Calcium in PDB 2xr6: Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic.

The structure of Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic., PDB code: 2xr6 was solved by M.Thepaut, I.Suitkeviciute, S.Sattin, J.Reina, A.Bernardi, F.Fieschi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.44 / 1.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.330, 71.330, 52.666, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.8

The structure of Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic. also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic. (pdb code 2xr6). 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 the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic., PDB code: 2xr6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic.


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 the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1389 b:10.4 occ:1.00 OE1 A:GLU353 2.1 23.4 0.5 OE1 A:GLU324 2.3 8.7 1.0 O A:HOH2148 2.4 18.6 1.0 O A:HOH2077 2.4 11.6 1.0 O A:HOH2149 2.4 15.2 1.0 OE2 A:GLU353 2.4 10.9 0.5 OD2 A:ASP355 2.5 11.7 1.0 OD1 A:ASP355 2.6 8.6 1.0 CG A:ASP355 2.9 9.1 1.0 CD A:GLU353 3.3 19.3 0.5 CD A:GLU324 3.5 7.9 1.0 CD A:GLU353 3.5 17.1 0.5 CA A:CA1390 3.9 7.8 1.0 CG A:GLU353 4.0 17.0 0.5 CB A:GLU324 4.1 11.3 1.0 OE2 A:GLU353 4.2 22.5 0.5 CG A:GLU324 4.2 11.6 1.0 OD1 A:ASN350 4.2 8.3 1.0 OE1 A:GLU353 4.3 15.4 0.5 O A:HOH2079 4.3 30.0 1.0 CB A:ASP355 4.4 8.5 1.0 O A:HOH2078 4.4 22.4 1.0 OE2 A:GLU324 4.5 10.2 1.0 CG A:GLU353 4.5 13.8 0.5 O A:ASP320 4.5 8.5 1.0 CB A:GLU353 4.5 14.5 0.5 O A:HOH2154 4.6 28.4 1.0 ND2 A:ASN350 4.7 11.8 1.0 CA A:GLU324 4.7 10.0 1.0 O A:HOH2165 4.7 41.8 1.0 OD1 A:ASP320 4.7 7.7 1.0 CG A:ASN350 4.9 7.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic.


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 the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1390 b:7.8 occ:1.00 O A:HOH2166 2.3 7.7 1.0 OD1 A:ASP355 2.4 8.6 1.0 O A:GLU354 2.4 7.9 1.0 OD1 A:ASN350 2.5 8.3 1.0 OE1 A:GLU324 2.5 8.7 1.0 OE2 A:GLU324 2.5 10.2 1.0 OD2 A:ASP320 2.5 8.6 1.0 OD1 A:ASP320 2.5 7.7 1.0 CD A:GLU324 2.8 7.9 1.0 CG A:ASP320 2.9 8.3 1.0 CG A:ASN350 3.4 7.8 1.0 C A:GLU354 3.4 6.5 1.0 CG A:ASP355 3.5 9.1 1.0 CA A:ASP355 3.8 6.4 1.0 CA A:CA1389 3.9 10.4 1.0 N A:ASP355 4.0 6.6 1.0 O A:HOH2094 4.0 14.1 1.0 CB A:ASN350 4.1 7.5 1.0 ND2 A:ASN350 4.2 11.8 1.0 CB A:ASP355 4.2 8.5 1.0 N A:GLU354 4.2 9.3 1.0 CZ2 A:TRP327 4.3 8.5 1.0 CG A:GLU324 4.3 11.6 1.0 OE1 A:GLU353 4.4 23.4 0.5 CB A:ASP320 4.4 7.6 1.0 CA A:GLU354 4.4 8.5 1.0 OD2 A:ASP355 4.5 11.7 1.0 OE2 A:GLU353 4.5 10.9 0.5 OD2 A:ASP366 4.5 7.0 1.0 CA A:ASN350 4.7 8.2 1.0 CH2 A:TRP327 4.8 8.4 1.0 N A:GLY325 4.8 11.1 1.0 O A:ASP320 4.9 8.5 1.0 O A:HOH2077 4.9 11.6 1.0 O A:HOH2086 4.9 27.5 1.0 CA A:GLU324 5.0 10.0 1.0 C A:ASP355 5.0 6.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic.


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 the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Trimannoside Mimic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1391 b:6.5 occ:1.00 OD1 A:ASP366 2.4 6.6 1.0 OD1 A:ASN365 2.4 6.7 1.0 OD1 A:ASN349 2.4 7.3 1.0 OE1 A:GLU354 2.4 7.8 1.0 O3 A:MAN1385 2.5 9.0 1.0 O A:ASP366 2.5 6.6 1.0 OE1 A:GLU347 2.5 7.8 1.0 O4 A:MAN1385 2.5 9.0 1.0 C3 A:MAN1385 3.4 9.4 1.0 CG A:ASP366 3.4 6.5 1.0 C4 A:MAN1385 3.4 10.1 1.0 CD A:GLU354 3.4 7.8 1.0 CG A:ASN349 3.4 7.3 1.0 CD A:GLU347 3.4 6.0 1.0 CG A:ASN365 3.4 7.4 1.0 C A:ASP366 3.6 5.8 1.0 OE2 A:GLU354 3.7 10.4 1.0 OE2 A:GLU347 3.7 8.6 1.0 ND2 A:ASN365 3.8 8.5 1.0 N A:ASP366 3.8 5.7 1.0 ND2 A:ASN349 3.9 8.9 1.0 CA A:ASP366 4.1 6.1 1.0 OD2 A:ASP366 4.1 7.0 1.0 N A:ASN349 4.2 6.8 1.0 CG1 A:VAL351 4.2 16.3 0.5 CB A:ASP366 4.3 5.8 1.0 N A:ASN350 4.6 7.5 1.0 CB A:ASN349 4.6 8.0 1.0 CG A:GLU354 4.6 7.5 1.0 CG2 A:VAL351 4.6 18.4 0.5 CG A:GLU347 4.7 7.2 1.0 CB A:ASN365 4.7 6.7 1.0 N A:ASP367 4.7 6.0 1.0 C A:ASN365 4.8 5.7 1.0 C2 A:MAN1385 4.8 12.2 1.0 CB A:GLU354 4.8 8.2 1.0 CA A:ASN349 4.8 7.6 1.0 C5 A:MAN1385 4.8 12.2 1.0 CA A:ASN365 4.9 5.7 1.0 N A:VAL351 4.9 8.4 1.0

I.Sutkeviciute, M.Thepaut, S.Sattin, A.Berzi, J.Mcgeagh, S.Grudinin, J.Weiser, A.Le Roy, J.J.Reina, J.Rojo, M.Clerici, A.Bernardi, C.Ebel, F.Fieschi. Unique Dc-Sign Clustering Activity of A Small Glycomimetic: A Lesson For Ligand Design. Acs Chem.Biol. V. 9 1377 2014.
ISSN: ISSN 1554-8929
PubMed: 24749535
DOI: 10.1021/CB500054H