Manganese in PDB 2zml: Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal, PDB code: 2zml 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)	29.55 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.928, 91.524, 73.654, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.7

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha 1,4 Gal 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 1,4 Gal (pdb code 2zml). 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 1,4 Gal, PDB code: 2zml:
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 1,4 Gal


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 1,4 Gal within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:27.4 occ:1.00 O A:HOH603 2.2 6.2 1.0 O A:HOH602 2.2 11.1 1.0 OD1 A:ASP131 2.2 24.8 1.0 NE2 A:HIS136 2.2 14.0 1.0 OD2 A:ASP124 2.3 21.1 1.0 OE2 A:GLU122 2.3 15.3 1.0 CG A:ASP131 3.1 22.9 1.0 CE1 A:HIS136 3.1 15.1 1.0 CG A:ASP124 3.2 19.5 1.0 CD2 A:HIS136 3.3 16.1 1.0 CD A:GLU122 3.4 15.6 1.0 CB A:ASP124 3.5 18.7 1.0 OD2 A:ASP131 3.5 21.3 1.0 OE1 A:GLU122 3.8 12.3 1.0 CB A:ASP131 4.2 23.4 1.0 OD1 A:ASP124 4.2 21.9 1.0 ND1 A:HIS136 4.3 17.6 1.0 O A:HOH604 4.3 9.7 1.0 OG A:SER146 4.3 21.7 1.0 O A:HOH639 4.4 24.8 1.0 CG A:HIS136 4.4 16.6 1.0 CA A:CA303 4.5 16.9 1.0 O A:VAL144 4.5 21.0 1.0 CD A:PRO132 4.7 24.3 1.0 CG A:GLU122 4.7 15.0 1.0 NE1 A:TRP130 4.8 26.8 1.0 CA A:ASP131 4.8 23.4 1.0 CD1 A:TRP130 4.9 27.0 1.0

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


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 1,4 Gal within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:21.8 occ:1.00 O B:HOH645 2.3 7.1 1.0 OD1 B:ASP131 2.3 19.4 1.0 OD2 B:ASP124 2.3 19.0 1.0 OE2 B:GLU122 2.3 12.8 1.0 O B:HOH646 2.4 9.0 1.0 NE2 B:HIS136 2.5 9.9 1.0 CG B:ASP131 3.1 20.1 1.0 CG B:ASP124 3.1 19.4 1.0 CE1 B:HIS136 3.3 10.2 1.0 CD B:GLU122 3.3 12.3 1.0 OD2 B:ASP131 3.5 21.9 1.0 CD2 B:HIS136 3.5 11.8 1.0 CB B:ASP124 3.6 19.2 1.0 OE1 B:GLU122 3.6 9.6 1.0 O B:HOH647 4.1 8.9 1.0 OD1 B:ASP124 4.1 21.6 1.0 CA B:CA303 4.2 16.4 1.0 CB B:ASP131 4.2 20.4 1.0 OG B:SER146 4.3 15.4 1.0 O B:VAL144 4.4 16.6 1.0 ND1 B:HIS136 4.5 12.1 1.0 O B:HOH661 4.5 17.1 1.0 CG B:HIS136 4.6 13.7 1.0 NE1 B:TRP130 4.7 24.7 1.0 CG B:GLU122 4.7 11.4 1.0 CD1 B:TRP130 4.8 24.4 1.0 CD B:PRO132 4.8 19.8 1.0 CA B:ASP131 4.9 21.4 1.0 CZ B:PHE107 4.9 8.8 1.0

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


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 1,4 Gal within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn300 b:30.4 occ:1.00 OD2 C:ASP124 2.2 24.9 1.0 OE2 C:GLU122 2.2 15.6 1.0 OD1 C:ASP131 2.2 25.5 1.0 O C:HOH602 2.3 7.8 1.0 NE2 C:HIS136 2.3 15.3 1.0 CG C:ASP124 3.1 22.1 1.0 CG C:ASP131 3.2 25.6 1.0 CE1 C:HIS136 3.2 16.5 1.0 CD C:GLU122 3.3 14.0 1.0 CD2 C:HIS136 3.4 16.3 1.0 CB C:ASP124 3.5 21.2 1.0 OE1 C:GLU122 3.6 13.2 1.0 OD2 C:ASP131 3.7 26.8 1.0 OD1 C:ASP124 4.2 23.6 1.0 OG C:SER146 4.3 24.1 1.0 CA C:CA303 4.3 25.1 1.0 CB C:ASP131 4.3 25.9 1.0 O C:HOH603 4.3 26.1 1.0 ND1 C:HIS136 4.4 15.8 1.0 O C:VAL144 4.5 20.3 1.0 CG C:HIS136 4.5 17.4 1.0 CG C:GLU122 4.6 15.0 1.0 CD C:PRO132 4.8 24.4 1.0 NE1 C:TRP130 4.8 29.7 1.0 CA C:ASP131 5.0 25.3 1.0 CZ C:PHE107 5.0 15.6 1.0 CA C:ASP124 5.0 19.3 1.0 CD1 C:TRP130 5.0 28.6 1.0

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


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 1,4 Gal within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn300 b:26.9 occ:1.00 O D:HOH602 2.2 2.9 1.0 OD1 D:ASP131 2.3 20.0 1.0 NE2 D:HIS136 2.3 15.4 1.0 OE2 D:GLU122 2.3 13.3 1.0 OD2 D:ASP124 2.3 20.4 1.0 O D:HOH603 2.5 13.7 1.0 CG D:ASP131 3.1 21.6 1.0 CE1 D:HIS136 3.2 15.9 1.0 CG D:ASP124 3.2 19.8 1.0 CD D:GLU122 3.4 11.6 1.0 CD2 D:HIS136 3.4 16.5 1.0 OD2 D:ASP131 3.6 20.6 1.0 CB D:ASP124 3.6 18.7 1.0 OE1 D:GLU122 3.7 10.5 1.0 O D:HOH604 4.1 9.8 1.0 OG D:SER146 4.2 18.8 1.0 CB D:ASP131 4.2 21.7 1.0 OD1 D:ASP124 4.3 20.5 1.0 ND1 D:HIS136 4.3 18.8 1.0 CA D:CA303 4.4 19.1 1.0 O D:VAL144 4.4 16.0 1.0 CG D:HIS136 4.5 18.7 1.0 CG D:GLU122 4.7 11.5 1.0 CD D:PRO132 4.7 20.6 1.0 NE1 D:TRP130 4.8 24.3 1.0 CA D:ASP131 4.9 22.0 1.0 CD1 D:TRP130 4.9 25.3 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