Calcium in PDB 2dvd: Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex, PDB code: 2dvd was solved by S.K.Natchiar, O.Srinivas, N.Mitra, A.Surolia, N.Jayaraman, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.440, 124.640, 75.690, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.2

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex (pdb code 2dvd). 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 Peanut Lectin Gal-Alpha-1,3-Gal Complex, PDB code: 2dvd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Peanut Lectin Gal-Alpha-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:28.7 occ:1.00 O A:HOH1242 2.4 20.0 1.0 O A:TYR125 2.5 33.7 1.0 O A:HOH1243 2.6 25.1 1.0 OD1 A:ASN127 2.6 28.9 1.0 OD2 A:ASP123 2.6 31.0 1.0 OD1 A:ASP123 2.6 34.5 1.0 OD2 A:ASP132 2.6 31.0 1.0 CG A:ASP123 3.0 31.4 1.0 CG A:ASN127 3.5 30.2 1.0 CG A:ASP132 3.5 31.0 1.0 C A:TYR125 3.7 31.9 1.0 N A:ASN127 3.9 28.9 1.0 CB A:ASN127 3.9 28.7 1.0 OD1 A:ASP132 4.0 30.8 1.0 MN A:MN238 4.1 47.4 1.0 O A:HOH1244 4.4 19.9 1.0 CA A:GLY104 4.4 24.0 1.0 CB A:ASP123 4.4 29.6 1.0 CA A:TYR125 4.5 31.2 1.0 CA A:ASN127 4.5 29.9 1.0 N A:TYR125 4.5 31.0 1.0 N A:SER126 4.6 29.8 1.0 CB A:TYR125 4.6 32.8 1.0 CA A:SER126 4.7 28.9 1.0 ND2 A:ASN127 4.7 31.6 1.0 CB A:ASP132 4.7 30.8 1.0 C A:SER126 4.7 29.6 1.0 OD1 A:ASP83 4.7 29.1 1.0 O A:GLY104 4.7 26.1 1.0 O A:ASP83 4.8 24.6 1.0 CD1 A:TYR125 4.9 34.9 1.0 CE1 A:HIS137 5.0 22.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Peanut Lectin Gal-Alpha-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:28.3 occ:1.00 O B:TYR125 2.5 29.8 1.0 OD2 B:ASP132 2.5 24.1 1.0 O B:HOH2243 2.6 19.8 1.0 OD1 B:ASN127 2.6 23.4 1.0 OD2 B:ASP123 2.6 21.2 1.0 OD1 B:ASP123 2.7 23.9 1.0 O B:HOH2242 2.7 24.8 1.0 CG B:ASP123 3.0 21.3 1.0 CG B:ASN127 3.6 26.4 1.0 CG B:ASP132 3.6 26.0 1.0 C B:TYR125 3.6 28.3 1.0 N B:ASN127 3.9 29.0 1.0 CB B:ASN127 4.0 26.8 1.0 MN B:MN238 4.1 43.3 1.0 OD1 B:ASP132 4.2 26.1 1.0 CA B:TYR125 4.4 28.8 1.0 CA B:GLY104 4.4 24.9 1.0 N B:TYR125 4.4 28.2 1.0 CB B:ASP123 4.5 23.3 1.0 O B:HOH2244 4.5 22.1 1.0 CB B:TYR125 4.5 30.4 1.0 CA B:ASN127 4.6 27.8 1.0 N B:SER126 4.6 28.0 1.0 OD1 B:ASP83 4.6 24.3 1.0 CA B:SER126 4.7 28.8 1.0 C B:SER126 4.7 30.1 1.0 O B:GLY104 4.7 25.3 1.0 O B:ASP83 4.7 23.0 1.0 CB B:ASP132 4.7 26.4 1.0 ND2 B:ASN127 4.8 25.2 1.0 CD1 B:TYR125 4.8 31.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Peanut Lectin Gal-Alpha-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:30.6 occ:1.00 O C:TYR125 2.5 34.7 1.0 OD2 C:ASP132 2.5 28.3 1.0 OD1 C:ASN127 2.6 30.2 1.0 OD1 C:ASP123 2.6 32.7 1.0 OD2 C:ASP123 2.7 33.0 1.0 O C:HOH3243 2.7 32.1 1.0 O C:HOH3242 2.7 27.4 1.0 CG C:ASP123 3.0 32.8 1.0 CG C:ASP132 3.5 32.0 1.0 CG C:ASN127 3.6 32.0 1.0 C C:TYR125 3.7 33.7 1.0 N C:ASN127 3.8 33.2 1.0 CB C:ASN127 4.0 31.8 1.0 OD1 C:ASP132 4.1 30.6 1.0 MN C:MN238 4.1 48.0 1.0 O C:HOH3244 4.3 22.3 1.0 CA C:GLY104 4.4 31.3 1.0 CB C:ASP123 4.5 32.1 1.0 CA C:TYR125 4.5 34.6 1.0 CA C:ASN127 4.6 32.3 1.0 N C:SER126 4.6 33.3 1.0 N C:TYR125 4.6 34.5 1.0 CA C:SER126 4.6 33.5 1.0 CB C:ASP132 4.6 32.6 1.0 C C:SER126 4.6 34.8 1.0 CB C:TYR125 4.7 36.7 1.0 O C:GLY104 4.7 32.7 1.0 ND2 C:ASN127 4.7 29.5 1.0 OD1 C:ASP83 4.8 31.0 1.0 CE1 C:HIS137 4.9 28.9 1.0 O C:ASP83 4.9 28.1 1.0 CD1 C:TYR125 4.9 41.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,3-Gal Complex


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 Peanut Lectin Gal-Alpha-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:28.1 occ:1.00 O D:TYR125 2.5 31.4 1.0 OD1 D:ASN127 2.6 25.1 1.0 O D:HOH4242 2.6 20.8 1.0 OD2 D:ASP123 2.6 25.8 1.0 OD1 D:ASP123 2.7 26.0 1.0 OD2 D:ASP132 2.7 33.3 1.0 O D:HOH4243 2.7 34.0 1.0 CG D:ASP123 3.0 26.9 1.0 CG D:ASP132 3.5 32.9 1.0 CG D:ASN127 3.6 29.4 1.0 C D:TYR125 3.6 30.4 1.0 OD1 D:ASP132 3.8 35.1 1.0 N D:ASN127 3.9 29.9 1.0 CB D:ASN127 4.0 29.8 1.0 O D:HOH4244 4.2 24.3 1.0 MN D:MN238 4.3 48.1 1.0 CA D:GLY104 4.4 26.8 1.0 CA D:TYR125 4.4 29.3 1.0 N D:TYR125 4.5 29.9 1.0 CB D:ASP123 4.5 25.4 1.0 CB D:TYR125 4.6 31.9 1.0 N D:SER126 4.6 30.2 1.0 CA D:ASN127 4.6 30.4 1.0 CB D:ASP132 4.7 30.6 1.0 OD1 D:ASP83 4.7 25.0 1.0 CA D:SER126 4.7 29.2 1.0 O D:GLY104 4.7 27.4 1.0 C D:SER126 4.7 29.5 1.0 ND2 D:ASN127 4.7 28.5 1.0 O D:ASP83 4.8 24.1 1.0 CD1 D:TYR125 4.8 34.9 1.0

S.K.Natchiar, O.Srinivas, N.Mitra, A.Surolia, N.Jayaraman, M.Vijayan. Structural Studies on Peanut Lectin Complexed with Disaccharides Involving Different Linkages: Further Insights Into the Structure and Interactions of the Lectin Acta Crystallogr.,Sect.D V. 62 1413 2006.
ISSN: ISSN 0907-4449
PubMed: 17057347
DOI: 10.1107/S0907444906035712