Calcium in PDB 2d3p: Cratylia Floribunda Seed Lectin Crystallized at Basic pH

The structure of Cratylia Floribunda Seed Lectin Crystallized at Basic pH, PDB code: 2d3p was solved by F.G.Del Sol, B.S.Cavada, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.367, 106.929, 119.625, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.7

The structure of Cratylia Floribunda Seed Lectin Crystallized at Basic pH also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Cratylia Floribunda Seed Lectin Crystallized at Basic pH (pdb code 2d3p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cratylia Floribunda Seed Lectin Crystallized at Basic pH, PDB code: 2d3p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cratylia Floribunda Seed Lectin Crystallized at Basic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cratylia Floribunda Seed Lectin Crystallized at Basic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:25.7 occ:1.00 OD1 A:ASN14 2.4 29.4 1.0 OD2 A:ASP19 2.4 28.4 1.0 O A:TYR12 2.4 23.4 1.0 OD1 A:ASP10 2.4 14.9 1.0 OD2 A:ASP10 2.6 15.6 1.0 CG A:ASP10 2.9 14.8 1.0 CG A:ASP19 3.5 27.5 1.0 CG A:ASN14 3.5 27.4 1.0 C A:TYR12 3.6 23.3 1.0 N A:ASN14 4.0 26.3 1.0 OD1 A:ASP19 4.0 28.2 1.0 CB A:ASN14 4.3 26.8 1.0 MN A:MN238 4.4 21.8 1.0 CB A:ASP10 4.4 15.2 1.0 OD1 A:ASP207 4.4 27.7 1.0 CA A:TYR12 4.5 22.6 1.0 N A:TYR12 4.5 20.6 1.0 O A:ARG227 4.6 19.0 1.0 ND2 A:ASN14 4.6 26.5 1.0 N A:PRO13 4.6 24.2 1.0 O A:ASP207 4.6 23.0 1.0 CB A:ARG227 4.7 19.6 1.0 CA A:PRO13 4.7 24.8 1.0 C A:PRO13 4.7 25.5 1.0 CE1 A:HIS24 4.7 13.0 1.0 CB A:ASP19 4.8 26.9 1.0 CA A:ASN14 4.8 27.0 1.0 CB A:TYR12 4.8 23.1 1.0 CA A:ARG227 4.8 19.4 1.0

Calcium binding site 2 out of 4 in the Cratylia Floribunda Seed Lectin Crystallized at Basic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cratylia Floribunda Seed Lectin Crystallized at Basic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:17.4 occ:1.00 OD1 B:ASP10 2.3 8.9 1.0 O B:TYR12 2.3 16.8 1.0 OD2 B:ASP19 2.5 17.5 1.0 OD1 B:ASN14 2.6 20.5 1.0 OD2 B:ASP10 2.7 8.9 1.0 CG B:ASP10 2.8 10.4 1.0 C B:TYR12 3.5 16.9 1.0 CG B:ASN14 3.7 18.7 1.0 CG B:ASP19 3.7 18.0 1.0 N B:ASN14 4.0 18.3 1.0 CB B:ASN14 4.2 18.6 1.0 OD1 B:ASP19 4.2 16.7 1.0 N B:TYR12 4.3 15.4 1.0 CA B:TYR12 4.3 16.3 1.0 MN B:MN240 4.3 13.2 1.0 CB B:ASP10 4.3 11.4 1.0 O B:ASP207 4.4 16.3 1.0 OD1 B:ASP207 4.5 22.1 1.0 N B:PRO13 4.5 17.5 1.0 CB B:TYR12 4.6 16.6 1.0 CE1 B:HIS24 4.6 12.2 1.0 O B:ARG227 4.7 13.7 1.0 CA B:PRO13 4.7 17.9 1.0 C B:PRO13 4.7 18.2 1.0 ND2 B:ASN14 4.8 17.8 1.0 CA B:ASN14 4.8 18.4 1.0 NE2 B:HIS24 4.9 12.0 1.0 CD2 B:TYR12 4.9 17.3 1.0 CB B:ASP19 4.9 19.4 1.0 CB B:ARG227 5.0 15.0 1.0

Calcium binding site 3 out of 4 in the Cratylia Floribunda Seed Lectin Crystallized at Basic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cratylia Floribunda Seed Lectin Crystallized at Basic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca241 b:14.3 occ:1.00 OD1 C:ASN14 2.3 32.6 1.0 OD1 C:ASP10 2.4 15.0 1.0 O C:TYR12 2.5 22.2 1.0 OD2 C:ASP19 2.6 22.4 1.0 OD2 C:ASP10 2.7 15.2 1.0 CG C:ASP10 2.9 14.7 1.0 O C:HOH244 2.9 13.0 1.0 CG C:ASN14 3.5 29.8 1.0 C C:TYR12 3.7 22.7 1.0 CG C:ASP19 3.7 23.7 1.0 N C:ASN14 4.1 26.6 1.0 OD1 C:ASP19 4.2 23.0 1.0 MN C:MN242 4.3 21.3 1.0 ND2 C:ASN14 4.3 31.3 1.0 O C:ASP207 4.4 24.9 1.0 CB C:ASP10 4.4 14.1 1.0 CB C:ASN14 4.4 28.1 1.0 CA C:TYR12 4.5 22.4 1.0 N C:TYR12 4.6 20.6 1.0 O C:ARG227 4.6 24.0 1.0 OD1 C:ASP207 4.6 27.7 1.0 N C:PRO13 4.6 23.7 1.0 CA C:PRO13 4.7 24.4 1.0 C C:PRO13 4.7 25.4 1.0 CE1 C:HIS24 4.7 13.3 1.0 CB C:ARG227 4.8 24.1 1.0 CA C:ARG227 4.8 23.9 1.0 CB C:TYR12 4.8 23.2 1.0 CA C:ASN14 4.9 27.8 1.0 CB C:ASP19 4.9 24.5 1.0

Calcium binding site 4 out of 4 in the Cratylia Floribunda Seed Lectin Crystallized at Basic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cratylia Floribunda Seed Lectin Crystallized at Basic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca243 b:27.8 occ:1.00 OD1 D:ASN14 2.2 33.0 1.0 O D:TYR12 2.4 26.4 1.0 OD1 D:ASP10 2.4 21.6 1.0 OD2 D:ASP19 2.5 27.2 1.0 OD2 D:ASP10 2.7 20.1 1.0 CG D:ASP10 2.9 21.3 1.0 CG D:ASN14 3.4 30.9 1.0 C D:TYR12 3.6 27.1 1.0 CG D:ASP19 3.6 28.1 1.0 N D:ASN14 3.9 29.8 1.0 CB D:ASN14 4.1 30.5 1.0 OD1 D:ASP19 4.1 29.2 1.0 MN D:MN244 4.3 24.9 1.0 O D:ARG227 4.4 31.1 1.0 CB D:ASP10 4.4 21.4 1.0 ND2 D:ASN14 4.5 29.8 1.0 CA D:TYR12 4.5 26.8 1.0 OD1 D:ASP207 4.5 24.6 1.0 N D:TYR12 4.5 26.0 1.0 N D:PRO13 4.5 27.8 1.0 O D:ASP207 4.6 22.0 1.0 CA D:ASN14 4.6 30.3 1.0 CA D:ARG227 4.6 31.5 1.0 CA D:PRO13 4.6 28.5 1.0 C D:PRO13 4.6 29.3 1.0 CB D:ARG227 4.6 31.7 1.0 CB D:TYR12 4.7 27.0 1.0 CE1 D:HIS24 4.8 17.8 1.0 CB D:ASP19 4.8 27.9 1.0 C D:ARG227 5.0 31.1 1.0

F.G.Del Sol, B.S.Cavada, J.J.Calvete. Crystal Structures of Cratylia Floribunda Seed Lectin at Acidic and Basic Phs. Insights Into the Structural Basis of the pH-Dependent Dimer-Tetramer Transition. J.Struct.Biol. V. 158 1 2007.
ISSN: ISSN 1047-8477
PubMed: 17251039
DOI: 10.1016/J.JSB.2006.08.014