Manganese in PDB 2e53: Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide, PDB code: 2e53 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)	29.93 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.367, 91.093, 73.399, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide 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 B Blood Group Disaccharide (pdb code 2e53). 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 B Blood Group Disaccharide, PDB code: 2e53:
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 B Blood Group Disaccharide


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1300 b:36.2 occ:1.00 OD1 A:ASP131 2.2 35.4 1.0 OD2 A:ASP124 2.2 28.0 1.0 OE2 A:GLU122 2.2 21.2 1.0 O A:HOH1362 2.3 16.9 1.0 O A:HOH1363 2.3 24.2 1.0 NE2 A:HIS136 2.5 25.7 1.0 CG A:ASP131 3.1 34.8 1.0 CD A:GLU122 3.2 23.7 1.0 CG A:ASP124 3.2 27.8 1.0 CE1 A:HIS136 3.3 25.7 1.0 OE1 A:GLU122 3.5 24.5 1.0 CB A:ASP124 3.6 28.3 1.0 OD2 A:ASP131 3.6 35.1 1.0 CD2 A:HIS136 3.6 26.5 1.0 O A:HOH1367 4.1 29.1 1.0 OG A:SER146 4.2 28.8 1.0 CA A:CA1303 4.3 28.9 1.0 CB A:ASP131 4.3 34.7 1.0 O A:VAL144 4.3 29.4 1.0 OD1 A:ASP124 4.3 30.5 1.0 ND1 A:HIS136 4.5 26.1 1.0 CG A:GLU122 4.6 24.7 1.0 O A:HOH1364 4.6 33.3 1.0 CG A:HIS136 4.7 27.5 1.0 NE1 A:TRP130 4.7 37.6 1.0 CD1 A:TRP130 4.9 37.6 1.0 CA A:ASP131 4.9 34.3 1.0 CZ A:PHE107 4.9 22.1 1.0 CD A:PRO132 4.9 33.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2300 b:34.6 occ:1.00 OD1 B:ASP131 2.2 31.6 1.0 O B:HOH2341 2.3 13.7 1.0 OD2 B:ASP124 2.3 27.9 1.0 OE2 B:GLU122 2.4 21.8 1.0 O B:HOH2340 2.4 22.8 1.0 NE2 B:HIS136 2.5 20.8 1.0 CG B:ASP131 3.0 31.0 1.0 CG B:ASP124 3.3 27.8 1.0 CE1 B:HIS136 3.3 21.7 1.0 CD B:GLU122 3.3 20.6 1.0 OD2 B:ASP131 3.4 32.1 1.0 OE1 B:GLU122 3.6 21.6 1.0 CD2 B:HIS136 3.6 21.1 1.0 CB B:ASP124 3.6 26.3 1.0 O B:HOH2338 3.8 20.2 1.0 CB B:ASP131 4.2 30.2 1.0 OG B:SER146 4.2 20.3 1.0 CA B:CA2303 4.3 25.6 1.0 O B:VAL144 4.3 25.6 1.0 OD1 B:ASP124 4.3 26.6 1.0 ND1 B:HIS136 4.5 23.2 1.0 CG B:HIS136 4.6 23.2 1.0 CG B:GLU122 4.7 20.7 1.0 NE1 B:TRP130 4.7 34.2 1.0 CA B:ASP131 4.8 29.6 1.0 CD1 B:TRP130 4.8 32.7 1.0 CD B:PRO132 4.8 28.1 1.0 CZ B:PHE107 5.0 20.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn3300 b:43.3 occ:1.00 O C:HOH3349 2.2 31.9 1.0 OD1 C:ASP131 2.2 37.2 1.0 OE2 C:GLU122 2.3 25.9 1.0 NE2 C:HIS136 2.3 25.5 1.0 OD2 C:ASP124 2.4 36.5 1.0 O C:HOH3359 2.4 40.2 1.0 CG C:ASP131 3.1 36.0 1.0 CE1 C:HIS136 3.1 27.0 1.0 CG C:ASP124 3.3 34.1 1.0 CD C:GLU122 3.3 27.3 1.0 CD2 C:HIS136 3.5 26.2 1.0 CB C:ASP124 3.6 32.0 1.0 OD2 C:ASP131 3.6 36.2 1.0 OE1 C:GLU122 3.6 26.8 1.0 CB C:ASP131 4.1 35.1 1.0 O C:HOH3347 4.2 31.1 1.0 OG C:SER146 4.3 32.0 1.0 CA C:CA3303 4.3 38.0 1.0 ND1 C:HIS136 4.3 26.1 1.0 OD1 C:ASP124 4.4 36.3 1.0 O C:VAL144 4.4 31.6 1.0 CG C:HIS136 4.5 26.9 1.0 CG C:GLU122 4.7 27.7 1.0 CD C:PRO132 4.7 34.0 1.0 CA C:ASP131 4.8 35.9 1.0 NE1 C:TRP130 4.8 39.0 1.0 CD1 C:TRP130 4.9 37.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn4300 b:39.3 occ:1.00 OD1 D:ASP131 2.2 32.0 1.0 OE2 D:GLU122 2.3 24.8 1.0 O D:HOH4351 2.3 29.8 1.0 NE2 D:HIS136 2.3 24.4 1.0 O D:HOH4353 2.4 23.6 1.0 OD2 D:ASP124 2.4 29.4 1.0 CG D:ASP131 3.1 32.2 1.0 CE1 D:HIS136 3.2 24.8 1.0 CD D:GLU122 3.3 24.0 1.0 CG D:ASP124 3.3 27.7 1.0 CD2 D:HIS136 3.4 27.2 1.0 OD2 D:ASP131 3.5 30.6 1.0 OE1 D:GLU122 3.6 23.9 1.0 CB D:ASP124 3.6 28.2 1.0 O D:HOH4350 4.1 19.3 1.0 OG D:SER146 4.2 28.4 1.0 CA D:CA4303 4.2 26.9 1.0 CB D:ASP131 4.2 32.1 1.0 ND1 D:HIS136 4.4 27.0 1.0 O D:VAL144 4.4 28.5 1.0 OD1 D:ASP124 4.4 28.5 1.0 O D:HOH4352 4.5 27.6 1.0 CG D:HIS136 4.5 27.4 1.0 CG D:GLU122 4.6 23.7 1.0 NE1 D:TRP130 4.7 32.7 1.0 CD D:PRO132 4.8 31.4 1.0 CA D:ASP131 4.8 33.9 1.0 CD1 D:TRP130 4.8 33.1 1.0

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Generation of Blood Group Specificity: New Insights From Structural Studies on the Complexes of A- and B-Reactive Saccharides with Basic Winged Bean Agglutinin. Proteins V. 68 762 2007.
ISSN: ISSN 0887-3585
PubMed: 17510954
DOI: 10.1002/PROT.21428