Calcium in PDB 2wn3: Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution.

The structure of Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution., PDB code: 2wn3 was solved by S.Mathieu, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	137.00 / 1.59
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.580, 274.000, 85.760, 90.00, 90.00, 90.00
R / Rfree (%)	15.159 / 18.023

The binding sites of Calcium atom in the Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution. (pdb code 2wn3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution., PDB code: 2wn3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution.


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 Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:8.2 occ:1.00 OD2 A:ASP203 2.3 8.9 1.0 OD1 A:ASP164 2.4 9.7 1.0 O B:HOH2309 2.4 8.6 1.0 OE1 B:GLN219 2.4 9.5 1.0 O B:HOH2310 2.4 8.9 1.0 OD1 A:ASP246 2.5 8.3 1.0 OD2 A:ASP246 2.5 8.2 1.0 CG A:ASP246 2.9 8.1 1.0 CG A:ASP203 3.4 13.0 1.0 CD B:GLN219 3.5 14.5 1.0 CG A:ASP164 3.6 12.1 1.0 NE2 B:GLN219 3.9 19.3 1.0 CB A:ASP203 4.0 9.9 1.0 CD B:PRO220 4.2 7.2 1.0 N A:ASP164 4.2 9.1 1.0 OD2 A:ASP164 4.2 14.9 1.0 OD1 A:ASP203 4.4 12.0 1.0 CB A:ASP246 4.4 7.6 1.0 NH2 A:ARG244 4.4 13.1 1.0 O B:VAL218 4.4 8.8 1.0 O A:HOH2294 4.5 26.9 1.0 CB A:ALA163 4.5 11.4 1.0 O B:LEU200 4.5 6.8 1.0 NE A:ARG244 4.6 16.0 1.0 CA A:ASP164 4.6 8.9 1.0 CB A:ASP164 4.7 10.0 1.0 O B:VAL198 4.8 10.0 1.0 CG B:GLN219 4.8 10.0 1.0 CA B:GLN219 4.8 8.7 1.0 CZ A:ARG244 4.9 14.5 1.0 CA A:ALA163 4.9 10.6 1.0 N B:LEU200 4.9 7.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution.


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 Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:8.7 occ:1.00 OD2 B:ASP203 2.2 11.9 1.0 OD1 B:ASP246 2.4 9.0 1.0 OE1 C:GLN219 2.4 11.1 1.0 OD1 B:ASP164 2.5 12.6 1.0 O C:HOH2285 2.5 9.4 1.0 O C:HOH2287 2.5 9.1 1.0 OD2 B:ASP246 2.5 10.3 1.0 CG B:ASP246 2.8 9.0 1.0 CG B:ASP203 3.3 12.6 1.0 CD C:GLN219 3.5 18.3 1.0 CG B:ASP164 3.7 14.4 1.0 O C:HOH2301 4.0 30.1 1.0 NE2 C:GLN219 4.0 22.4 1.0 CB B:ASP203 4.0 10.3 1.0 N B:ASP164 4.2 10.6 1.0 CD C:PRO220 4.3 11.2 1.0 OD2 B:ASP164 4.3 16.3 1.0 OD1 B:ASP203 4.3 14.4 1.0 CB B:ASP246 4.4 7.7 1.0 NH2 B:ARG244 4.4 17.4 1.0 O C:VAL218 4.4 9.3 1.0 CB B:ALA163 4.5 11.5 1.0 O C:LEU200 4.5 8.0 1.0 NE B:ARG244 4.5 14.4 1.0 CA B:ASP164 4.6 10.7 1.0 CB B:ASP164 4.8 10.8 1.0 CG C:GLN219 4.8 15.0 1.0 CZ B:ARG244 4.8 16.3 1.0 N C:LEU200 4.9 8.3 1.0 CA B:ALA163 4.9 10.8 1.0 CA C:GLN219 4.9 9.7 1.0 O C:VAL198 4.9 10.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution.


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 Discoidin I From Dictyostelium Discoideum in Complex with the Disaccharide Galnac Beta 1- 3 Galactose, at 1.6 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:7.8 occ:1.00 OD2 C:ASP203 2.3 9.7 1.0 OE1 A:GLN219 2.4 10.7 1.0 O A:HOH2352 2.4 8.6 1.0 O A:HOH2351 2.4 8.8 1.0 OD1 C:ASP164 2.4 11.6 1.0 OD1 C:ASP246 2.5 8.8 1.0 OD2 C:ASP246 2.6 10.2 1.0 CG C:ASP246 2.9 10.4 1.0 CG C:ASP203 3.4 11.0 1.0 CD A:GLN219 3.5 15.6 1.0 CG C:ASP164 3.7 13.7 1.0 NE2 A:GLN219 4.0 21.4 1.0 CB C:ASP203 4.0 9.2 1.0 CD A:PRO220 4.2 7.8 1.0 N C:ASP164 4.3 10.2 1.0 OD2 C:ASP164 4.3 17.5 1.0 OD1 C:ASP203 4.4 12.6 1.0 NH2 C:ARG244 4.4 16.7 1.0 CB C:ASP246 4.4 7.8 1.0 O A:VAL218 4.4 7.4 1.0 CB C:ALA163 4.5 10.7 1.0 NE C:ARG244 4.5 11.7 1.0 O A:LEU200 4.5 8.6 1.0 CA C:ASP164 4.6 11.1 1.0 CB C:ASP164 4.7 11.0 1.0 O A:HOH2167 4.8 23.3 1.0 CG A:GLN219 4.8 9.8 1.0 O A:VAL198 4.8 10.4 1.0 CZ C:ARG244 4.9 15.3 1.0 N A:LEU200 4.9 7.8 1.0 CA A:GLN219 4.9 8.8 1.0 CA C:ALA163 4.9 10.5 1.0

S.Mathieu, K.Saboia Aragao, A.Imberty, A.Varrot. Discoidin I From Dictyostelium Discoideum and Interactions with Oligosaccharides: Specificity, Affinity, Crystal Structures and Comparison with Discoidin II. J.Mol.Biol. V. 400 540 2010.
ISSN: ISSN 0022-2836
PubMed: 20580724
DOI: 10.1016/J.JMB.2010.05.042