Calcium in PDB 1n47: Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen

The structure of Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen, PDB code: 1n47 was solved by A.Babino, D.Tello, A.Rojas, S.Bay, E.Osinaga, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	85.510, 85.510, 153.650, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.8

The structure of Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen (pdb code 1n47). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen, PDB code: 1n47:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca252 b:35.3 occ:1.00 OD1 A:ASP132 2.3 38.5 1.0 OD1 A:ASP125 2.4 31.3 1.0 O A:HOH1403 2.5 37.5 1.0 O A:TYR127 2.6 37.9 1.0 OD2 A:ASP125 2.6 27.9 1.0 OD1 A:ASN129 2.7 43.4 1.0 CG A:ASP125 2.9 31.0 1.0 CG A:ASP132 3.5 40.1 1.0 C A:TYR127 3.8 37.4 1.0 CG A:ASN129 3.8 42.2 1.0 MN A:MN253 4.0 36.5 1.0 OD2 A:ASP132 4.1 41.2 1.0 N A:ASN129 4.1 40.3 1.0 CB A:ASN129 4.3 41.5 1.0 NE1 A:TRP131 4.4 37.1 1.0 CB A:ASP125 4.4 31.9 1.0 N A:TYR127 4.5 35.9 1.0 O A:HOH1407 4.5 31.8 1.0 CB A:ASP132 4.6 39.2 1.0 CA A:TYR127 4.6 36.3 1.0 O A:ASP85 4.6 34.8 1.0 O A:GLY103 4.7 38.8 1.0 CA A:SER128 4.7 39.0 1.0 N A:SER128 4.7 38.0 1.0 CE1 A:HIS137 4.8 29.9 1.0 C A:SER128 4.8 39.8 1.0 CA A:ASN129 4.9 40.8 1.0 ND2 A:ASN129 4.9 42.6 1.0 OD1 A:ASP85 4.9 35.8 1.0 CB A:TYR127 5.0 36.2 1.0

Calcium binding site 2 out of 4 in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca252 b:31.1 occ:1.00 O B:HOH2410 2.3 36.3 1.0 OD1 B:ASP132 2.4 28.8 1.0 O B:TYR127 2.4 35.6 1.0 O B:HOH2405 2.4 29.8 1.0 OD1 B:ASP125 2.5 28.6 1.0 OD1 B:ASN129 2.5 39.7 1.0 OD2 B:ASP125 2.8 25.7 1.0 CG B:ASP125 3.0 29.5 1.0 CG B:ASN129 3.4 37.9 1.0 CG B:ASP132 3.5 31.1 1.0 C B:TYR127 3.6 35.5 1.0 N B:ASN129 3.9 37.1 1.0 OD2 B:ASP132 4.0 32.0 1.0 CB B:ASN129 4.1 36.6 1.0 NE1 B:TRP131 4.3 34.1 1.0 CA B:TYR127 4.3 34.7 1.0 ND2 B:ASN129 4.3 40.5 1.0 N B:TYR127 4.4 34.3 1.0 MN B:MN253 4.4 36.5 1.0 CB B:TYR127 4.5 34.6 1.0 CB B:ASP125 4.5 29.9 1.0 O B:GLY103 4.6 35.1 1.0 O B:HOH2415 4.6 36.9 1.0 N B:SER128 4.6 36.0 1.0 CA B:ASN129 4.6 36.7 1.0 OD1 B:ASP85 4.7 34.4 1.0 CB B:ASP132 4.7 32.0 1.0 CD1 B:TYR127 4.7 34.6 1.0 CA B:SER128 4.7 36.6 1.0 C B:SER128 4.8 37.1 1.0 O B:ASP85 4.8 33.2 1.0 CA B:GLY103 4.9 33.6 1.0 CE2 B:TRP131 5.0 34.3 1.0

Calcium binding site 3 out of 4 in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca252 b:28.3 occ:1.00 OD1 C:ASP132 2.3 23.9 1.0 O C:HOH3414 2.4 25.3 1.0 OD1 C:ASN129 2.5 35.7 1.0 O C:HOH3402 2.5 29.8 1.0 O C:TYR127 2.6 31.3 1.0 OD1 C:ASP125 2.6 26.9 1.0 OD2 C:ASP125 2.6 22.9 1.0 CG C:ASP125 3.0 27.4 1.0 CG C:ASP132 3.4 27.1 1.0 CG C:ASN129 3.6 33.0 1.0 C C:TYR127 3.8 31.4 1.0 OD2 C:ASP132 3.8 23.2 1.0 N C:ASN129 4.1 33.9 1.0 MN C:MN253 4.2 36.9 1.0 CB C:ASN129 4.2 33.0 1.0 O C:HOH3418 4.3 33.2 1.0 NE1 C:TRP131 4.4 36.8 1.0 CB C:ASP125 4.5 27.5 1.0 CB C:ASP132 4.6 29.0 1.0 N C:TYR127 4.6 31.0 1.0 CA C:SER128 4.6 32.7 1.0 C C:SER128 4.6 33.7 1.0 N C:SER128 4.7 31.6 1.0 O C:GLY103 4.7 34.8 1.0 CA C:TYR127 4.7 31.5 1.0 ND2 C:ASN129 4.7 32.6 1.0 CE1 C:HIS137 4.7 30.1 1.0 CA C:ASN129 4.8 33.4 1.0 O C:ASP85 4.8 30.6 1.0 CA C:GLY103 4.8 34.5 1.0 OD1 C:ASP85 4.9 26.4 1.0 CE2 C:TRP131 5.0 35.3 1.0

Calcium binding site 4 out of 4 in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca252 b:32.9 occ:1.00 OD1 D:ASP132 2.4 29.4 1.0 O D:HOH4413 2.4 39.0 1.0 O D:TYR127 2.4 32.0 1.0 OD1 D:ASP125 2.5 33.0 1.0 OD2 D:ASP125 2.6 34.1 1.0 OD1 D:ASN129 2.6 35.0 1.0 CG D:ASP125 2.9 32.0 1.0 CG D:ASP132 3.6 32.4 1.0 C D:TYR127 3.6 31.4 1.0 CG D:ASN129 3.7 33.9 1.0 N D:ASN129 3.9 32.7 1.0 MN D:MN253 4.0 39.5 1.0 CB D:ASN129 4.1 33.0 1.0 OD2 D:ASP132 4.1 35.7 1.0 CB D:ASP125 4.5 29.9 1.0 O D:HOH4411 4.5 29.4 1.0 N D:TYR127 4.5 30.4 1.0 CA D:TYR127 4.5 30.7 1.0 NE1 D:TRP131 4.5 31.4 1.0 O D:GLY103 4.5 34.9 1.0 N D:SER128 4.6 31.2 1.0 CA D:SER128 4.6 31.7 1.0 C D:SER128 4.6 32.4 1.0 CA D:ASN129 4.6 32.9 1.0 CB D:ASP132 4.7 32.6 1.0 CB D:TYR127 4.8 30.9 1.0 OD1 D:ASP85 4.8 32.7 1.0 ND2 D:ASN129 4.9 35.4 1.0 CE1 D:HIS137 4.9 27.4 1.0 O D:ASP85 4.9 29.0 1.0 CD1 D:TYR127 4.9 33.4 1.0

A.Babino, D.Tello, A.Rojas, S.Bay, E.Osinaga, P.M.Alzari. The Crystal Structure of A Plant Lectin in Complex with the Tn Antigen Febs Lett. V. 536 106 2003.
ISSN: ISSN 0014-5793
PubMed: 12586347
DOI: 10.1016/S0014-5793(03)00037-1