Calcium in PDB 2dvf: Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal

The structure of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal, PDB code: 2dvf 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)	19.94 / 2.74
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.810, 124.060, 75.400, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 26.3

The structure of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal (pdb code 2dvf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal, PDB code: 2dvf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:37.6 occ:1.00 O A:TYR125 2.5 45.9 1.0 OD1 A:ASP123 2.5 39.3 1.0 OD2 A:ASP132 2.6 42.2 1.0 OD1 A:ASN127 2.7 24.5 1.0 OD2 A:ASP123 2.8 42.1 1.0 CG A:ASP123 3.0 40.6 1.0 CG A:ASN127 3.5 23.5 1.0 CG A:ASP132 3.7 47.1 1.0 C A:TYR125 3.7 43.4 1.0 CA A:GLY104 3.8 38.3 1.0 CB A:ASN127 4.0 19.1 1.0 OD1 A:ASP83 4.0 48.2 1.0 OD1 A:ASP132 4.1 47.5 1.0 N A:ASN127 4.1 40.5 1.0 CB A:TYR125 4.3 64.2 1.0 CA A:TYR125 4.4 43.7 1.0 N A:TYR125 4.4 46.8 1.0 ND2 A:ASN127 4.5 23.2 1.0 CB A:ASP123 4.5 38.5 1.0 O A:GLY104 4.5 40.1 1.0 O A:ASP83 4.5 46.4 1.0 C A:GLY104 4.7 39.5 1.0 CA A:ASN127 4.7 35.5 1.0 CD1 A:TYR125 4.7 65.3 1.0 N A:SER126 4.7 41.8 1.0 N A:GLY104 4.8 41.3 1.0 MN A:MN238 4.9 58.5 1.0 CB A:ASP132 4.9 45.3 1.0 C A:SER126 4.9 48.9 1.0 CA A:SER126 4.9 46.5 1.0 CD2 A:LEU106 5.0 26.1 1.0

Calcium binding site 2 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:38.9 occ:1.00 OD1 B:ASP123 2.6 25.2 1.0 O B:TYR125 2.7 33.8 1.0 OD2 B:ASP132 2.7 43.3 1.0 OD1 B:ASN127 2.8 38.1 1.0 OD2 B:ASP123 3.0 25.4 1.0 CG B:ASP123 3.2 26.0 1.0 CG B:ASN127 3.4 37.5 1.0 CB B:ASN127 3.7 36.2 1.0 C B:TYR125 3.8 33.5 1.0 CG B:ASP132 3.8 46.0 1.0 N B:ASN127 3.9 35.1 1.0 CA B:GLY104 4.0 28.7 1.0 OD1 B:ASP83 4.1 38.9 1.0 OD1 B:ASP132 4.3 46.4 1.0 O B:GLY104 4.4 29.4 1.0 CA B:ASN127 4.4 32.6 1.0 CB B:TYR125 4.5 40.3 1.0 ND2 B:ASN127 4.5 36.5 1.0 CA B:TYR125 4.5 34.2 1.0 N B:TYR125 4.6 36.9 1.0 CB B:ASP123 4.7 26.2 1.0 C B:SER126 4.7 40.0 1.0 C B:GLY104 4.7 32.0 1.0 CD1 B:TYR125 4.7 43.0 1.0 N B:SER126 4.7 37.2 1.0 MN B:MN238 4.8 53.9 1.0 O B:ASP83 4.8 44.9 1.0 CA B:SER126 4.9 40.2 1.0 CB B:ASP132 4.9 43.6 1.0

Calcium binding site 3 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:41.7 occ:1.00 OD1 C:ASP123 2.6 43.7 1.0 O C:TYR125 2.7 87.3 1.0 OD2 C:ASP132 2.8 53.1 1.0 OD1 C:ASN127 2.9 35.8 1.0 OD2 C:ASP123 3.0 45.5 1.0 CG C:ASP123 3.2 41.2 1.0 CG C:ASN127 3.4 35.1 1.0 CG C:ASP132 3.4 57.2 1.0 CB C:ASN127 3.6 35.2 1.0 C C:TYR125 3.7 88.0 1.0 OD1 C:ASP132 3.7 53.7 1.0 N C:ASN127 3.7 61.9 1.0 CA C:GLY104 4.1 53.0 1.0 CB C:TYR125 4.2 64.3 1.0 ND2 C:ASN127 4.3 38.7 1.0 CA C:ASN127 4.3 58.2 1.0 CA C:TYR125 4.4 85.2 1.0 OD1 C:ASP83 4.4 54.8 1.0 N C:SER126 4.5 39.9 1.0 CD1 C:TYR125 4.6 69.7 1.0 N C:TYR125 4.6 84.2 1.0 CB C:ASP132 4.6 54.7 1.0 C C:SER126 4.6 46.3 1.0 O C:GLY104 4.6 56.1 1.0 CA C:SER126 4.7 42.3 1.0 CB C:ASP123 4.7 38.2 1.0 MN C:MN238 4.8 59.0 1.0 C C:GLY104 4.9 54.3 1.0 O C:ASP83 4.9 54.2 1.0 CG C:TYR125 4.9 66.5 1.0

Calcium binding site 4 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:38.9 occ:1.00 OD1 D:ASP123 2.6 28.8 1.0 O D:TYR125 2.7 39.0 1.0 OD2 D:ASP132 2.8 48.2 1.0 OD2 D:ASP123 2.8 32.8 1.0 OD1 D:ASN127 2.9 49.3 1.0 CG D:ASP123 3.1 31.1 1.0 CG D:ASN127 3.4 47.2 1.0 CG D:ASP132 3.6 46.8 1.0 CB D:ASN127 3.6 48.9 1.0 C D:TYR125 3.8 41.2 1.0 N D:ASN127 3.8 30.5 1.0 OD1 D:ASP132 4.0 43.6 1.0 OD1 D:ASP83 4.2 43.3 1.0 CA D:GLY104 4.3 36.9 1.0 CA D:ASN127 4.4 30.1 1.0 ND2 D:ASN127 4.4 47.1 1.0 CB D:ASP123 4.5 30.9 1.0 CA D:TYR125 4.6 39.3 1.0 N D:TYR125 4.6 37.9 1.0 CB D:TYR125 4.6 43.2 1.0 O D:GLY104 4.6 37.1 1.0 C D:SER126 4.7 33.0 1.0 N D:SER126 4.7 26.6 1.0 CB D:ASP132 4.7 47.0 1.0 MN D:MN238 4.7 59.2 1.0 CA D:SER126 4.8 29.9 1.0 O D:ASP83 4.8 45.8 1.0 CD1 D:TYR125 4.8 45.3 1.0 C D:GLY104 5.0 36.3 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