Manganese in PDB 2dtw: Crystal Structure of Basic Winged Bean Lectin in Complex with 2ME-O-D- Galactose

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with 2ME-O-D- Galactose, PDB code: 2dtw 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 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.431, 91.061, 73.383, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.3

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with 2ME-O-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 2ME-O-D- Galactose (pdb code 2dtw). 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 2ME-O-D- Galactose, PDB code: 2dtw:
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 2ME-O-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 2ME-O-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1300 b:36.7 occ:1.00 OD1 A:ASP131 2.2 37.9 1.0 OE2 A:GLU122 2.3 23.9 1.0 O A:HOH1451 2.3 17.3 1.0 O A:HOH1452 2.3 23.0 1.0 OD2 A:ASP124 2.3 29.1 1.0 NE2 A:HIS136 2.3 23.1 1.0 CE1 A:HIS136 3.1 23.1 1.0 CG A:ASP131 3.1 36.4 1.0 CG A:ASP124 3.2 28.9 1.0 CD A:GLU122 3.2 24.8 1.0 CD2 A:HIS136 3.4 25.6 1.0 CB A:ASP124 3.5 28.1 1.0 OE1 A:GLU122 3.5 25.3 1.0 OD2 A:ASP131 3.7 36.2 1.0 O A:HOH1456 4.1 23.6 1.0 CB A:ASP131 4.2 35.9 1.0 ND1 A:HIS136 4.3 23.9 1.0 CA A:CA1303 4.3 29.1 1.0 OD1 A:ASP124 4.3 28.5 1.0 O A:HOH1453 4.3 30.3 1.0 OG A:SER146 4.4 29.7 1.0 CG A:HIS136 4.5 26.1 1.0 O A:VAL144 4.5 29.7 1.0 CG A:GLU122 4.6 23.1 1.0 CD A:PRO132 4.7 34.5 1.0 NE1 A:TRP130 4.7 40.5 1.0 CA A:ASP131 4.7 36.0 1.0 CD1 A:TRP130 4.8 39.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with 2ME-O-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 2ME-O-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2300 b:31.8 occ:1.00 OD2 B:ASP124 2.2 32.9 1.0 OD1 B:ASP131 2.2 29.2 1.0 O B:HOH2437 2.2 18.6 1.0 OE2 B:GLU122 2.3 22.6 1.0 NE2 B:HIS136 2.3 18.2 1.0 O B:HOH2438 2.4 16.6 1.0 CG B:ASP131 2.9 30.4 1.0 CE1 B:HIS136 3.0 19.4 1.0 CG B:ASP124 3.1 29.8 1.0 CD B:GLU122 3.3 21.2 1.0 OD2 B:ASP131 3.3 34.2 1.0 CB B:ASP124 3.4 28.6 1.0 CD2 B:HIS136 3.5 18.9 1.0 OE1 B:GLU122 3.7 21.1 1.0 O B:HOH2435 3.9 22.2 1.0 CB B:ASP131 4.1 30.3 1.0 OD1 B:ASP124 4.1 31.2 1.0 CA B:CA2303 4.2 26.8 1.0 ND1 B:HIS136 4.2 21.0 1.0 OG B:SER146 4.4 21.9 1.0 O B:VAL144 4.5 24.3 1.0 CG B:HIS136 4.5 20.6 1.0 O B:HOH2464 4.5 33.4 1.0 CG B:GLU122 4.6 18.8 1.0 CA B:ASP131 4.8 30.2 1.0 NE1 B:TRP130 4.8 28.7 1.0 CD B:PRO132 4.8 25.3 1.0 CA B:ASP124 4.9 27.1 1.0 CZ B:PHE107 4.9 22.6 1.0 CD1 B:TRP130 4.9 29.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with 2ME-O-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 2ME-O-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn3300 b:38.0 occ:1.00 OD1 C:ASP131 2.2 33.9 1.0 OD2 C:ASP124 2.2 34.1 1.0 O C:HOH3441 2.2 26.0 1.0 OE2 C:GLU122 2.3 23.2 1.0 NE2 C:HIS136 2.3 32.4 1.0 O C:HOH3447 2.4 31.8 1.0 CG C:ASP131 3.0 35.1 1.0 CE1 C:HIS136 3.0 33.8 1.0 CG C:ASP124 3.2 32.8 1.0 CD C:GLU122 3.3 26.0 1.0 OD2 C:ASP131 3.3 35.0 1.0 CD2 C:HIS136 3.5 32.6 1.0 CB C:ASP124 3.5 30.5 1.0 OE1 C:GLU122 3.6 25.6 1.0 CB C:ASP131 4.1 35.4 1.0 O C:HOH3439 4.2 26.3 1.0 ND1 C:HIS136 4.2 32.0 1.0 CA C:CA3303 4.3 34.1 1.0 OD1 C:ASP124 4.4 35.0 1.0 OG C:SER146 4.4 36.0 1.0 O C:VAL144 4.5 31.6 1.0 CG C:HIS136 4.5 32.0 1.0 CG C:GLU122 4.6 27.5 1.0 NE1 C:TRP130 4.7 45.8 1.0 CD C:PRO132 4.7 35.6 1.0 CA C:ASP131 4.8 35.8 1.0 CD1 C:TRP130 4.8 45.1 1.0 CZ C:PHE107 5.0 28.5 1.0 CA C:ASP124 5.0 29.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with 2ME-O-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 2ME-O-D- Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn4300 b:40.7 occ:1.00 O D:HOH4436 2.2 26.4 1.0 OD1 D:ASP131 2.2 30.4 1.0 OE2 D:GLU122 2.3 24.0 1.0 O D:HOH4435 2.3 29.2 1.0 OD2 D:ASP124 2.3 31.1 1.0 NE2 D:HIS136 2.4 29.1 1.0 CG D:ASP131 3.0 30.2 1.0 CE1 D:HIS136 3.1 29.2 1.0 OD2 D:ASP131 3.2 29.5 1.0 CD D:GLU122 3.2 23.1 1.0 CG D:ASP124 3.3 30.8 1.0 OE1 D:GLU122 3.5 23.0 1.0 CD2 D:HIS136 3.5 29.9 1.0 CB D:ASP124 3.6 30.2 1.0 O D:HOH4434 4.0 18.6 1.0 CA D:CA4303 4.2 27.9 1.0 OG D:SER146 4.2 30.1 1.0 CB D:ASP131 4.2 30.1 1.0 O D:VAL144 4.3 29.6 1.0 ND1 D:HIS136 4.3 30.6 1.0 OD1 D:ASP124 4.4 33.7 1.0 O D:HOH4453 4.5 39.6 1.0 CG D:HIS136 4.6 31.0 1.0 CG D:GLU122 4.6 24.3 1.0 NE1 D:TRP130 4.7 29.7 1.0 CD D:PRO132 4.8 29.0 1.0 CA D:ASP131 4.8 32.2 1.0 CD1 D:TRP130 4.8 31.5 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