Manganese in PDB 2d3s: Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen

The structure of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen, PDB code: 2d3s was solved by K.A.Kulkarni, S.Sinha, 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 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.866, 91.897, 73.503, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.4

The structure of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen 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 with Tn-Antigen (pdb code 2d3s). 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 with Tn-Antigen, PDB code: 2d3s:
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 with Tn-Antigen


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 with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:43.8 occ:1.00 O A:HOH651 2.2 20.1 1.0 O A:HOH650 2.3 30.1 1.0 OD2 A:ASP124 2.3 36.4 1.0 OD1 A:ASP131 2.4 39.4 1.0 NE2 A:HIS136 2.4 33.2 1.0 OE2 A:GLU122 2.4 29.6 1.0 CG A:ASP131 3.1 39.9 1.0 CE1 A:HIS136 3.1 33.8 1.0 CG A:ASP124 3.2 35.1 1.0 CD A:GLU122 3.4 31.6 1.0 CD2 A:HIS136 3.5 32.5 1.0 CB A:ASP124 3.6 35.5 1.0 OE1 A:GLU122 3.7 31.8 1.0 OD2 A:ASP131 3.7 38.6 1.0 CB A:ASP131 4.0 41.5 1.0 O A:HOH652 4.2 28.5 1.0 OG A:SER146 4.3 39.2 1.0 CA A:CA303 4.3 34.6 1.0 OD1 A:ASP124 4.3 36.5 1.0 ND1 A:HIS136 4.3 34.3 1.0 O A:VAL144 4.5 34.0 1.0 CG A:HIS136 4.5 34.5 1.0 O A:HOH632 4.6 38.7 1.0 NE1 A:TRP130 4.6 47.3 1.0 CG A:GLU122 4.7 28.6 1.0 CA A:ASP131 4.8 43.3 1.0 CD A:PRO132 4.8 42.9 1.0 CD1 A:TRP130 4.8 47.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


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 with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1300 b:35.2 occ:1.00 OD2 B:ASP124 2.1 30.4 1.0 O B:HOH1439 2.2 21.4 1.0 OD1 B:ASP131 2.2 24.9 1.0 O B:HOH1440 2.3 18.3 1.0 OE2 B:GLU122 2.3 21.6 1.0 NE2 B:HIS136 2.4 24.1 1.0 CG B:ASP131 3.2 27.7 1.0 CG B:ASP124 3.2 30.5 1.0 CD B:GLU122 3.2 22.5 1.0 CE1 B:HIS136 3.2 27.9 1.0 OE1 B:GLU122 3.4 21.4 1.0 CD2 B:HIS136 3.5 23.0 1.0 CB B:ASP124 3.6 27.9 1.0 OD2 B:ASP131 3.7 26.1 1.0 OG B:SER146 4.1 22.9 1.0 O B:HOH1441 4.2 28.0 1.0 CA B:CA1303 4.2 34.2 1.0 OD1 B:ASP124 4.3 29.8 1.0 CB B:ASP131 4.3 26.3 1.0 O B:VAL144 4.3 29.7 1.0 ND1 B:HIS136 4.4 26.2 1.0 O B:HOH1438 4.6 34.1 1.0 CG B:GLU122 4.6 18.5 1.0 CG B:HIS136 4.6 26.3 1.0 NE1 B:TRP130 4.7 36.7 1.0 CZ B:PHE107 4.8 25.9 1.0 CD1 B:TRP130 4.9 35.2 1.0 CA B:ASP131 4.9 27.9 1.0 CD B:PRO132 5.0 27.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


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 with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn2300 b:49.9 occ:1.00 OD1 C:ASP131 2.1 51.7 1.0 O C:HOH2436 2.3 35.2 1.0 NE2 C:HIS136 2.3 35.3 1.0 OE2 C:GLU122 2.3 34.8 1.0 OD2 C:ASP124 2.4 45.4 1.0 CE1 C:HIS136 3.1 34.5 1.0 CG C:ASP131 3.2 51.1 1.0 CG C:ASP124 3.2 40.8 1.0 CD C:GLU122 3.3 33.1 1.0 CD2 C:HIS136 3.5 36.6 1.0 CB C:ASP124 3.5 39.6 1.0 OE1 C:GLU122 3.6 28.0 1.0 OD2 C:ASP131 3.7 52.1 1.0 OG C:SER146 4.2 40.7 1.0 ND1 C:HIS136 4.3 36.0 1.0 O C:HOH2437 4.3 32.2 1.0 OD1 C:ASP124 4.3 44.9 1.0 CB C:ASP131 4.3 50.6 1.0 CA C:CA2303 4.4 43.8 1.0 CG C:HIS136 4.5 35.2 1.0 O C:VAL144 4.5 37.6 1.0 CG C:GLU122 4.7 32.9 1.0 CD C:PRO132 4.7 44.3 1.0 NE1 C:TRP130 5.0 54.0 1.0 CA C:ASP131 5.0 47.9 1.0 CZ C:PHE107 5.0 31.4 1.0 CD1 C:TRP130 5.0 54.0 1.0 CA C:ASP124 5.0 35.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


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 with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn3300 b:49.7 occ:1.00 OD1 D:ASP131 2.2 35.8 1.0 OE2 D:GLU122 2.3 23.9 1.0 O D:HOH3427 2.3 33.3 1.0 O D:HOH3428 2.3 34.4 1.0 NE2 D:HIS136 2.3 29.3 1.0 OD2 D:ASP124 2.4 42.1 1.0 CG D:ASP131 3.1 34.3 1.0 CE1 D:HIS136 3.2 29.4 1.0 CG D:ASP124 3.2 41.0 1.0 CD D:GLU122 3.4 30.0 1.0 CD2 D:HIS136 3.5 29.3 1.0 OD2 D:ASP131 3.5 33.3 1.0 CB D:ASP124 3.5 40.0 1.0 OE1 D:GLU122 3.8 28.5 1.0 CB D:ASP131 4.2 35.6 1.0 OD1 D:ASP124 4.2 42.9 1.0 CA D:CA3303 4.3 38.8 1.0 O D:HOH3429 4.3 26.0 1.0 OG D:SER146 4.3 34.6 1.0 ND1 D:HIS136 4.4 30.8 1.0 O D:VAL144 4.4 31.4 1.0 CG D:HIS136 4.5 31.3 1.0 CG D:GLU122 4.6 30.0 1.0 NE1 D:TRP130 4.7 43.9 1.0 CD1 D:TRP130 4.9 43.7 1.0 CZ D:PHE107 4.9 28.4 1.0 CD D:PRO132 4.9 35.3 1.0 CA D:ASP131 4.9 38.1 1.0

K.A.Kulkarni, S.Sinha, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structural Basis For the Specificity of Basic Winged Bean Lectin For the Tn-Antigen: A Crystallographic, Thermodynamic and Modelling Study Febs Lett. V. 579 6775 2005.
ISSN: ISSN 0014-5793
PubMed: 16310781
DOI: 10.1016/J.FEBSLET.2005.11.011