Calcium in PDB 2wn2: Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution.

The structure of Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution., PDB code: 2wn2 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)	47.33 / 1.82
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.470, 273.700, 85.800, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 18

The binding sites of Calcium atom in the Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution. (pdb code 2wn2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution., PDB code: 2wn2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:7.5 occ:1.00 OD2 A:ASP203 2.3 7.4 1.0 O B:HOH2299 2.4 6.4 1.0 OD1 A:ASP164 2.4 7.5 1.0 OE1 B:GLN219 2.4 6.0 1.0 O B:HOH2300 2.4 5.4 1.0 OD1 A:ASP246 2.5 6.9 1.0 OD2 A:ASP246 2.5 6.0 1.0 CG A:ASP246 2.8 5.5 1.0 CG A:ASP203 3.4 9.0 1.0 CD B:GLN219 3.5 12.9 1.0 CG A:ASP164 3.6 10.3 1.0 CB A:ASP203 4.0 6.3 1.0 NE2 B:GLN219 4.0 15.6 1.0 N A:ASP164 4.2 7.0 1.0 CD B:PRO220 4.2 8.8 1.0 OD2 A:ASP164 4.2 11.7 1.0 OD1 A:ASP203 4.3 9.6 1.0 NH2 A:ARG244 4.3 9.1 1.0 CB A:ASP246 4.3 6.0 1.0 O A:HOH2263 4.4 22.6 1.0 O B:VAL218 4.4 6.0 1.0 CB A:ALA163 4.5 8.7 1.0 O B:LEU200 4.5 5.8 1.0 NE A:ARG244 4.6 12.9 1.0 CA A:ASP164 4.6 7.5 1.0 CB A:ASP164 4.7 7.3 1.0 CZ A:ARG244 4.8 9.9 1.0 CG B:GLN219 4.8 8.4 1.0 O B:VAL198 4.8 7.8 1.0 CA B:GLN219 4.8 6.9 1.0 CA A:ALA163 4.9 8.7 1.0 N B:LEU200 4.9 5.7 1.0

Calcium binding site 2 out of 3 in the Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:8.9 occ:1.00 OD2 B:ASP203 2.3 6.7 1.0 OD1 B:ASP164 2.4 8.2 1.0 OE1 C:GLN219 2.4 7.9 1.0 O C:HOH2271 2.5 7.1 1.0 O C:HOH2270 2.5 5.8 1.0 OD1 B:ASP246 2.5 5.7 1.0 OD2 B:ASP246 2.6 7.2 1.0 CG B:ASP246 2.9 5.9 1.0 CG B:ASP203 3.4 9.8 1.0 CD C:GLN219 3.5 15.0 1.0 CG B:ASP164 3.6 12.3 1.0 CB B:ASP203 4.0 8.9 1.0 NE2 C:GLN219 4.0 17.4 1.0 O B:HOH2239 4.1 24.9 1.0 N B:ASP164 4.2 7.9 1.0 OD2 B:ASP164 4.2 11.9 1.0 CD C:PRO220 4.3 7.6 1.0 OD1 B:ASP203 4.3 11.1 1.0 NH2 B:ARG244 4.3 9.7 1.0 O C:VAL218 4.4 6.7 1.0 CB B:ASP246 4.4 5.4 1.0 NE B:ARG244 4.5 10.4 1.0 O C:LEU200 4.5 5.8 1.0 CA B:ASP164 4.6 8.2 1.0 CB B:ALA163 4.6 7.9 1.0 CB B:ASP164 4.7 8.6 1.0 CZ B:ARG244 4.8 9.7 1.0 CG C:GLN219 4.8 12.9 1.0 CA C:GLN219 4.9 7.4 1.0 CA B:ALA163 4.9 7.9 1.0 O C:VAL198 4.9 8.0 1.0 N C:LEU200 4.9 6.6 1.0

Calcium binding site 3 out of 3 in the Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Discoidin I From Dictyostelium Discoideum in Complex with Galactose Beta 1-3 Galnac at 1.8 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:7.6 occ:1.00 OD2 C:ASP203 2.3 7.5 1.0 OD1 C:ASP164 2.4 6.8 1.0 O A:HOH2321 2.4 4.8 1.0 O A:HOH2322 2.4 4.5 1.0 OE1 A:GLN219 2.4 7.5 1.0 OD1 C:ASP246 2.5 6.7 1.0 OD2 C:ASP246 2.6 8.1 1.0 CG C:ASP246 2.9 7.5 1.0 CG C:ASP203 3.4 8.8 1.0 CD A:GLN219 3.5 13.0 1.0 CG C:ASP164 3.6 10.2 1.0 NE2 A:GLN219 4.0 16.6 1.0 CB C:ASP203 4.0 8.1 1.0 CD A:PRO220 4.2 6.2 1.0 N C:ASP164 4.2 6.6 1.0 OD2 C:ASP164 4.3 10.5 1.0 OD1 C:ASP203 4.3 12.2 1.0 NH2 C:ARG244 4.4 11.9 1.0 CB C:ASP246 4.4 6.4 1.0 O A:VAL218 4.4 6.5 1.0 CB C:ALA163 4.5 6.4 1.0 O A:LEU200 4.5 5.8 1.0 NE C:ARG244 4.6 12.5 1.0 CA C:ASP164 4.6 8.4 1.0 O A:HOH2142 4.6 20.7 1.0 CB C:ASP164 4.7 8.9 1.0 O A:VAL198 4.8 7.5 1.0 CG A:GLN219 4.8 6.1 1.0 CZ C:ARG244 4.8 11.8 1.0 CA C:ALA163 4.8 7.9 1.0 N A:LEU200 4.9 5.9 1.0 CA A:GLN219 4.9 6.2 1.0 C C:ALA163 5.0 6.8 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