Calcium in PDB 2dvg: Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex, PDB code: 2dvg 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)	19.93 / 2.78
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.190, 124.660, 75.740, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 27.4

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc 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-1,6-Glc Complex (pdb code 2dvg). 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-1,6-Glc Complex, PDB code: 2dvg:
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-1,6-Glc 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-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:23.6 occ:1.00 OD2 A:ASP132 2.6 42.4 1.0 OD1 A:ASP123 2.6 25.4 1.0 O A:TYR125 2.6 38.1 1.0 O A:HOH469 2.7 17.5 1.0 OD1 A:ASN127 2.8 23.0 1.0 OD2 A:ASP123 2.9 28.2 1.0 CG A:ASP123 3.1 26.8 1.0 CG A:ASN127 3.4 21.9 1.0 CG A:ASP132 3.4 47.2 1.0 CB A:ASN127 3.5 17.6 1.0 N A:ASN127 3.6 39.5 1.0 OD1 A:ASP132 3.8 47.7 1.0 C A:TYR125 3.8 35.6 1.0 O A:HOH470 3.9 21.6 1.0 CA A:ASN127 4.2 34.5 1.0 CA A:GLY104 4.3 28.5 1.0 OD1 A:ASP83 4.4 35.5 1.0 C A:SER126 4.4 35.8 1.0 CA A:SER126 4.5 33.4 1.0 ND2 A:ASN127 4.5 21.7 1.0 CB A:ASP132 4.5 45.4 1.0 CB A:ASP123 4.6 24.7 1.0 MN A:MN238 4.6 43.1 1.0 N A:SER126 4.6 28.7 1.0 O A:GLY104 4.7 30.4 1.0 CD1 A:TYR125 4.8 48.5 1.0 CA A:TYR125 4.8 36.0 1.0 N A:TYR125 4.9 39.0 1.0 CD2 A:TYR130 4.9 24.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc 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-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:24.3 occ:1.00 OD2 B:ASP132 2.6 26.8 1.0 OD1 B:ASP123 2.6 22.1 1.0 O B:HOH478 2.7 32.9 1.0 O B:TYR125 2.7 30.2 1.0 OD1 B:ASN127 2.8 27.8 1.0 OD2 B:ASP123 2.9 22.3 1.0 CG B:ASP123 3.1 22.9 1.0 CG B:ASN127 3.3 27.1 1.0 CB B:ASN127 3.5 25.9 1.0 CG B:ASP132 3.7 29.4 1.0 N B:ASN127 3.8 23.5 1.0 C B:TYR125 4.0 29.9 1.0 CA B:GLY104 4.0 40.5 1.0 OD1 B:ASP132 4.3 29.9 1.0 CA B:ASN127 4.3 21.0 1.0 ND2 B:ASN127 4.4 26.1 1.0 O B:GLY104 4.4 41.1 1.0 MN B:MN238 4.4 42.3 1.0 CB B:ASP123 4.5 23.2 1.0 OD1 B:ASP83 4.6 31.8 1.0 C B:GLY104 4.7 43.7 1.0 CB B:ASP132 4.7 27.1 1.0 CA B:TYR125 4.8 30.6 1.0 C B:SER126 4.8 18.8 1.0 CB B:TYR125 4.9 32.9 1.0 N B:TYR125 4.9 33.3 1.0 N B:SER126 4.9 15.9 1.0 CA B:SER126 5.0 19.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc 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-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:26.2 occ:1.00 OD1 C:ASP123 2.6 45.3 1.0 OD1 C:ASN127 2.7 30.7 1.0 OD2 C:ASP132 2.8 27.9 1.0 O C:HOH484 2.8 40.1 1.0 O C:TYR125 2.8 52.2 1.0 OD2 C:ASP123 3.0 47.0 1.0 CG C:ASP123 3.1 42.8 1.0 CG C:ASN127 3.4 30.0 1.0 CG C:ASP132 3.6 32.0 1.0 N C:ASN127 3.8 51.5 1.0 CB C:ASN127 3.8 30.1 1.0 OD1 C:ASP132 3.9 28.4 1.0 C C:TYR125 3.9 52.9 1.0 MN C:MN238 4.3 45.2 1.0 CA C:ASN127 4.4 47.8 1.0 ND2 C:ASN127 4.4 33.6 1.0 CA C:GLY104 4.5 67.8 1.0 O C:GLY104 4.5 70.9 1.0 CB C:ASP123 4.5 39.8 1.0 CB C:ASP132 4.7 29.5 1.0 N C:SER126 4.7 44.5 1.0 C C:SER126 4.7 50.8 1.0 CA C:SER126 4.7 46.8 1.0 CD1 C:TYR125 4.8 73.0 1.0 CA C:TYR125 4.8 50.0 1.0 CB C:TYR125 4.8 67.6 1.0 N C:TYR125 4.9 49.1 1.0 CE1 C:HIS137 4.9 34.1 1.0 C C:GLY104 5.0 69.0 1.0 OD1 C:ASP83 5.0 36.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc 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-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:25.2 occ:1.00 OD1 D:ASP123 2.5 30.9 1.0 O D:TYR125 2.6 26.4 1.0 O D:HOH492 2.7 30.2 1.0 OD2 D:ASP123 2.7 34.9 1.0 O D:HOH493 2.8 37.8 1.0 OD1 D:ASN127 2.8 48.3 1.0 CG D:ASP123 3.0 33.2 1.0 OD2 D:ASP132 3.0 49.8 1.0 CG D:ASN127 3.3 46.3 1.0 CG D:ASP132 3.4 48.4 1.0 OD1 D:ASP132 3.5 45.2 1.0 CB D:ASN127 3.5 48.0 1.0 N D:ASN127 3.7 28.0 1.0 C D:TYR125 3.8 28.6 1.0 CA D:ASN127 4.3 27.6 1.0 ND2 D:ASN127 4.3 46.1 1.0 CB D:ASP123 4.4 33.0 1.0 CB D:ASP132 4.5 48.6 1.0 N D:TYR125 4.5 25.2 1.0 CA D:GLY104 4.5 38.5 1.0 C D:SER126 4.6 22.5 1.0 O D:HOH495 4.6 20.7 1.0 CA D:TYR125 4.6 26.7 1.0 N D:SER126 4.7 16.0 1.0 CA D:SER126 4.7 19.3 1.0 OD1 D:ASP83 4.8 44.5 1.0 O D:GLY104 4.8 38.8 1.0 CB D:TYR125 4.8 36.7 1.0 MN D:MN238 4.8 42.8 1.0 CD1 D:TYR125 4.9 38.8 1.0 O D:ASP83 4.9 31.9 1.0 CE1 D:HIS137 5.0 35.6 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