Cadmium in PDB 3r52: Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato

The structure of Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato, PDB code: 3r52 was solved by K.L.Liu, W.C.Chang, S.T.Jeng, Y.S.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.98 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.280, 83.710, 65.060, 90.00, 112.76, 90.00
R / Rfree (%)	18.8 / 24.3

The binding sites of Cadmium atom in the Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato (pdb code 3r52). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato, PDB code: 3r52:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd250 b:59.2 occ:1.00 O B:ASN19 2.4 20.9 1.0 OG B:SER18 2.7 27.6 1.0 O B:HOH158 2.7 30.5 1.0 O B:HOH166 2.8 15.6 1.0 O B:HOH167 2.9 12.6 1.0 CB B:SER18 3.5 25.4 1.0 C B:ASN19 3.6 22.3 1.0 N B:ASN19 3.8 21.1 1.0 C B:SER18 3.9 22.1 1.0 CA B:ASN19 4.1 21.8 1.0 OD1 B:ASP145 4.2 26.4 1.0 CA B:SER18 4.4 22.2 1.0 O B:SER18 4.4 22.6 1.0 O B:ASN98 4.4 25.9 1.0 O B:HOH402 4.5 48.5 1.0 O4 B:GYP200 4.6 32.1 1.0 CB B:ASN19 4.6 21.2 1.0 N B:GLY20 4.7 20.2 1.0 CD2 B:TYR97 4.7 35.0 1.0 N B:ASN98 4.8 29.7 1.0 CB B:TYR97 4.9 33.3 1.0 CG B:ASP145 4.9 23.5 1.0 CB B:ASP145 4.9 21.2 1.0 CA B:GLY20 5.0 21.4 1.0

Cadmium binding site 2 out of 3 in the Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd250 b:36.6 occ:1.00 O D:HOH201 2.5 10.3 1.0 O C:ASN19 2.6 21.4 1.0 O C:HOH426 2.7 29.8 1.0 OG C:SER18 2.7 24.5 1.0 O D:HOH258 2.8 19.7 1.0 CB C:SER18 3.4 18.4 1.0 C C:ASN19 3.7 23.2 1.0 N C:ASN19 3.8 21.6 1.0 C C:SER18 4.0 20.3 1.0 O D:LEU3 4.0 45.7 1.0 O C:ASN98 4.1 21.1 1.0 O C:HOH259 4.2 31.4 1.0 CA C:ASN19 4.3 23.7 1.0 OD1 C:ASP145 4.3 24.1 1.0 CA C:SER18 4.3 19.2 1.0 O C:SER18 4.4 18.0 1.0 O C:HOH257 4.5 30.7 1.0 O4 C:GYP200 4.5 29.4 1.0 N C:ASN98 4.7 26.3 1.0 CD1 C:TYR97 4.8 29.5 1.0 N C:GLY20 4.8 23.4 1.0 C D:LEU3 4.8 46.3 1.0 CB C:ASN19 4.8 21.7 1.0

Cadmium binding site 3 out of 3 in the Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure Analysis of A Wound-Inducible Lectin Ipomoelin From Sweet Potato within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd250 b:41.5 occ:1.00 O D:ASN19 2.5 14.0 1.0 O C:HOH175 2.6 10.6 1.0 O D:HOH155 2.6 37.8 1.0 O C:HOH171 2.7 18.9 1.0 O D:HOH346 2.7 37.2 1.0 OG D:SER18 2.8 17.7 1.0 C D:ASN19 3.6 17.3 1.0 CB D:SER18 3.7 19.6 1.0 N D:ASN19 3.9 19.1 1.0 C D:SER18 4.1 19.6 1.0 OD1 D:ASP145 4.1 19.2 1.0 O D:ASN98 4.2 25.5 1.0 CA D:ASN19 4.2 17.7 1.0 O C:LEU3 4.3 49.4 1.0 O D:SER18 4.4 20.8 1.0 O D:HOH284 4.4 32.5 1.0 CA D:SER18 4.5 19.2 1.0 CD1 D:TYR97 4.5 35.6 1.0 O4 D:GYP200 4.6 38.7 1.0 N D:ASN98 4.7 29.1 1.0 CB D:ASN19 4.7 16.8 1.0 N D:GLY20 4.7 14.8 1.0 O D:HOH464 4.8 40.8 1.0 CG D:ASP145 4.8 19.5 1.0 O D:HOH280 4.9 34.1 1.0 CB D:ASP145 5.0 18.5 1.0

W.C.Chang, K.L.Liu, F.C.Hsu, S.T.Jeng, Y.S.Cheng. Ipomoelin, A Jacalin-Related Lectin with A Compact Tetrameric Association and Versatile Carbohydrate Binding Properties Regulated By Its N Terminus. Plos One V. 7 40618 2012.
ISSN: ESSN 1932-6203
PubMed: 22808208
DOI: 10.1371/JOURNAL.PONE.0040618