Calcium in PDB 2dv9: Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal Complex

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal Complex, PDB code: 2dv9 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)	19.89 / 2.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	127.770, 124.910, 76.280, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.7

The structure of Crystal Structure of Peanut Lectin Gal-Beta-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-Beta-1,3-Gal Complex (pdb code 2dv9). 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-Beta-1,3-Gal Complex, PDB code: 2dv9:
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-Beta-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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:36.9 occ:1.00 O A:TYR125 2.6 33.3 1.0 OD1 A:ASP123 2.6 35.2 1.0 OD1 A:ASN127 2.6 30.4 1.0 OD2 A:ASP123 2.7 32.8 1.0 OD2 A:ASP132 2.7 39.0 1.0 O A:HOH337 2.7 46.0 1.0 O A:HOH338 2.8 26.2 1.0 CG A:ASP123 3.0 32.7 1.0 CG A:ASN127 3.4 30.8 1.0 CG A:ASP132 3.6 38.5 1.0 C A:TYR125 3.7 32.5 1.0 N A:ASN127 3.7 31.2 1.0 CB A:ASN127 3.8 30.2 1.0 OD1 A:ASP132 4.1 39.7 1.0 CA A:GLY104 4.3 26.2 1.0 MN A:MN238 4.3 46.0 1.0 O A:HOH438 4.4 26.5 1.0 CA A:ASN127 4.4 29.1 1.0 CB A:ASP123 4.4 31.6 1.0 N A:SER126 4.5 31.1 1.0 CA A:TYR125 4.5 32.4 1.0 CD1 A:TYR125 4.6 36.7 1.0 CA A:SER126 4.6 29.8 1.0 N A:TYR125 4.6 32.9 1.0 C A:SER126 4.6 30.8 1.0 ND2 A:ASN127 4.6 32.0 1.0 CB A:TYR125 4.7 32.3 1.0 CB A:ASP132 4.7 36.7 1.0 OD1 A:ASP83 4.7 31.7 1.0 O A:GLY104 4.8 26.9 1.0 O A:ASP83 5.0 30.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:25.8 occ:1.00 OD2 B:ASP132 2.6 26.1 1.0 O B:TYR125 2.6 32.3 1.0 OD2 B:ASP123 2.7 25.8 1.0 OD1 B:ASP123 2.7 28.0 1.0 OD1 B:ASN127 2.7 24.4 1.0 O B:HOH1392 2.7 18.2 1.0 O B:HOH1494 2.7 36.5 1.0 CG B:ASP123 3.0 25.2 1.0 CG B:ASN127 3.6 27.5 1.0 C B:TYR125 3.7 31.1 1.0 CG B:ASP132 3.7 27.5 1.0 N B:ASN127 4.0 30.4 1.0 CB B:ASN127 4.0 27.5 1.0 MN B:MN238 4.1 39.1 1.0 OD1 B:ASP132 4.3 28.9 1.0 O B:HOH1393 4.3 25.8 1.0 CA B:GLY104 4.4 27.6 1.0 CA B:TYR125 4.5 30.9 1.0 CB B:ASP123 4.5 27.1 1.0 CB B:TYR125 4.6 30.9 1.0 N B:TYR125 4.6 29.6 1.0 CA B:ASN127 4.6 29.5 1.0 O B:GLY104 4.7 27.9 1.0 N B:SER126 4.7 30.6 1.0 CD1 B:TYR125 4.7 31.6 1.0 CA B:SER126 4.8 31.4 1.0 ND2 B:ASN127 4.8 27.6 1.0 C B:SER126 4.8 31.6 1.0 CB B:ASP132 4.8 27.6 1.0 OD1 B:ASP83 4.9 22.9 1.0 O B:ASP83 4.9 23.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:40.2 occ:1.00 O C:TYR125 2.5 47.7 1.0 OD2 C:ASP132 2.5 43.5 1.0 O C:HOH2332 2.6 23.6 1.0 OD1 C:ASN127 2.8 40.4 1.0 OD1 C:ASP123 2.8 44.7 1.0 OD2 C:ASP123 2.9 42.9 1.0 O C:HOH2397 3.0 40.9 1.0 CG C:ASP123 3.1 42.6 1.0 CG C:ASP132 3.3 41.7 1.0 CG C:ASN127 3.5 38.6 1.0 N C:ASN127 3.6 44.8 1.0 OD1 C:ASP132 3.7 45.1 1.0 C C:TYR125 3.7 48.1 1.0 CB C:ASN127 3.8 39.1 1.0 MN C:MN238 3.9 56.4 1.0 O C:HOH2396 3.9 34.7 1.0 CA C:ASN127 4.3 41.9 1.0 CB C:ASP132 4.4 40.5 1.0 CA C:SER126 4.4 45.3 1.0 C C:SER126 4.4 45.7 1.0 N C:SER126 4.5 45.9 1.0 CB C:ASP123 4.5 41.4 1.0 ND2 C:ASN127 4.6 38.0 1.0 CA C:TYR125 4.7 49.7 1.0 N C:TYR125 4.8 50.1 1.0 CE1 C:HIS137 4.8 36.6 1.0 CA C:GLY104 4.9 36.8 1.0 CD1 C:TYR125 4.9 58.2 1.0 O C:GLY104 4.9 37.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:31.7 occ:1.00 O D:TYR125 2.5 31.6 1.0 OD2 D:ASP132 2.7 35.4 1.0 OD2 D:ASP123 2.7 33.7 1.0 O D:HOH352 2.7 24.3 1.0 OD1 D:ASP123 2.7 32.9 1.0 OD1 D:ASN127 2.7 38.6 1.0 O D:HOH353 2.8 38.0 1.0 CG D:ASP123 3.1 32.2 1.0 CG D:ASN127 3.6 37.5 1.0 C D:TYR125 3.6 31.5 1.0 CG D:ASP132 3.6 37.8 1.0 N D:ASN127 3.7 34.7 1.0 CB D:ASN127 3.9 36.7 1.0 OD1 D:ASP132 4.1 39.4 1.0 MN D:MN238 4.3 49.6 1.0 CA D:GLY104 4.4 32.7 1.0 CA D:ASN127 4.4 35.3 1.0 CA D:TYR125 4.4 29.3 1.0 N D:TYR125 4.5 28.7 1.0 N D:SER126 4.5 32.0 1.0 CB D:TYR125 4.5 31.0 1.0 CB D:ASP123 4.5 29.7 1.0 CA D:SER126 4.5 32.1 1.0 O D:HOH354 4.6 18.2 1.0 C D:SER126 4.6 33.8 1.0 CD1 D:TYR125 4.6 31.4 1.0 OD1 D:ASP83 4.7 30.1 1.0 CB D:ASP132 4.7 36.2 1.0 ND2 D:ASN127 4.7 38.1 1.0 O D:GLY104 4.7 31.6 1.0 O D:ASP83 4.9 29.7 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