Calcium in PDB 1sl4: Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4

The structure of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4, PDB code: 1sl4 was solved by Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.51 / 1.55
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	55.660, 55.660, 53.330, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.5

The binding sites of Calcium atom in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4 (pdb code 1sl4). 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 Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4, PDB code: 1sl4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4


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 Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:15.3 occ:1.00 O A:HOH412 2.4 16.5 1.0 OD1 A:ASP355 2.4 17.4 1.0 O A:GLU354 2.4 15.6 1.0 OD1 A:ASN350 2.5 17.6 1.0 OE1 A:GLU324 2.5 18.5 1.0 OD2 A:ASP320 2.5 15.3 1.0 OE2 A:GLU324 2.5 17.2 1.0 OD1 A:ASP320 2.6 15.4 1.0 CD A:GLU324 2.8 17.2 1.0 CG A:ASP320 2.9 16.2 1.0 CG A:ASN350 3.3 18.1 1.0 C A:GLU354 3.3 15.9 1.0 CG A:ASP355 3.5 17.7 1.0 CA A:ASP355 3.7 14.5 1.0 CA A:CA407 3.9 21.4 1.0 N A:ASP355 3.9 15.9 1.0 CB A:ASN350 4.0 18.2 1.0 O A:HOH425 4.1 18.2 1.0 CB A:ASP355 4.2 16.5 1.0 ND2 A:ASN350 4.2 19.4 1.0 N A:GLU354 4.3 19.3 1.0 CZ2 A:TRP327 4.3 14.7 1.0 OE2 A:GLU353 4.3 27.9 1.0 CG A:GLU324 4.3 18.4 1.0 CA A:GLU354 4.4 18.1 1.0 CB A:ASP320 4.4 13.8 1.0 OD2 A:ASP355 4.5 19.9 1.0 CA A:ASN350 4.5 19.3 1.0 OD2 A:ASP366 4.6 15.3 1.0 CH2 A:TRP327 4.7 16.2 1.0 O A:ASP320 4.8 18.6 1.0 O A:HOH530 4.8 36.6 1.0 O A:HOH409 4.9 23.1 1.0 N A:GLY325 4.9 18.9 1.0 CA A:GLU324 5.0 18.4 1.0 C A:ASP355 5.0 14.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4


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 Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:18.4 occ:1.00 OD1 A:ASP366 2.4 17.2 1.0 OD1 A:ASN349 2.4 22.7 1.0 OD1 A:ASN365 2.4 19.2 1.0 O A:ASP366 2.5 15.6 1.0 OE1 A:GLU347 2.5 24.1 1.0 O3 A:MAN3 2.5 25.1 1.0 OE1 A:GLU354 2.6 19.0 1.0 O4 A:MAN3 2.6 22.0 1.0 CG A:ASP366 3.3 16.2 1.0 C3 A:MAN3 3.3 26.5 1.0 C4 A:MAN3 3.4 25.1 1.0 CG A:ASN365 3.4 19.4 1.0 CD A:GLU347 3.4 24.4 1.0 CG A:ASN349 3.4 24.4 1.0 CD A:GLU354 3.5 20.9 1.0 C A:ASP366 3.6 13.6 1.0 N A:ASP366 3.7 13.6 1.0 ND2 A:ASN365 3.7 17.0 1.0 OE2 A:GLU347 3.7 26.6 1.0 OE2 A:GLU354 3.7 23.4 1.0 ND2 A:ASN349 3.8 23.4 1.0 OD2 A:ASP366 4.0 15.3 1.0 CA A:ASP366 4.1 14.2 1.0 N A:ASN349 4.1 20.6 1.0 CB A:ASP366 4.3 14.7 1.0 CG2 A:VAL351 4.5 27.6 1.0 CG A:GLU347 4.6 24.0 1.0 CB A:ASN349 4.7 23.1 1.0 C A:ASN365 4.7 15.3 1.0 CB A:ASN365 4.7 17.4 1.0 N A:ASN350 4.7 20.5 1.0 CG A:GLU354 4.7 19.3 1.0 N A:ASP367 4.7 15.0 1.0 C2 A:MAN3 4.7 27.8 1.0 C5 A:MAN3 4.8 27.5 1.0 CA A:ASN349 4.8 21.9 1.0 CB A:GLU354 4.9 17.9 1.0 CA A:ASN365 4.9 15.9 1.0 CB A:GLU347 5.0 21.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4


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 Dc-Sign Carbohydrate Recognition Domain Complexed with MAN4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:21.4 occ:1.00 OE2 A:GLU353 2.1 27.9 1.0 O A:HOH411 2.3 35.4 1.0 OE1 A:GLU324 2.3 18.5 1.0 O A:HOH410 2.4 19.8 1.0 O A:HOH409 2.4 23.1 1.0 OD2 A:ASP355 2.6 19.9 1.0 OD1 A:ASP355 2.6 17.4 1.0 CG A:ASP355 2.9 17.7 1.0 CD A:GLU353 3.1 30.2 1.0 CD A:GLU324 3.5 17.2 1.0 CG A:GLU353 3.9 29.0 1.0 CA A:CA405 3.9 15.3 1.0 OE1 A:GLU353 4.0 32.8 1.0 OD1 A:ASN350 4.1 17.6 1.0 CB A:GLU324 4.1 17.5 1.0 CG A:GLU324 4.2 18.4 1.0 CB A:ASP355 4.4 16.5 1.0 O A:HOH474 4.4 37.4 1.0 OE2 A:GLU324 4.5 17.2 1.0 O A:ASP320 4.5 18.6 1.0 O A:HOH490 4.6 43.6 1.0 ND2 A:ASN350 4.6 19.4 1.0 CA A:GLU324 4.6 18.4 1.0 OD1 A:ASP320 4.7 15.4 1.0 CG A:ASN350 4.8 18.1 1.0

Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer. Structural Basis For Distinct Ligand-Binding and Targeting Properties of the Receptors Dc-Sign and Dc-Signr Nat.Struct.Mol.Biol. V. 11 591 2004.
ISSN: ISSN 1545-9993
PubMed: 15195147
DOI: 10.1038/NSMB784