Manganese in PDB 2dty: Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine

The structure of Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine, PDB code: 2dty 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)	25.00 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.725, 91.864, 73.549, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.9

The structure of Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine 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 Complexed with N-Acetyl- D-Galactosamine (pdb code 2dty). 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 Complexed with N-Acetyl- D-Galactosamine, PDB code: 2dty:
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 Complexed with N-Acetyl- D-Galactosamine


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 Complexed with N-Acetyl- D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1300 b:39.6 occ:1.00 OD1 A:ASP131 2.2 37.4 1.0 OE2 A:GLU122 2.3 27.7 1.0 OD2 A:ASP124 2.3 24.6 1.0 NE2 A:HIS136 2.3 26.0 1.0 O A:HOH1402 2.4 34.1 1.0 O A:HOH1403 2.5 14.6 1.0 CG A:ASP131 3.2 35.4 1.0 CD A:GLU122 3.2 27.3 1.0 CE1 A:HIS136 3.2 26.1 1.0 CG A:ASP124 3.3 27.3 1.0 CD2 A:HIS136 3.4 26.4 1.0 OE1 A:GLU122 3.5 27.9 1.0 CB A:ASP124 3.6 27.9 1.0 OD2 A:ASP131 3.7 34.9 1.0 OG A:SER146 4.2 31.1 1.0 CB A:ASP131 4.3 35.5 1.0 O A:HOH1404 4.4 25.5 1.0 ND1 A:HIS136 4.4 28.8 1.0 CA A:CA1303 4.4 24.2 1.0 OD1 A:ASP124 4.4 27.9 1.0 O A:VAL144 4.5 32.6 1.0 CG A:HIS136 4.5 27.7 1.0 CG A:GLU122 4.6 27.0 1.0 CD A:PRO132 4.8 35.3 1.0 CA A:ASP131 4.8 34.6 1.0 NE1 A:TRP130 4.9 37.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine


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 Complexed with N-Acetyl- D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2300 b:31.9 occ:1.00 OE2 B:GLU122 2.2 20.1 1.0 OD1 B:ASP131 2.2 24.8 1.0 O B:HOH2403 2.4 11.7 1.0 NE2 B:HIS136 2.5 16.2 1.0 OD2 B:ASP124 2.5 27.0 1.0 O B:HOH2402 2.5 29.4 1.0 CG B:ASP131 3.0 25.7 1.0 OD2 B:ASP131 3.3 24.7 1.0 CD B:GLU122 3.3 20.0 1.0 CE1 B:HIS136 3.3 16.2 1.0 CG B:ASP124 3.4 27.2 1.0 CD2 B:HIS136 3.6 15.8 1.0 OE1 B:GLU122 3.6 20.4 1.0 CB B:ASP124 3.7 27.5 1.0 O B:HOH2404 4.1 26.4 1.0 CB B:ASP131 4.2 25.6 1.0 OG B:SER146 4.2 23.3 1.0 O B:VAL144 4.3 30.5 1.0 CA B:CA2303 4.4 23.4 1.0 ND1 B:HIS136 4.5 19.1 1.0 CG B:GLU122 4.6 18.9 1.0 OD1 B:ASP124 4.6 28.1 1.0 CG B:HIS136 4.7 19.2 1.0 NE1 B:TRP130 4.7 29.5 1.0 CD1 B:TRP130 4.8 29.1 1.0 CA B:ASP131 4.8 28.1 1.0 CD B:PRO132 4.9 26.2 1.0 CZ B:PHE107 5.0 18.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine


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 Complexed with N-Acetyl- D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn3300 b:43.9 occ:1.00 OD1 C:ASP131 2.2 41.3 1.0 OE2 C:GLU122 2.4 27.6 1.0 OD2 C:ASP124 2.4 34.6 1.0 NE2 C:HIS136 2.4 24.9 1.0 O C:HOH3402 2.4 27.8 1.0 CG C:ASP131 3.0 39.3 1.0 CE1 C:HIS136 3.2 27.4 1.0 CG C:ASP124 3.3 34.0 1.0 OD2 C:ASP131 3.3 40.3 1.0 CD C:GLU122 3.4 27.5 1.0 CD2 C:HIS136 3.5 26.7 1.0 CB C:ASP124 3.6 32.9 1.0 OE1 C:GLU122 3.6 27.3 1.0 OG C:SER146 4.1 33.3 1.0 CA C:CA3303 4.2 32.8 1.0 CB C:ASP131 4.2 37.3 1.0 O C:HOH3403 4.2 13.3 1.0 OD1 C:ASP124 4.4 36.0 1.0 ND1 C:HIS136 4.4 27.8 1.0 O C:VAL144 4.4 32.0 1.0 CG C:HIS136 4.6 28.4 1.0 CG C:GLU122 4.7 26.8 1.0 CD C:PRO132 4.8 33.1 1.0 CA C:ASP131 4.8 34.9 1.0 NE1 C:TRP130 4.9 39.0 1.0 CD1 C:TRP130 4.9 37.1 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine


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 Complexed with N-Acetyl- D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn4300 b:40.6 occ:1.00 OD1 D:ASP131 2.2 30.8 1.0 OE2 D:GLU122 2.3 28.4 1.0 NE2 D:HIS136 2.3 27.7 1.0 O D:HOH4402 2.3 8.8 1.0 O D:HOH4403 2.4 28.6 1.0 OD2 D:ASP124 2.5 32.3 1.0 CE1 D:HIS136 2.9 27.7 1.0 CG D:ASP131 3.1 31.5 1.0 CG D:ASP124 3.3 32.7 1.0 CD D:GLU122 3.4 28.7 1.0 CD2 D:HIS136 3.5 27.2 1.0 OD2 D:ASP131 3.6 30.2 1.0 CB D:ASP124 3.6 31.8 1.0 OE1 D:GLU122 3.8 27.9 1.0 O D:HOH4404 4.0 7.5 1.0 ND1 D:HIS136 4.2 28.6 1.0 OG D:SER146 4.3 31.7 1.0 CB D:ASP131 4.3 31.2 1.0 CA D:CA4303 4.3 27.9 1.0 OD1 D:ASP124 4.4 33.2 1.0 CG D:HIS136 4.5 28.6 1.0 O D:VAL144 4.5 31.2 1.0 CG D:GLU122 4.6 27.3 1.0 CD D:PRO132 4.7 30.3 1.0 NE1 D:TRP130 4.8 32.2 1.0 CA D:ASP131 4.8 33.5 1.0 CD1 D:TRP130 4.9 31.9 1.0 CZ D:PHE107 5.0 25.0 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