Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Isolectin B4 From Vicia Villosa in Complex with the Tn Antigen, PDB code: 1n47:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn253 b:36.5 occ:1.00 OD2 A:ASP125 1.9 27.9 1.0 O A:HOH1408 2.1 23.3 1.0 OE2 A:GLU123 2.3 34.1 1.0 OD2 A:ASP132 2.4 41.2 1.0 O A:HOH1407 2.4 31.8 1.0 NE2 A:HIS137 2.5 29.0 1.0 CG A:ASP125 3.0 31.0 1.0 CG A:ASP132 3.0 40.1 1.0 OD1 A:ASP132 3.1 38.5 1.0 CD A:GLU123 3.3 34.0 1.0 CE1 A:HIS137 3.3 29.9 1.0 OE1 A:GLU123 3.5 32.9 1.0 CD2 A:HIS137 3.6 29.7 1.0 CB A:ASP125 3.6 31.9 1.0 CA A:CA252 4.0 35.3 1.0 OD1 A:ASP125 4.1 31.3 1.0 OG A:SER147 4.3 32.5 1.0 CB A:ASP132 4.4 39.2 1.0 O A:ILE145 4.4 33.2 1.0 ND1 A:HIS137 4.5 29.8 1.0 CG A:HIS137 4.7 30.4 1.0 CG A:GLU123 4.7 30.7 1.0 CD1 A:TRP131 4.7 37.5 1.0 NE1 A:TRP131 4.8 37.1 1.0 CA A:ASP132 5.0 39.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn253 b:36.5 occ:1.00 OD2 B:ASP125 2.2 25.7 1.0 OE2 B:GLU123 2.3 34.2 1.0 NE2 B:HIS137 2.3 31.2 1.0 OD2 B:ASP132 2.3 32.0 1.0 O B:HOH2409 2.4 29.4 1.0 O B:HOH2415 2.5 36.9 1.0 CG B:ASP125 3.2 29.5 1.0 CE1 B:HIS137 3.2 31.4 1.0 CG B:ASP132 3.2 31.1 1.0 CD2 B:HIS137 3.3 30.8 1.0 CD B:GLU123 3.4 33.7 1.0 CB B:ASP125 3.6 29.9 1.0 OD1 B:ASP132 3.6 28.8 1.0 OE1 B:GLU123 3.9 34.5 1.0 O B:HOH2405 4.0 29.8 1.0 OD1 B:ASP125 4.2 28.6 1.0 CB B:ASP132 4.3 32.0 1.0 ND1 B:HIS137 4.3 32.2 1.0 OG B:SER147 4.4 28.5 1.0 CA B:CA252 4.4 31.1 1.0 CG B:HIS137 4.4 30.9 1.0 O B:ILE145 4.6 30.9 1.0 CG B:GLU123 4.7 30.9 1.0 O B:HOH2411 4.7 30.1 1.0 CD1 B:TRP131 4.7 33.5 1.0 NE1 B:TRP131 4.8 34.1 1.0 CA B:ASP132 4.9 32.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn253 b:36.9 occ:1.00 O C:HOH3413 2.1 32.2 1.0 OD2 C:ASP125 2.1 22.9 1.0 OE2 C:GLU123 2.2 28.6 1.0 NE2 C:HIS137 2.2 30.6 1.0 OD2 C:ASP132 2.3 23.2 1.0 O C:HOH3418 2.3 33.2 1.0 CE1 C:HIS137 3.1 30.1 1.0 CD C:GLU123 3.2 29.1 1.0 CG C:ASP125 3.2 27.4 1.0 CG C:ASP132 3.3 27.1 1.0 CD2 C:HIS137 3.3 31.3 1.0 OE1 C:GLU123 3.4 25.3 1.0 OD1 C:ASP132 3.7 23.9 1.0 CB C:ASP125 3.8 27.5 1.0 OG C:SER147 3.9 31.9 1.0 CA C:CA252 4.2 28.3 1.0 ND1 C:HIS137 4.3 31.1 1.0 O C:HOH3402 4.3 29.8 1.0 OD1 C:ASP125 4.3 26.9 1.0 O C:ILE145 4.4 31.0 1.0 CG C:HIS137 4.4 31.2 1.0 CB C:ASP132 4.4 29.0 1.0 O C:HOH3411 4.5 27.7 1.0 CG C:GLU123 4.5 28.0 1.0 NE1 C:TRP131 4.6 36.8 1.0 CD1 C:TRP131 4.7 35.0 1.0 CA C:ASP132 5.0 29.9 1.0 CD C:PRO133 5.0 31.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn253 b:39.5 occ:1.00 OD2 D:ASP125 1.9 34.1 1.0 O D:HOH4414 2.1 26.0 1.0 O D:HOH4411 2.2 29.4 1.0 NE2 D:HIS137 2.3 27.1 1.0 OE2 D:GLU123 2.6 28.3 1.0 OD2 D:ASP132 2.6 35.7 1.0 CE1 D:HIS137 2.9 27.4 1.0 CG D:ASP125 3.0 32.0 1.0 CG D:ASP132 3.2 32.4 1.0 OD1 D:ASP132 3.3 29.4 1.0 CD2 D:HIS137 3.5 27.1 1.0 CB D:ASP125 3.5 29.9 1.0 CD D:GLU123 3.6 29.7 1.0 OE1 D:GLU123 3.8 32.0 1.0 CA D:CA252 4.0 32.9 1.0 OD1 D:ASP125 4.1 33.0 1.0 ND1 D:HIS137 4.2 27.0 1.0 OG D:SER147 4.3 28.2 1.0 CB D:ASP132 4.4 32.6 1.0 CG D:HIS137 4.5 28.6 1.0 O D:ILE145 4.7 28.6 1.0 NE1 D:TRP131 4.8 31.4 1.0 CD1 D:TRP131 4.9 32.7 1.0 CG D:GLU123 4.9 28.4 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