Calcium in PDB 2it6: Crystal Structure of Dcsign-Crd with MAN2

The structure of Crystal Structure of Dcsign-Crd with MAN2, PDB code: 2it6 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)	55.64 / 1.95
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	55.640, 55.640, 53.200, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.1

The binding sites of Calcium atom in the Crystal Structure of Dcsign-Crd with MAN2 (pdb code 2it6). 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 MAN2, PDB code: 2it6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Dcsign-Crd with MAN2


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 MAN2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:18.4 occ:1.00 O A:HOH411 2.2 20.1 1.0 OD1 A:ASP355 2.3 18.8 1.0 OD2 A:ASP320 2.4 19.6 1.0 OD1 A:ASN350 2.4 22.2 1.0 O A:GLU354 2.5 16.9 1.0 OE2 A:GLU324 2.5 18.8 1.0 OE1 A:GLU324 2.6 19.0 1.0 OD1 A:ASP320 2.7 19.6 1.0 CD A:GLU324 2.9 19.5 1.0 CG A:ASP320 2.9 20.4 1.0 CG A:ASN350 3.3 21.7 1.0 C A:GLU354 3.4 20.4 1.0 CG A:ASP355 3.5 18.2 1.0 CA A:ASP355 3.7 17.9 1.0 CA A:CA407 3.9 23.1 1.0 CB A:ASN350 3.9 21.2 1.0 N A:ASP355 4.0 18.4 1.0 CB A:ASP355 4.1 18.8 1.0 O A:HOH428 4.1 19.6 1.0 ND2 A:ASN350 4.1 23.1 1.0 CZ2 A:TRP327 4.3 21.4 1.0 CG A:GLU324 4.3 21.1 1.0 OE2 A:GLU353 4.4 31.7 1.0 N A:GLU354 4.4 23.0 1.0 CB A:ASP320 4.4 19.6 1.0 OD2 A:ASP355 4.4 21.8 1.0 CA A:GLU354 4.5 21.4 1.0 CA A:ASN350 4.6 21.6 1.0 OD2 A:ASP366 4.7 20.2 1.0 CH2 A:TRP327 4.7 20.8 1.0 O A:HOH408 4.8 24.5 1.0 N A:GLY325 4.8 21.8 1.0 O A:ASP320 4.9 23.1 1.0 CA A:GLU324 4.9 23.4 1.0 C A:ASP355 4.9 17.3 1.0 O A:HOH434 5.0 31.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Dcsign-Crd with MAN2


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 MAN2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:20.8 occ:1.00 OD1 A:ASP366 2.3 18.6 1.0 O3 A:MAN3 2.3 27.4 0.2 OE1 A:GLU354 2.4 26.0 1.0 OD1 A:ASN349 2.5 24.1 1.0 O4 A:MAN3 2.5 30.0 0.8 O A:ASP366 2.5 17.1 1.0 OD1 A:ASN365 2.5 21.1 1.0 OE1 A:GLU347 2.5 27.6 1.0 O3 A:MAN3 2.5 23.7 0.8 O4 A:MAN3 2.6 26.3 0.2 C3 A:MAN3 3.2 27.3 0.2 CG A:ASP366 3.2 19.4 1.0 C4 A:MAN3 3.3 28.3 0.8 C3 A:MAN3 3.3 29.8 0.8 C4 A:MAN3 3.3 26.9 0.2 CD A:GLU354 3.3 26.2 1.0 CD A:GLU347 3.4 25.2 1.0 CG A:ASN349 3.4 26.1 1.0 CG A:ASN365 3.4 22.9 1.0 C A:ASP366 3.6 18.7 1.0 OE2 A:GLU347 3.7 27.5 1.0 OE2 A:GLU354 3.7 26.7 1.0 N A:ASP366 3.7 19.8 1.0 ND2 A:ASN365 3.8 21.6 1.0 ND2 A:ASN349 3.8 25.2 1.0 OD2 A:ASP366 3.9 20.2 1.0 CA A:ASP366 4.1 18.6 1.0 N A:ASN349 4.2 21.8 1.0 CB A:ASP366 4.2 19.3 1.0 CG2 A:VAL351 4.5 30.7 1.0 CG A:GLU347 4.6 24.5 1.0 C2 A:MAN3 4.6 27.6 0.2 CG A:GLU354 4.6 24.7 1.0 N A:ASN350 4.7 19.9 1.0 CB A:ASN349 4.7 23.5 1.0 C A:ASN365 4.7 19.6 1.0 C5 A:MAN3 4.7 30.8 0.8 N A:ASP367 4.7 19.3 1.0 C2 A:MAN3 4.7 31.1 0.8 C5 A:MAN3 4.7 26.8 0.2 CB A:ASN365 4.7 19.3 1.0 CA A:ASN349 4.8 22.4 1.0 CB A:GLU354 4.8 21.6 1.0 O2 A:MAN3 4.9 27.6 0.2 CA A:ASN365 5.0 20.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Dcsign-Crd with MAN2


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 MAN2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:23.1 occ:1.00 OE2 A:GLU353 2.1 31.7 1.0 O A:HOH410 2.2 30.9 1.0 OE1 A:GLU324 2.2 19.0 1.0 O A:HOH408 2.3 24.5 1.0 O A:HOH409 2.5 23.9 1.0 OD2 A:ASP355 2.6 21.8 1.0 OD1 A:ASP355 2.6 18.8 1.0 CG A:ASP355 2.9 18.2 1.0 CD A:GLU353 3.2 33.7 1.0 CD A:GLU324 3.4 19.5 1.0 CA A:CA405 3.9 18.4 1.0 CG A:GLU353 3.9 31.4 1.0 CB A:GLU324 4.1 21.3 1.0 OD1 A:ASN350 4.1 22.2 1.0 O A:HOH517 4.1 41.3 1.0 OE1 A:GLU353 4.1 34.3 1.0 CG A:GLU324 4.2 21.1 1.0 CB A:ASP355 4.4 18.8 1.0 OE2 A:GLU324 4.4 18.8 1.0 ND2 A:ASN350 4.5 23.1 1.0 CA A:GLU324 4.6 23.4 1.0 O A:ASP320 4.6 23.1 1.0 CG A:ASN350 4.7 21.7 1.0 OD1 A:ASP320 4.7 19.6 1.0 O A:HOH512 4.8 47.3 1.0 OD2 A:ASP320 4.9 19.6 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