Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Basic Winged Bean Lectin Complexed with N-Acetyl- D-Galactosamine, PDB code: 2dty:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca1303 b:24.2 occ:1.00 OD2 A:ASP131 2.4 34.9 1.0 O A:PHE126 2.4 35.5 1.0 O A:HOH1405 2.4 49.0 1.0 O A:HOH1404 2.5 25.5 1.0 OD1 A:ASP124 2.5 27.9 1.0 OD1 A:ASN128 2.5 38.2 1.0 OD2 A:ASP124 2.6 24.6 1.0 CG A:ASP124 2.9 27.3 1.0 CG A:ASP131 3.5 35.4 1.0 C A:PHE126 3.5 34.6 1.0 CG A:ASN128 3.7 37.4 1.0 N A:ASN128 3.9 35.5 1.0 OD1 A:ASP131 4.0 37.4 1.0 CB A:ASN128 4.2 36.3 1.0 O A:HOH1403 4.2 14.6 1.0 CA A:PHE126 4.3 33.7 1.0 CB A:PHE126 4.4 33.5 1.0 CB A:ASP124 4.4 27.9 1.0 N A:PHE126 4.4 33.3 1.0 CD2 A:PHE126 4.4 32.6 1.0 MN A:MN1300 4.4 39.6 1.0 N A:ARG127 4.4 35.1 1.0 CZ A:PHE107 4.5 23.0 1.0 CA A:ARG127 4.6 35.8 1.0 CB A:ASP131 4.6 35.5 1.0 C A:ARG127 4.7 35.3 1.0 CA A:ASN128 4.7 36.2 1.0 NE1 A:TRP130 4.7 37.9 1.0 CA A:GLY105 4.7 29.8 1.0 ND2 A:ASN128 4.8 36.6 1.0 OD2 A:ASP87 4.8 31.4 1.0 O A:GLY105 4.8 29.6 1.0 O A:ASP87 4.8 32.1 1.0 CG A:PHE126 4.9 32.4 1.0 CE1 A:PHE107 5.0 25.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca2303 b:23.4 occ:1.00 O B:HOH2405 2.4 32.4 1.0 O B:PHE126 2.4 30.4 1.0 O B:HOH2404 2.4 26.4 1.0 OD1 B:ASN128 2.4 33.8 1.0 OD2 B:ASP124 2.4 27.0 1.0 OD2 B:ASP131 2.5 24.7 1.0 OD1 B:ASP124 2.5 28.1 1.0 CG B:ASP124 2.8 27.2 1.0 C B:PHE126 3.5 31.0 1.0 CG B:ASN128 3.5 34.0 1.0 CG B:ASP131 3.7 25.7 1.0 N B:ASN128 4.0 33.8 1.0 CB B:ASN128 4.2 32.8 1.0 CA B:PHE126 4.3 30.6 1.0 CB B:PHE126 4.3 29.9 1.0 CB B:ASP124 4.3 27.5 1.0 N B:PHE126 4.3 31.8 1.0 OD2 B:ASP87 4.4 35.4 1.0 OD1 B:ASP131 4.4 24.8 1.0 MN B:MN2300 4.4 31.9 1.0 N B:ARG127 4.4 32.2 1.0 CZ B:PHE107 4.5 18.0 1.0 CD2 B:PHE126 4.6 27.4 1.0 CA B:ARG127 4.6 33.1 1.0 CA B:GLY105 4.6 30.1 1.0 O B:HOH2403 4.6 11.7 1.0 ND2 B:ASN128 4.6 35.0 1.0 CB B:ASP131 4.7 25.6 1.0 O B:ASP87 4.7 30.3 1.0 O B:GLY105 4.7 28.9 1.0 C B:ARG127 4.7 33.8 1.0 CA B:ASN128 4.7 34.3 1.0 NE1 B:TRP130 4.7 29.5 1.0 CE1 B:PHE107 4.9 20.6 1.0 CG B:PHE126 5.0 29.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca3303 b:32.8 occ:1.00 OD1 C:ASN128 2.4 43.0 1.0 OD2 C:ASP131 2.4 40.3 1.0 O C:HOH3404 2.4 23.3 1.0 O C:HOH3403 2.4 13.3 1.0 OD2 C:ASP124 2.5 34.6 1.0 OD1 C:ASP124 2.5 36.0 1.0 O C:PHE126 2.7 36.4 1.0 CG C:ASP124 2.8 34.0 1.0 CG C:ASN128 3.5 41.2 1.0 CG C:ASP131 3.5 39.3 1.0 C C:PHE126 3.8 36.7 1.0 O C:HOH3402 4.0 27.8 1.0 OD1 C:ASP131 4.1 41.3 1.0 CZ C:PHE107 4.1 29.5 1.0 N C:ASN128 4.2 37.4 1.0 MN C:MN3300 4.2 43.9 1.0 CB C:ASN128 4.2 39.9 1.0 CB C:ASP124 4.3 32.9 1.0 NE1 C:TRP130 4.4 39.0 1.0 ND2 C:ASN128 4.5 39.6 1.0 O C:GLY105 4.5 32.4 1.0 CA C:PHE126 4.6 37.2 1.0 CA C:GLY105 4.6 32.0 1.0 CB C:PHE126 4.6 39.3 1.0 N C:PHE126 4.6 36.0 1.0 OD2 C:ASP87 4.7 38.0 1.0 CB C:ASP131 4.7 37.3 1.0 CE1 C:PHE107 4.7 29.7 1.0 N C:ARG127 4.8 36.6 1.0 CA C:ARG127 4.8 36.4 1.0 CA C:ASN128 4.9 37.6 1.0 O C:ASP87 4.9 33.3 1.0 CD2 C:PHE126 4.9 43.5 1.0 CE2 C:PHE107 4.9 29.7 1.0 C C:ARG127 4.9 37.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca4303 b:27.9 occ:1.00 OD2 D:ASP131 2.4 30.2 1.0 O D:HOH4404 2.4 7.5 1.0 OD1 D:ASP124 2.4 33.2 1.0 OD2 D:ASP124 2.4 32.3 1.0 O D:PHE126 2.5 34.2 1.0 OD1 D:ASN128 2.5 31.1 1.0 CG D:ASP124 2.8 32.7 1.0 CG D:ASP131 3.5 31.5 1.0 C D:PHE126 3.6 34.9 1.0 CG D:ASN128 3.6 31.9 1.0 N D:ASN128 4.1 35.2 1.0 OD1 D:ASP131 4.1 30.8 1.0 CB D:ASN128 4.2 33.8 1.0 CB D:ASP124 4.3 31.8 1.0 CZ D:PHE107 4.3 25.0 1.0 MN D:MN4300 4.3 40.6 1.0 O D:HOH4402 4.3 8.8 1.0 CA D:PHE126 4.4 34.0 1.0 N D:PHE126 4.4 33.9 1.0 CB D:PHE126 4.4 33.9 1.0 O D:GLY105 4.5 31.5 1.0 CA D:GLY105 4.5 33.4 1.0 N D:ARG127 4.6 35.6 1.0 OD2 D:ASP87 4.6 38.1 1.0 CD2 D:PHE126 4.6 35.7 1.0 CB D:ASP131 4.7 31.2 1.0 NE1 D:TRP130 4.7 32.2 1.0 O D:ASP87 4.7 35.6 1.0 CA D:ARG127 4.7 34.4 1.0 CE1 D:PHE107 4.7 26.7 1.0 ND2 D:ASN128 4.7 30.9 1.0 CA D:ASN128 4.8 34.8 1.0 C D:ARG127 4.8 34.5 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