Calcium in PDB 2xr5: Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Dimannoside Mimic.

The structure of Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Dimannoside Mimic., PDB code: 2xr5 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)	42.41 / 1.42
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.450, 71.450, 52.670, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.1

The structure of Crystal Structure of the Complex of the Carbohydrate Recognition Domain of Human Dc-Sign with Pseudo Dimannoside 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 Dimannoside Mimic. (pdb code 2xr5). 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 Dimannoside Mimic., PDB code: 2xr5:
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 Dimannoside 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 Dimannoside Mimic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1387 b:6.4 occ:1.00 OD1 A:ASP366 2.3 6.1 1.0 OD1 A:ASN365 2.4 6.5 1.0 OD1 A:ASN349 2.4 6.5 1.0 OE1 A:GLU354 2.4 6.8 1.0 O4 A:MAN1384 2.4 8.3 1.0 O A:ASP366 2.5 5.2 1.0 O3 A:MAN1384 2.5 8.8 1.0 OE1 A:GLU347 2.5 7.9 1.0 CG A:ASP366 3.3 5.7 1.0 C3 A:MAN1384 3.4 9.9 1.0 CD A:GLU354 3.4 8.1 1.0 C4 A:MAN1384 3.4 9.3 1.0 CG A:ASN365 3.4 6.1 1.0 CD A:GLU347 3.4 6.5 1.0 CG A:ASN349 3.4 7.1 1.0 C A:ASP366 3.5 5.4 1.0 OE2 A:GLU354 3.7 10.4 1.0 OE2 A:GLU347 3.7 9.7 1.0 ND2 A:ASN365 3.8 8.0 1.0 N A:ASP366 3.8 4.4 1.0 ND2 A:ASN349 3.9 8.5 1.0 CA A:ASP366 4.0 5.2 1.0 OD2 A:ASP366 4.1 6.3 1.0 N A:ASN349 4.2 6.5 1.0 CB A:ASP366 4.3 5.7 1.0 CG1 A:VAL351 4.3 15.7 0.5 CG A:GLU354 4.6 7.6 1.0 CB A:ASN349 4.6 7.5 1.0 CG A:GLU347 4.6 6.9 1.0 N A:ASN350 4.7 7.8 1.0 CG2 A:VAL351 4.7 17.5 0.5 N A:ASP367 4.7 5.7 1.0 CB A:ASN365 4.7 5.4 1.0 C A:ASN365 4.7 5.3 1.0 C2 A:MAN1384 4.8 12.3 1.0 CB A:GLU354 4.8 8.2 1.0 C5 A:MAN1384 4.8 13.0 1.0 CA A:ASN349 4.8 7.6 1.0 CA A:ASN365 4.9 5.2 1.0 N A:VAL351 5.0 10.4 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 Dimannoside 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 Dimannoside Mimic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1388 b:7.5 occ:1.00 OD1 A:ASP355 2.3 8.3 1.0 O A:HOH2147 2.4 7.5 1.0 OD1 A:ASN350 2.4 7.5 1.0 OE1 A:GLU324 2.4 8.3 1.0 O A:GLU354 2.4 7.5 1.0 OE2 A:GLU324 2.5 11.1 1.0 OD2 A:ASP320 2.5 7.9 1.0 OD1 A:ASP320 2.6 7.3 1.0 CD A:GLU324 2.8 8.0 1.0 CG A:ASP320 2.9 7.8 1.0 CG A:ASN350 3.3 9.3 1.0 C A:GLU354 3.4 6.6 1.0 CG A:ASP355 3.5 9.1 1.0 CA A:ASP355 3.8 5.3 1.0 CA A:CA1389 3.9 11.0 1.0 N A:ASP355 4.0 5.8 1.0 O A:HOH2082 4.1 6.4 0.5 CB A:ASN350 4.1 7.9 1.0 CB A:ASP355 4.1 7.7 1.0 ND2 A:ASN350 4.2 12.0 1.0 N A:GLU354 4.2 9.2 1.0 CG A:GLU324 4.3 11.6 1.0 CZ2 A:TRP327 4.3 6.7 1.0 CA A:GLU354 4.4 8.6 1.0 OD2 A:ASP355 4.4 10.2 1.0 CB A:ASP320 4.4 8.2 1.0 OE1 A:GLU353 4.5 16.4 1.0 O A:HOH2076 4.5 19.4 0.5 OD2 A:ASP366 4.5 6.3 1.0 CA A:ASN350 4.6 7.8 1.0 CH2 A:TRP327 4.8 7.7 1.0 O A:HOH2075 4.8 27.7 1.0 O A:HOH2066 4.8 9.5 1.0 O A:ASP320 4.8 7.6 1.0 N A:GLY325 4.8 10.8 1.0 CA A:GLU324 4.9 11.0 1.0 C A:ASP355 5.0 5.6 1.0 CB A:GLU324 5.0 11.8 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 Dimannoside 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 Dimannoside Mimic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1389 b:11.0 occ:1.00 O A:HOH2135 2.4 18.4 1.0 OE1 A:GLU353 2.4 16.4 1.0 OE1 A:GLU324 2.4 8.3 1.0 O A:HOH2066 2.4 9.5 1.0 O A:HOH2131 2.4 15.7 1.0 OD2 A:ASP355 2.5 10.2 1.0 OD1 A:ASP355 2.6 8.3 1.0 CG A:ASP355 2.9 9.1 1.0 CD A:GLU324 3.5 8.0 1.0 CD A:GLU353 3.5 20.4 1.0 CA A:CA1388 3.9 7.5 1.0 CB A:GLU324 4.1 11.8 1.0 OD1 A:ASN350 4.2 7.5 1.0 O A:HOH2067 4.2 21.0 1.0 CG A:GLU324 4.2 11.6 1.0 OE2 A:GLU353 4.2 23.7 1.0 CB A:ASP355 4.4 7.7 1.0 O A:HOH2068 4.4 18.8 1.0 OE2 A:GLU324 4.5 11.1 1.0 CG A:GLU353 4.5 20.6 1.0 O A:ASP320 4.5 7.6 1.0 O A:HOH2145 4.6 44.1 1.0 ND2 A:ASN350 4.7 12.0 1.0 CA A:GLU324 4.7 11.0 1.0 CB A:GLU353 4.7 16.6 1.0 OD1 A:ASP320 4.7 7.3 1.0 O A:HOH2134 4.8 27.4 1.0 CG A:ASN350 4.9 9.3 1.0

M.Thepaut, C.Guzzi, I.Sutkeviciute, S.Sattin, R.Ribeiro-Viana, N.Varga, E.Chabrol, J.Rojo, A.Bernardi, J.Angulo, P.M.Nieto, F.Fieschi. Structure of A Glycomimetic Ligand in the Carbohydrate Recognition Domain of C-Type Lectin Dc-Sign. Structural Requirements For Selectivity and Ligand Design. J.Am.Chem.Soc. V. 135 2518 2013.
ISSN: ISSN 0002-7863
PubMed: 23360500
DOI: 10.1021/JA3053305