Manganese in PDB 2du0: Crystal Structure of Basic Winged Bean Lectin in Complex with Alpha-D- Galactose

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Alpha-D- Galactose, PDB code: 2du0 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.552, 89.957, 73.404, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.5

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Alpha-D- Galactose 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 Alpha-D- Galactose (pdb code 2du0). 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 Alpha-D- Galactose, PDB code: 2du0:
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 Alpha-D- Galactose


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 Alpha-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1300 b:38.2 occ:1.00 NE2 A:HIS136 2.2 25.6 1.0 OD1 A:ASP131 2.3 39.2 1.0 OE2 A:GLU122 2.3 23.7 1.0 OD2 A:ASP124 2.3 28.0 1.0 O A:HOH1402 2.3 31.0 1.0 O A:HOH1403 2.5 12.0 1.0 CE1 A:HIS136 3.0 25.2 1.0 CG A:ASP131 3.1 35.9 1.0 CG A:ASP124 3.2 28.4 1.0 CD2 A:HIS136 3.3 26.5 1.0 CD A:GLU122 3.4 23.4 1.0 CB A:ASP124 3.5 27.5 1.0 OD2 A:ASP131 3.6 35.0 1.0 OE1 A:GLU122 3.9 23.0 1.0 CB A:ASP131 4.1 34.7 1.0 ND1 A:HIS136 4.2 27.3 1.0 O A:HOH1404 4.3 28.2 1.0 CA A:CA1303 4.3 31.6 1.0 OD1 A:ASP124 4.3 28.6 1.0 OG A:SER146 4.4 31.9 1.0 CG A:HIS136 4.4 26.2 1.0 O A:VAL144 4.5 31.9 1.0 NE1 A:TRP130 4.6 36.5 1.0 O A:HOH1432 4.6 18.2 1.0 CA A:ASP131 4.7 35.5 1.0 CG A:GLU122 4.7 21.9 1.0 CD A:PRO132 4.7 33.5 1.0 CD1 A:TRP130 4.8 36.6 1.0 CA A:ASP124 5.0 26.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Alpha-D- Galactose


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 Alpha-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2300 b:35.1 occ:1.00 OD2 B:ASP124 2.2 30.7 1.0 O B:HOH2403 2.2 14.8 1.0 OD1 B:ASP131 2.2 29.1 1.0 OE2 B:GLU122 2.3 16.0 1.0 O B:HOH2402 2.3 26.9 1.0 NE2 B:HIS136 2.4 13.8 1.0 CG B:ASP131 2.9 28.6 1.0 OD2 B:ASP131 3.1 30.7 1.0 CG B:ASP124 3.1 28.8 1.0 CE1 B:HIS136 3.3 13.3 1.0 CD B:GLU122 3.3 18.3 1.0 CD2 B:HIS136 3.5 14.5 1.0 CB B:ASP124 3.5 29.4 1.0 OE1 B:GLU122 3.7 18.8 1.0 O B:HOH2404 4.0 14.8 1.0 CB B:ASP131 4.1 30.5 1.0 OD1 B:ASP124 4.2 32.1 1.0 OG B:SER146 4.3 23.2 1.0 CA B:CA2303 4.3 26.8 1.0 O B:VAL144 4.4 26.8 1.0 ND1 B:HIS136 4.5 14.7 1.0 CG B:HIS136 4.6 17.1 1.0 O B:HOH2450 4.6 33.5 1.0 NE1 B:TRP130 4.6 28.7 1.0 CG B:GLU122 4.7 16.9 1.0 CA B:ASP131 4.7 31.4 1.0 CD1 B:TRP130 4.8 28.9 1.0 CD B:PRO132 4.8 27.0 1.0 CZ B:PHE107 4.8 24.6 1.0 CA B:ASP124 5.0 27.5 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Alpha-D- Galactose


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 Alpha-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn3300 b:51.4 occ:1.00 OD1 C:ASP131 2.2 39.3 1.0 OE2 C:GLU122 2.3 25.6 1.0 O C:HOH3402 2.4 20.8 1.0 NE2 C:HIS136 2.7 33.5 1.0 OD2 C:ASP124 2.8 37.6 1.0 CD C:GLU122 3.0 27.1 1.0 OE1 C:GLU122 3.1 26.9 1.0 OG C:SER146 3.4 37.1 1.0 CG C:ASP131 3.4 41.1 1.0 CE1 C:HIS136 3.5 33.3 1.0 O C:VAL144 3.8 33.6 1.0 CD2 C:HIS136 3.8 32.3 1.0 CG C:ASP124 3.8 35.8 1.0 OD2 C:ASP131 3.9 42.0 1.0 CB C:ASP124 4.1 34.5 1.0 CG C:GLU122 4.3 25.0 1.0 CB C:ASP131 4.5 39.0 1.0 O C:HOH3403 4.6 25.9 1.0 CB C:SER146 4.6 33.2 1.0 NE1 C:TRP130 4.6 43.9 1.0 CA C:CA3303 4.7 32.2 1.0 ND1 C:HIS136 4.7 32.5 1.0 CD1 C:TRP130 4.7 43.8 1.0 CD C:PRO132 4.8 34.0 1.0 CG C:HIS136 4.8 31.9 1.0 N C:SER146 4.9 33.5 1.0 CG1 C:VAL144 4.9 35.2 1.0 OD1 C:ASP124 4.9 34.9 1.0 CA C:ASP131 5.0 37.5 1.0 C C:VAL144 5.0 33.2 1.0 OD1 C:ASP140 5.0 29.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with Alpha-D- Galactose


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 Alpha-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn4300 b:36.3 occ:1.00 NE2 D:HIS136 2.3 28.1 1.0 O D:HOH4403 2.3 29.6 1.0 OD1 D:ASP131 2.3 29.7 1.0 OE2 D:GLU122 2.4 27.8 1.0 OD2 D:ASP124 2.5 29.4 1.0 O D:HOH4402 2.6 19.3 1.0 CE1 D:HIS136 3.1 25.8 1.0 CD D:GLU122 3.2 26.7 1.0 OE1 D:GLU122 3.2 25.3 1.0 CG D:ASP124 3.3 28.5 1.0 CD2 D:HIS136 3.3 26.6 1.0 CG D:ASP131 3.3 30.0 1.0 CB D:ASP124 3.5 29.0 1.0 OD2 D:ASP131 3.9 27.9 1.0 OG D:SER146 4.1 24.3 1.0 ND1 D:HIS136 4.3 26.6 1.0 O D:HOH4404 4.3 16.1 1.0 O D:VAL144 4.3 29.0 1.0 CA D:CA4303 4.3 28.8 1.0 CB D:ASP131 4.4 31.5 1.0 CG D:HIS136 4.4 26.3 1.0 OD1 D:ASP124 4.5 30.7 1.0 CG D:GLU122 4.6 24.9 1.0 NE1 D:TRP130 4.8 35.3 1.0 CD D:PRO132 4.8 30.8 1.0 CA D:ASP131 4.9 32.4 1.0 CZ D:PHE107 4.9 25.7 1.0 CD1 D:TRP130 5.0 33.7 1.0 CA D:ASP124 5.0 29.9 1.0

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structural Basis For the Carbohydrate-Specificity of Basic Winged-Bean Lectin and Its Differential Affinity For Gal and Galnac Acta Crystallogr.,Sect.D V. 62 1319 2006.
ISSN: ISSN 0907-4449
PubMed: 17057334
DOI: 10.1107/S0907444906028198