Calcium in PDB 2w94: Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution

The structure of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution, PDB code: 2w94 was solved by K.Saboia Aragao, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.60 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.530, 274.371, 85.928, 90.00, 90.00, 90.00
R / Rfree (%)	16.474 / 20.593

The structure of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Calcium atom in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution (pdb code 2w94). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution, PDB code: 2w94:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1257 b:15.3 occ:1.00 OD1 A:ASP164 2.3 17.8 1.0 O B:HOH2281 2.4 14.6 1.0 OD2 A:ASP203 2.4 21.9 1.0 O B:HOH2282 2.4 12.7 1.0 OE1 B:GLN219 2.4 16.2 1.0 OD1 A:ASP246 2.5 13.9 1.0 OD2 A:ASP246 2.6 12.8 1.0 CG A:ASP246 2.9 13.3 1.0 CG A:ASP203 3.4 19.1 1.0 CD B:GLN219 3.4 19.8 1.0 CG A:ASP164 3.5 17.9 1.0 NE2 B:GLN219 3.9 26.2 1.0 CB A:ASP203 4.0 16.3 1.0 OD2 A:ASP164 4.2 20.9 1.0 CD B:PRO220 4.2 18.1 1.0 N A:ASP164 4.2 15.2 1.0 OD1 A:ASP203 4.4 21.1 1.0 CB A:ASP246 4.4 13.0 1.0 NH2 A:ARG244 4.4 25.8 1.0 O B:VAL218 4.4 12.3 1.0 O B:LEU200 4.5 14.0 1.0 CB A:ALA163 4.5 16.6 1.0 NE A:ARG244 4.5 23.9 1.0 CA A:ASP164 4.6 16.8 1.0 CB A:ASP164 4.6 16.5 1.0 O B:HOH2128 4.7 31.7 1.0 CG B:GLN219 4.8 18.0 1.0 CA B:GLN219 4.8 15.2 1.0 CZ A:ARG244 4.8 24.0 1.0 O B:VAL198 4.9 14.1 1.0 N B:LEU200 4.9 13.2 1.0 CA A:ALA163 4.9 15.8 1.0

Calcium binding site 2 out of 3 in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1256 b:17.1 occ:1.00 O C:HOH2263 2.4 10.8 1.0 OD1 B:ASP164 2.4 19.4 1.0 OD2 B:ASP203 2.4 19.8 1.0 OE1 C:GLN219 2.4 18.3 1.0 O C:HOH2264 2.4 17.0 1.0 OD1 B:ASP246 2.5 16.0 1.0 OD2 B:ASP246 2.6 14.3 1.0 CG B:ASP246 2.9 15.0 1.0 CG B:ASP203 3.5 20.3 1.0 CD C:GLN219 3.5 21.5 1.0 CG B:ASP164 3.6 21.3 1.0 NE2 C:GLN219 3.9 23.8 1.0 CB B:ASP203 4.0 17.0 1.0 N B:ASP164 4.2 18.8 1.0 CD C:PRO220 4.2 17.8 1.0 OD2 B:ASP164 4.2 20.8 1.0 NH2 B:ARG244 4.4 24.0 1.0 CB B:ASP246 4.4 14.4 1.0 OD1 B:ASP203 4.5 22.6 1.0 O C:VAL218 4.5 15.6 1.0 CB B:ALA163 4.5 20.0 1.0 NE B:ARG244 4.5 23.7 1.0 CA B:ASP164 4.6 19.4 1.0 O C:LEU200 4.7 15.8 1.0 CB B:ASP164 4.7 19.8 1.0 O C:HOH2115 4.8 32.2 1.0 CG C:GLN219 4.8 20.9 1.0 CZ B:ARG244 4.8 23.3 1.0 CA B:ALA163 4.9 18.9 1.0 N C:LEU200 4.9 14.6 1.0 CA C:GLN219 4.9 18.0 1.0 C B:ALA163 5.0 18.8 1.0 O C:VAL198 5.0 15.0 1.0

Calcium binding site 3 out of 3 in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1257 b:16.1 occ:1.00 O A:HOH2288 2.4 14.6 1.0 OE1 A:GLN219 2.4 17.1 1.0 OD1 C:ASP164 2.4 19.1 1.0 OD2 C:ASP203 2.4 17.5 1.0 O A:HOH2289 2.5 14.6 1.0 OD1 C:ASP246 2.6 15.2 1.0 OD2 C:ASP246 2.7 15.1 1.0 CG C:ASP246 3.0 16.0 1.0 CD A:GLN219 3.4 21.6 1.0 CG C:ASP203 3.4 17.6 1.0 CG C:ASP164 3.6 18.2 1.0 NE2 A:GLN219 3.9 25.8 1.0 CB C:ASP203 4.0 17.1 1.0 CD A:PRO220 4.2 14.7 1.0 OD2 C:ASP164 4.2 20.2 1.0 N C:ASP164 4.2 17.4 1.0 O A:VAL218 4.4 14.6 1.0 NH2 C:ARG244 4.4 25.0 1.0 OD1 C:ASP203 4.5 19.3 1.0 NE C:ARG244 4.5 23.5 1.0 CB C:ASP246 4.5 13.7 1.0 O A:LEU200 4.5 13.2 1.0 CA C:ASP164 4.6 16.9 1.0 CB C:ALA163 4.6 17.1 1.0 CB C:ASP164 4.7 18.1 1.0 CG A:GLN219 4.8 18.1 1.0 O A:HOH2130 4.8 28.7 1.0 CZ C:ARG244 4.8 25.2 1.0 CA A:GLN219 4.9 15.4 1.0 CA C:ALA163 4.9 16.8 1.0 N A:LEU200 4.9 12.1 1.0 O A:VAL198 4.9 14.7 1.0 C C:ALA163 5.0 17.4 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