4.3 22.1 1.0 CD D:PRO132 4.4 26.8 1.0 CG D:HIS136 4.5 21.6 1.0 O D:HOH606 4.6 20.7 1.0 CG D:GLU122 4.6 18.7 1.0 CA D:ASP131 4.7 29.5 1.0 CB D:SER146 4.8 20.9 1.0 CD1 D:TRP130 4.8 29.0 1.0 CA D:CA303 4.8 18.3 1.0 NE1 D:TRP130 4.8 29.0 1.0 OG1 D:THR149 4.9 27.4 1.0 OD1 D:ASP124 4.9 25.5 1.0

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structure and Sugar-Specificity of Basic Winged-Bean Lectin: Structures of New Disaccharide Complexes and A Comparative Study with Other Known Disaccharide Complexes of the Lectin. Acta Crystallogr.,Sect.D V. 64 730 2008.
ISSN: ISSN 0907-4449
PubMed: 18566508
DOI: 10.1107/S0907444908011323