Calcium in PDB 2it5: Crystal Structure of Dcsign-Crd with MAN6

The structure of Crystal Structure of Dcsign-Crd with MAN6, PDB code: 2it5 was solved by W.I.Weis, H.Feinberg, R.Castelli, K.Drickamer, P.H.Seeberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.98 / 2.40
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	55.960, 55.960, 53.260, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.2

The binding sites of Calcium atom in the Crystal Structure of Dcsign-Crd with MAN6 (pdb code 2it5). 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 Dcsign-Crd with MAN6, PDB code: 2it5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Dcsign-Crd with MAN6


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 Dcsign-Crd with MAN6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:19.5 occ:1.00 O A:HOH391 2.1 14.0 1.0 OD1 A:ASN350 2.2 25.7 1.0 OD1 A:ASP355 2.3 17.1 1.0 OD2 A:ASP320 2.4 21.4 1.0 O A:GLU354 2.6 19.3 1.0 OE1 A:GLU324 2.6 23.4 1.0 OD1 A:ASP320 2.7 24.1 1.0 OE2 A:GLU324 2.8 22.9 1.0 CG A:ASP320 2.9 23.4 1.0 CD A:GLU324 3.0 24.5 1.0 CG A:ASN350 3.2 23.5 1.0 C A:GLU354 3.4 22.4 1.0 CG A:ASP355 3.5 18.9 1.0 CA A:ASP355 3.7 19.9 1.0 CA A:CA103 3.8 33.0 1.0 N A:ASP355 3.9 19.3 1.0 ND2 A:ASN350 4.0 21.8 1.0 OE2 A:GLU353 4.0 43.9 1.0 CB A:ASN350 4.1 23.2 1.0 CB A:ASP355 4.1 18.6 1.0 N A:GLU354 4.3 28.6 1.0 CZ2 A:TRP327 4.4 23.5 1.0 CB A:ASP320 4.4 20.6 1.0 OD2 A:ASP355 4.4 19.6 1.0 O A:HOH415 4.4 28.5 1.0 CA A:GLU354 4.5 25.1 1.0 CG A:GLU324 4.5 23.9 1.0 CA A:ASN350 4.7 25.1 1.0 OD2 A:ASP366 4.7 18.6 1.0 CH2 A:TRP327 4.8 22.7 1.0 O A:HOH389 4.9 20.1 1.0 C A:ASP355 4.9 18.6 1.0 O A:ASP320 4.9 22.3 1.0 O A:HOH423 5.0 30.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Dcsign-Crd with MAN6


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 Dcsign-Crd with MAN6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:24.8 occ:1.00 OD1 A:ASP366 2.3 15.4 1.0 OD1 A:ASN365 2.4 18.3 1.0 OE1 A:GLU354 2.5 33.0 1.0 OE1 A:GLU347 2.5 36.1 1.0 O A:ASP366 2.5 17.9 1.0 O3 A:MAN3 2.6 35.8 0.8 O4 A:MAN3 2.6 33.8 0.8 O3 A:MAN3 2.6 13.6 0.2 OD1 A:ASN349 2.7 27.2 1.0 O4 A:MAN3 2.8 14.8 0.2 CG A:ASP366 3.2 16.0 1.0 CG A:ASN365 3.3 18.7 1.0 C3 A:MAN3 3.4 36.8 0.8 CD A:GLU347 3.4 33.1 1.0 C4 A:MAN3 3.4 34.9 0.8 CG A:ASN349 3.5 27.5 1.0 CD A:GLU354 3.5 32.9 1.0 C4 A:MAN3 3.5 14.2 0.2 C3 A:MAN3 3.5 14.3 0.2 C A:ASP366 3.6 17.9 1.0 N A:ASP366 3.6 17.0 1.0 ND2 A:ASN365 3.7 14.7 1.0 OE2 A:GLU347 3.8 35.5 1.0 ND2 A:ASN349 3.9 30.0 1.0 OD2 A:ASP366 3.9 18.6 1.0 OE2 A:GLU354 3.9 35.3 1.0 CA A:ASP366 4.0 18.2 1.0 N A:ASN349 4.1 25.1 1.0 CB A:ASP366 4.2 17.6 1.0 C A:ASN365 4.6 18.4 1.0 CG A:GLU347 4.6 30.1 1.0 CB A:ASN365 4.6 19.1 1.0 CB A:ASN349 4.6 26.6 1.0 N A:ASN350 4.7 24.8 1.0 N A:ASP367 4.7 20.5 1.0 CG A:GLU354 4.7 29.4 1.0 CA A:ASN349 4.8 25.8 1.0 C2 A:MAN3 4.8 39.2 0.8 CG2 A:VAL351 4.8 29.8 1.0 C5 A:MAN3 4.8 35.1 0.8 CA A:ASN365 4.8 20.1 1.0 C2 A:MAN3 4.9 14.7 0.2 CB A:GLU354 4.9 26.1 1.0 C5 A:MAN3 5.0 14.2 0.2 CA A:PRO348 5.0 26.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Dcsign-Crd with MAN6


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 Dcsign-Crd with MAN6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:33.0 occ:1.00 OE2 A:GLU353 2.1 43.9 1.0 OE1 A:GLU324 2.3 23.4 1.0 O A:HOH440 2.3 42.1 1.0 O A:HOH389 2.4 20.1 1.0 O A:HOH390 2.5 24.1 1.0 OD1 A:ASP355 2.7 17.1 1.0 OD2 A:ASP355 2.7 19.6 1.0 CG A:ASP355 3.0 18.9 1.0 CD A:GLU353 3.0 43.5 1.0 CD A:GLU324 3.5 24.5 1.0 OE1 A:GLU353 3.7 44.6 1.0 CA A:CA101 3.8 19.5 1.0 CG A:GLU353 4.0 40.4 1.0 CB A:GLU324 4.2 26.1 1.0 OD1 A:ASN350 4.2 25.7 1.0 CG A:GLU324 4.2 23.9 1.0 OE2 A:GLU324 4.4 22.9 1.0 CB A:ASP355 4.5 18.6 1.0 ND2 A:ASN350 4.6 21.8 1.0 O A:ASP320 4.6 22.3 1.0 OD1 A:ASP320 4.6 24.1 1.0 CA A:GLU324 4.7 27.2 1.0 CG A:ASN350 4.8 23.5 1.0 OD2 A:ASP320 4.9 21.4 1.0

H.Feinberg, R.Castelli, K.Drickamer, P.H.Seeberger, W.I.Weis. Multiple Modes of Binding Enhance the Affinity of Dc-Sign For High Mannose N-Linked Glycans Found on Viral Glycoproteins. J.Biol.Chem. V. 282 4202 2007.
ISSN: ISSN 0021-9258
PubMed: 17150970
DOI: 10.1074/JBC.M609689200