Calcium in PDB 1k9j: Complex of Dc-Signr and GLCNAC2MAN3

The structure of Complex of Dc-Signr and GLCNAC2MAN3, PDB code: 1k9j was solved by H.Feinberg, D.A.Mitchell, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.77 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.226, 57.039, 89.263, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24

The binding sites of Calcium atom in the Complex of Dc-Signr and GLCNAC2MAN3 (pdb code 1k9j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex of Dc-Signr and GLCNAC2MAN3, PDB code: 1k9j:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Complex of Dc-Signr and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Dc-Signr and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:15.7 occ:1.00 O A:HOH441 2.3 11.8 1.0 OD1 A:ASP367 2.3 19.2 1.0 OD1 A:ASN362 2.4 16.9 1.0 O A:GLU366 2.4 16.5 1.0 OE1 A:GLU336 2.5 20.8 1.0 OD2 A:ASP332 2.5 11.9 1.0 OD1 A:ASP332 2.6 12.6 1.0 OE2 A:GLU336 2.6 17.7 1.0 CD A:GLU336 2.9 18.4 1.0 CG A:ASP332 2.9 12.8 1.0 CG A:ASN362 3.3 19.0 1.0 C A:GLU366 3.4 17.2 1.0 CG A:ASP367 3.5 19.0 1.0 CA A:ASP367 3.8 17.7 1.0 CA A:CA403 3.9 18.5 1.0 N A:ASP367 4.0 17.6 1.0 CB A:ASN362 4.0 18.6 1.0 CB A:ASP367 4.1 18.7 1.0 O A:HOH410 4.2 18.1 1.0 ND2 A:ASN362 4.2 18.9 1.0 N A:GLU366 4.3 18.6 1.0 CZ2 A:TRP339 4.3 17.1 1.0 CG A:GLU336 4.3 19.8 1.0 CB A:ASP332 4.4 9.6 1.0 OD2 A:ASP367 4.5 18.9 1.0 CA A:GLU366 4.5 17.3 1.0 CA A:ASN362 4.6 19.3 1.0 CH2 A:TRP339 4.6 15.0 1.0 OD2 A:ASP378 4.7 17.6 1.0 OD1 A:ASN365 4.8 20.4 1.0 O A:ASP332 4.8 14.9 1.0 O A:HOH525 4.8 12.9 1.0 N A:GLY337 4.9 17.5 1.0 CA A:GLU336 4.9 17.8 1.0 O A:HOH492 4.9 31.1 1.0

Calcium binding site 2 out of 3 in the Complex of Dc-Signr and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Dc-Signr and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.1 occ:1.00 OD1 A:ASP378 2.3 17.9 1.0 O A:ASP378 2.4 14.2 1.0 OE1 A:GLU366 2.4 17.2 1.0 OD1 A:ASN361 2.4 18.8 1.0 OD1 A:ASN377 2.5 15.7 1.0 O3 A:MAN2 2.5 18.6 1.0 O4 A:MAN2 2.6 17.4 1.0 OE1 A:GLU359 2.6 17.2 1.0 CG A:ASP378 3.2 16.8 1.0 C3 A:MAN2 3.3 21.1 1.0 CD A:GLU366 3.3 18.9 1.0 C4 A:MAN2 3.3 20.6 1.0 CG A:ASN377 3.4 15.2 1.0 CG A:ASN361 3.4 17.8 1.0 CD A:GLU359 3.5 17.4 1.0 C A:ASP378 3.5 14.5 1.0 OE2 A:GLU366 3.6 18.4 1.0 ND2 A:ASN377 3.7 15.2 1.0 N A:ASP378 3.7 14.8 1.0 OE2 A:GLU359 3.7 17.4 1.0 OD2 A:ASP378 3.8 17.6 1.0 ND2 A:ASN361 3.9 19.2 1.0 CA A:ASP378 4.1 14.5 1.0 N A:ASN361 4.2 16.4 1.0 CB A:ASP378 4.2 15.3 1.0 CG A:GLU366 4.6 18.8 1.0 CB A:ASN361 4.6 17.4 1.0 N A:ASN379 4.7 15.5 1.0 C A:ASN377 4.7 16.6 1.0 CG A:GLU359 4.7 16.5 1.0 C2 A:MAN2 4.7 21.2 1.0 CB A:ASN377 4.7 15.9 1.0 N A:ASN362 4.8 18.4 1.0 C5 A:MAN2 4.8 22.3 1.0 CB A:GLU366 4.8 18.8 1.0 CA A:ASN361 4.8 17.9 1.0 N A:SER363 4.9 18.1 1.0 CB A:SER363 4.9 20.6 1.0 CA A:ASN377 5.0 16.8 1.0 O2 A:MAN2 5.0 24.4 1.0

Calcium binding site 3 out of 3 in the Complex of Dc-Signr and GLCNAC2MAN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Dc-Signr and GLCNAC2MAN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:18.5 occ:1.00 OE1 A:GLU336 2.3 20.8 1.0 O A:HOH525 2.4 12.9 1.0 O A:HOH526 2.4 14.1 1.0 O A:HOH527 2.5 17.6 1.0 OD1 A:ASN365 2.5 20.4 1.0 OD2 A:ASP367 2.5 18.9 1.0 OD1 A:ASP367 2.6 19.2 1.0 CG A:ASP367 2.9 19.0 1.0 CD A:GLU336 3.5 18.4 1.0 CG A:ASN365 3.5 22.9 1.0 ND2 A:ASN365 3.8 25.0 1.0 CA A:CA401 3.9 15.7 1.0 OD1 A:ASN362 4.0 16.9 1.0 CB A:GLU336 4.0 18.5 1.0 CG A:GLU336 4.1 19.8 1.0 O A:HOH491 4.3 25.5 1.0 CB A:ASP367 4.4 18.7 1.0 OE2 A:GLU336 4.4 17.7 1.0 O A:ASP332 4.5 14.9 1.0 ND2 A:ASN362 4.5 18.9 1.0 CA A:GLU336 4.6 17.8 1.0 O A:HOH500 4.6 42.2 1.0 CG A:ASN362 4.7 19.0 1.0 OD1 A:ASP332 4.7 12.6 1.0 CB A:ASN365 4.8 19.6 1.0 OD2 A:ASP332 4.9 11.9 1.0

H.Feinberg, D.A.Mitchell, K.Drickamer, W.I.Weis. Structural Basis For Selective Recognition of Oligosaccharides By Dc-Sign and Dc-Signr. Science V. 294 2163 2001.
ISSN: ISSN 0036-8075
PubMed: 11739956
DOI: 10.1126/SCIENCE.1066371