Calcium in PDB 1sl5: Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504).

The structure of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504)., PDB code: 1sl5 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)	44.02 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.570, 55.370, 29.630, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.3

The structure of Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504). also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504). (pdb code 1sl5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504)., PDB code: 1sl5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504).


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 Lnfp III (Dextra L504). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.5 occ:1.00 O A:HOH407 2.2 7.8 1.0 OE1 A:GLU324 2.4 15.3 1.0 OD1 A:ASN350 2.4 16.2 1.0 OE2 A:GLU324 2.5 14.3 1.0 OD2 A:ASP320 2.5 13.7 1.0 OD1 A:ASP355 2.5 12.5 1.0 O A:GLU354 2.5 12.0 1.0 OD1 A:ASP320 2.7 16.7 1.0 CD A:GLU324 2.8 15.3 1.0 CG A:ASP320 2.9 15.4 1.0 CG A:ASN350 3.2 16.3 1.0 C A:GLU354 3.4 13.0 1.0 CG A:ASP355 3.6 13.2 1.0 CA A:ASP355 3.7 11.0 1.0 CB A:ASN350 3.9 16.1 1.0 N A:ASP355 3.9 12.2 1.0 O A:HOH405 4.1 12.8 1.0 CB A:ASP355 4.1 12.4 1.0 ND2 A:ASN350 4.1 15.7 1.0 O A:HOH461 4.1 25.5 1.0 CZ2 A:TRP327 4.2 12.4 1.0 N A:GLU354 4.2 12.4 1.0 CG A:GLU324 4.3 17.2 1.0 O A:HOH404 4.3 14.8 1.0 CB A:ASP320 4.5 16.3 1.0 CA A:GLU354 4.5 12.3 1.0 CA A:ASN350 4.5 16.6 1.0 OD2 A:ASP355 4.6 13.8 1.0 OD2 A:ASP366 4.6 13.9 1.0 CH2 A:TRP327 4.7 10.9 1.0 O A:ASP320 4.8 16.8 1.0 N A:GLY325 4.9 19.3 1.0 CA A:GLU324 4.9 20.1 1.0 C A:ASP355 5.0 10.6 1.0 CE2 A:TRP327 5.0 10.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Dc-Sign Carbohydrate Recognition Domain Complexed with Lnfp III (Dextra L504).


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 Lnfp III (Dextra L504). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:11.8 occ:1.00 OD1 A:ASN349 2.3 12.7 1.0 OD1 A:ASP366 2.3 11.7 1.0 OE1 A:GLU354 2.3 13.3 1.0 O4 A:FUC3 2.4 11.7 1.0 OD1 A:ASN365 2.4 11.4 1.0 O A:ASP366 2.5 12.2 1.0 O3 A:FUC3 2.5 12.5 1.0 OE1 A:GLU347 2.5 12.7 1.0 C4 A:FUC3 3.3 10.6 1.0 C3 A:FUC3 3.3 12.1 1.0 CG A:ASN349 3.3 12.8 1.0 CG A:ASP366 3.3 12.4 1.0 CD A:GLU354 3.3 16.9 1.0 CD A:GLU347 3.4 13.3 1.0 CG A:ASN365 3.5 10.5 1.0 C A:ASP366 3.6 10.7 1.0 ND2 A:ASN349 3.7 9.4 1.0 C2 A:FUC3 3.7 12.5 1.0 N A:ASP366 3.7 10.8 1.0 OE2 A:GLU347 3.8 12.8 1.0 OE2 A:GLU354 3.8 19.4 1.0 ND2 A:ASN365 3.9 9.4 1.0 OD2 A:ASP366 4.0 13.9 1.0 CA A:ASP366 4.1 11.3 1.0 N A:ASN349 4.1 14.1 1.0 CB A:ASP366 4.3 12.5 1.0 O2 A:FUC3 4.5 12.3 1.0 CB A:ASN349 4.6 14.2 1.0 CG A:GLU354 4.6 15.3 1.0 N A:ASN350 4.6 16.5 1.0 C5 A:FUC3 4.6 14.1 1.0 N A:ASP367 4.7 9.7 1.0 CB A:GLU354 4.7 13.9 1.0 C A:ASN365 4.7 11.9 1.0 CG A:GLU347 4.7 11.7 1.0 CA A:ASN349 4.8 14.5 1.0 CB A:ASN365 4.8 9.7 1.0 O5 A:FUC3 4.8 14.7 1.0 C1 A:FUC3 4.9 13.3 1.0 CA A:ASP367 5.0 8.2 1.0 CA A:ASN365 5.0 10.5 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