Calcium in PDB 2dvb: Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac Complex

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac Complex, PDB code: 2dvb 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)	19.98 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.740, 124.330, 75.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.6

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex (pdb code 2dvb). 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-1,6-Galnac Complex, PDB code: 2dvb:
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-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:36.3 occ:1.00 O A:TYR125 2.6 33.2 1.0 OD2 A:ASP132 2.6 34.7 1.0 OD1 A:ASN127 2.6 29.8 1.0 OD2 A:ASP123 2.6 30.4 1.0 O A:HOH1355 2.7 27.6 1.0 OD1 A:ASP123 2.7 35.1 1.0 O A:HOH1348 2.7 31.0 1.0 CG A:ASP123 3.0 29.1 1.0 CG A:ASN127 3.5 25.6 1.0 CG A:ASP132 3.5 34.8 1.0 C A:TYR125 3.8 33.1 1.0 N A:ASN127 3.9 30.9 1.0 CB A:ASN127 3.9 28.7 1.0 OD1 A:ASP132 3.9 33.2 1.0 MN A:MN238 4.1 57.7 1.0 O A:HOH1347 4.1 26.1 1.0 CA A:GLY104 4.3 24.4 1.0 CB A:ASP123 4.5 30.2 1.0 ND2 A:ASN127 4.6 25.8 1.0 CA A:ASN127 4.6 29.6 1.0 O A:GLY104 4.6 24.0 1.0 N A:TYR125 4.6 33.4 1.0 CB A:ASP132 4.7 34.9 1.0 CA A:TYR125 4.7 32.3 1.0 CA A:SER126 4.7 32.0 1.0 N A:SER126 4.7 32.2 1.0 OD1 A:ASP83 4.7 30.6 1.0 C A:SER126 4.7 32.9 1.0 CB A:TYR125 4.9 31.6 1.0 CD1 A:TYR125 5.0 30.5 1.0 C A:GLY104 5.0 25.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:31.5 occ:1.00 O B:TYR125 2.6 32.8 1.0 OD2 B:ASP132 2.6 32.3 1.0 OD1 B:ASN127 2.6 29.3 1.0 OD1 B:ASP123 2.7 31.4 1.0 O B:HOH2384 2.7 27.2 1.0 O B:HOH2383 2.7 24.4 1.0 OD2 B:ASP123 2.8 33.0 1.0 CG B:ASP123 3.1 29.7 1.0 CG B:ASP132 3.5 33.4 1.0 CG B:ASN127 3.5 29.3 1.0 C B:TYR125 3.7 32.0 1.0 N B:ASN127 3.8 32.4 1.0 CB B:ASN127 3.9 31.6 1.0 OD1 B:ASP132 3.9 32.8 1.0 O B:HOH2386 4.1 42.4 1.0 MN B:MN238 4.3 47.8 1.0 CA B:GLY104 4.3 21.0 1.0 CA B:TYR125 4.5 31.7 1.0 CA B:ASN127 4.5 31.1 1.0 CB B:TYR125 4.5 32.1 1.0 CB B:ASP123 4.5 30.7 1.0 N B:TYR125 4.5 30.5 1.0 N B:SER126 4.6 32.2 1.0 CA B:SER126 4.6 32.1 1.0 OD1 B:ASP83 4.7 31.1 1.0 CD1 B:TYR125 4.7 30.8 1.0 C B:SER126 4.7 33.1 1.0 CB B:ASP132 4.7 31.5 1.0 ND2 B:ASN127 4.7 29.1 1.0 O B:GLY104 4.8 23.6 1.0 O B:ASP83 4.8 28.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:36.1 occ:1.00 OD2 C:ASP132 2.6 34.4 1.0 O C:HOH3397 2.6 30.0 1.0 O C:TYR125 2.6 35.6 1.0 OD1 C:ASN127 2.7 33.5 1.0 OD2 C:ASP123 2.7 32.0 1.0 O C:HOH3396 2.7 43.2 1.0 OD1 C:ASP123 2.8 32.5 1.0 CG C:ASP123 3.1 31.6 1.0 CG C:ASN127 3.5 34.3 1.0 CG C:ASP132 3.6 33.4 1.0 C C:TYR125 3.7 36.8 1.0 N C:ASN127 3.8 37.0 1.0 CB C:ASN127 3.9 35.4 1.0 OD1 C:ASP132 4.1 33.7 1.0 MN C:MN238 4.2 42.3 1.0 O C:HOH3389 4.2 28.0 1.0 CA C:GLY104 4.2 29.8 1.0 CA C:ASN127 4.5 35.5 1.0 CA C:TYR125 4.5 37.0 1.0 N C:SER126 4.6 37.4 1.0 ND2 C:ASN127 4.6 32.3 1.0 CB C:ASP123 4.6 32.2 1.0 CB C:TYR125 4.6 39.5 1.0 CA C:SER126 4.6 37.3 1.0 C C:SER126 4.6 37.2 1.0 N C:TYR125 4.6 36.6 1.0 CB C:ASP132 4.7 33.7 1.0 CD1 C:TYR125 4.7 43.2 1.0 O C:GLY104 4.7 32.9 1.0 OD1 C:ASP83 4.7 29.2 1.0 CE1 C:HIS137 4.9 25.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:32.4 occ:1.00 OD1 D:ASN127 2.6 26.5 1.0 O D:TYR125 2.6 32.7 1.0 OD1 D:ASP123 2.6 29.7 1.0 O D:HOH4372 2.6 28.4 1.0 OD2 D:ASP132 2.7 35.6 1.0 O D:HOH4371 2.7 33.6 1.0 OD2 D:ASP123 2.7 31.5 1.0 CG D:ASP123 3.0 30.0 1.0 CG D:ASN127 3.4 29.5 1.0 CG D:ASP132 3.6 31.7 1.0 C D:TYR125 3.7 33.1 1.0 CB D:ASN127 3.9 31.2 1.0 N D:ASN127 3.9 32.4 1.0 MN D:MN238 4.1 44.4 1.0 OD1 D:ASP132 4.1 34.2 1.0 O D:HOH4374 4.3 19.5 1.0 CA D:GLY104 4.4 30.7 1.0 CB D:ASP123 4.5 29.1 1.0 ND2 D:ASN127 4.5 26.1 1.0 CA D:TYR125 4.5 32.8 1.0 CA D:ASN127 4.5 31.7 1.0 N D:TYR125 4.6 32.2 1.0 CB D:TYR125 4.6 34.5 1.0 O D:GLY104 4.6 30.9 1.0 CB D:ASP132 4.6 31.6 1.0 N D:SER126 4.7 33.2 1.0 CA D:SER126 4.7 31.9 1.0 C D:SER126 4.7 33.2 1.0 CD1 D:TYR125 4.9 39.7 1.0 O D:ASP83 4.9 28.5 1.0 OD1 D:ASP83 4.9 31.1 1.0 CE1 D:HIS137 4.9 18.9 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