Manganese in PDB 1wbl: Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose

The structure of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1wbl was solved by M.M.Prabu, R.Sankaranarayanan, K.D.Puri, V.Sharma, 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)	100.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.585, 91.908, 73.283, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 25.9

The structure of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose (pdb code 1wbl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1wbl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Winged Bean Lectin Complexed with Methyl-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 Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:32.0 occ:1.00 OD1 A:ASP131 2.2 16.9 1.0 O A:HOH604 2.3 12.9 1.0 OE2 A:GLU122 2.5 16.9 1.0 NE2 A:HIS136 2.5 3.8 1.0 OD2 A:ASP124 2.5 23.0 1.0 O A:HOH605 2.6 19.2 1.0 CG A:ASP131 3.3 9.3 1.0 CE1 A:HIS136 3.4 2.1 1.0 CD A:GLU122 3.4 17.5 1.0 CD2 A:HIS136 3.5 10.2 1.0 CG A:ASP124 3.6 24.2 1.0 OD2 A:ASP131 3.7 2.5 1.0 OE1 A:GLU122 3.7 16.8 1.0 OG A:SER146 3.9 16.6 1.0 CB A:ASP124 3.9 18.5 1.0 O A:VAL144 4.2 17.3 1.0 O A:HOH606 4.3 28.0 1.0 NE1 A:TRP130 4.4 13.6 1.0 CA A:CA303 4.5 13.8 1.0 ND1 A:HIS136 4.5 7.3 1.0 CD1 A:TRP130 4.5 13.5 1.0 CB A:ASP131 4.5 10.0 1.0 CD A:PRO132 4.6 13.2 1.0 CG A:HIS136 4.6 7.8 1.0 OD1 A:ASP124 4.7 13.7 1.0 CG A:GLU122 4.7 15.8 1.0 CA A:ASP131 4.9 8.1 1.0

Manganese binding site 2 out of 4 in the Winged Bean Lectin Complexed with Methyl-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 Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:13.1 occ:1.00 O B:HOH605 2.3 2.7 1.0 OD1 B:ASP131 2.3 18.1 1.0 OE2 B:GLU122 2.4 2.0 1.0 O B:HOH604 2.5 40.5 1.0 OD2 B:ASP124 2.7 17.0 1.0 NE2 B:HIS136 2.8 2.0 1.0 CD B:GLU122 3.1 2.0 1.0 OE1 B:GLU122 3.2 2.0 1.0 CG B:ASP131 3.3 16.4 1.0 OD2 B:ASP131 3.5 24.4 1.0 CG B:ASP124 3.6 15.0 1.0 CD2 B:HIS136 3.6 2.0 1.0 OG B:SER146 3.8 11.9 1.0 CE1 B:HIS136 3.8 2.0 1.0 CB B:ASP124 3.8 14.7 1.0 O B:VAL144 4.1 8.8 1.0 O B:HOH606 4.3 2.0 1.0 CG B:GLU122 4.6 5.7 1.0 CB B:ASP131 4.6 10.8 1.0 CA B:CA303 4.6 28.3 1.0 OD1 B:ASP124 4.7 22.5 1.0 NE1 B:TRP130 4.7 14.7 1.0 CG B:HIS136 4.8 8.1 1.0 CD1 B:TRP130 4.9 18.2 1.0 ND1 B:HIS136 4.9 2.9 1.0 CZ B:PHE107 5.0 2.0 1.0

Manganese binding site 3 out of 4 in the Winged Bean Lectin Complexed with Methyl-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 Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn300 b:29.8 occ:1.00 O C:HOH504 2.3 25.3 1.0 OD1 C:ASP131 2.3 3.1 1.0 OE2 C:GLU122 2.5 10.4 1.0 OD2 C:ASP124 2.8 38.8 1.0 NE2 C:HIS136 2.8 2.6 1.0 OE1 C:GLU122 3.1 6.8 1.0 CD C:GLU122 3.1 2.9 1.0 CG C:ASP131 3.1 4.5 1.0 OD2 C:ASP131 3.3 14.4 1.0 OG C:SER146 3.6 24.1 1.0 CE1 C:HIS136 3.7 2.8 1.0 CG C:ASP124 3.7 22.8 1.0 CD2 C:HIS136 3.8 3.8 1.0 CB C:ASP124 4.0 18.7 1.0 O C:VAL144 4.0 16.3 1.0 CA C:CA303 4.3 22.7 1.0 O C:HOH505 4.3 2.3 1.0 CB C:ASP131 4.5 7.3 1.0 CG C:GLU122 4.6 2.9 1.0 NE1 C:TRP130 4.6 24.0 1.0 CD1 C:TRP130 4.7 20.1 1.0 CD C:PRO132 4.8 18.5 1.0 ND1 C:HIS136 4.9 7.4 1.0 OD1 C:ASP124 4.9 34.5 1.0 CB C:SER146 4.9 24.7 1.0 CG C:HIS136 5.0 6.5 1.0

Manganese binding site 4 out of 4 in the Winged Bean Lectin Complexed with Methyl-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 Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn300 b:34.6 occ:1.00 OE2 D:GLU122 2.3 7.4 1.0 O D:HOH604 2.3 15.5 1.0 OD1 D:ASP131 2.4 11.8 1.0 O D:HOH605 2.6 11.8 1.0 NE2 D:HIS136 2.7 3.0 1.0 OD2 D:ASP124 2.8 31.7 1.0 CD D:GLU122 3.1 6.1 1.0 CG D:ASP131 3.2 8.8 1.0 OD2 D:ASP131 3.3 4.0 1.0 OE1 D:GLU122 3.3 7.9 1.0 CE1 D:HIS136 3.6 6.7 1.0 CG D:ASP124 3.6 29.3 1.0 CD2 D:HIS136 3.7 9.3 1.0 OG D:SER146 3.8 7.2 1.0 CB D:ASP124 3.9 16.9 1.0 O D:VAL144 4.0 9.7 1.0 O D:HOH606 4.3 9.7 1.0 CG D:GLU122 4.5 6.5 1.0 NE1 D:TRP130 4.5 6.1 1.0 CB D:ASP131 4.6 9.5 1.0 CA D:CA303 4.6 28.3 1.0 CD1 D:TRP130 4.6 2.9 1.0 ND1 D:HIS136 4.7 14.6 1.0 OD1 D:ASP124 4.8 30.8 1.0 CG D:HIS136 4.8 13.2 1.0 CD D:PRO132 4.9 2.0 1.0

M.M.Prabu, R.Sankaranarayanan, K.D.Puri, V.Sharma, A.Surolia, M.Vijayan, K.Suguna. Carbohydrate Specificity and Quaternary Association in Basic Winged Bean Lectin: X-Ray Analysis of the Lectin at 2.5 A Resolution. J.Mol.Biol. V. 276 787 1998.
ISSN: ISSN 0022-2836
PubMed: 9500920
DOI: 10.1006/JMBI.1997.1568