Calcium in PDB 4r9j: L-Ficolin Complexed to Glucosamine-6-Sulfate

The structure of L-Ficolin Complexed to Glucosamine-6-Sulfate, PDB code: 4r9j was solved by E.Laffly, M.Lacroix, L.Martin, E.Vassal-Stermann, N.Thielens, C.Gaboriaud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.170, 97.170, 139.990, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.3

The binding sites of Calcium atom in the L-Ficolin Complexed to Glucosamine-6-Sulfate (pdb code 4r9j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the L-Ficolin Complexed to Glucosamine-6-Sulfate, PDB code: 4r9j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the L-Ficolin Complexed to Glucosamine-6-Sulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of L-Ficolin Complexed to Glucosamine-6-Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca301 b:11.6 occ:1.00 O G:ASN228 2.3 13.5 1.0 O G:GLY230 2.3 13.4 1.0 OD1 G:ASP226 2.3 11.4 1.0 O G:HOH402 2.3 9.2 1.0 O G:HOH401 2.4 9.6 1.0 OD1 G:ASP224 2.4 11.4 1.0 OD2 G:ASP224 2.4 13.7 1.0 CG G:ASP224 2.8 12.2 1.0 CG G:ASP226 3.1 11.4 1.0 C G:ASN228 3.4 14.6 1.0 OD2 G:ASP226 3.4 12.1 1.0 C G:GLY230 3.5 13.0 1.0 O G:HOH483 4.1 19.7 1.0 N G:ASN228 4.1 13.7 1.0 O G:ASP226 4.2 12.5 1.0 CA G:ASN228 4.2 13.6 1.0 CB G:ASP224 4.2 11.2 1.0 C G:THR229 4.3 15.0 1.0 N G:ASN231 4.3 12.9 1.0 N G:GLY230 4.4 13.4 1.0 CA G:ASN231 4.4 12.7 1.0 N G:THR229 4.4 15.3 1.0 CB G:ASN228 4.4 14.3 1.0 CA G:GLY230 4.4 13.3 1.0 C G:ASP226 4.5 11.5 1.0 CB G:ASP226 4.5 10.6 1.0 O G:THR229 4.5 15.3 1.0 O G:HOH468 4.5 17.6 1.0 CA G:THR229 4.6 16.6 1.0 N G:ASP226 4.6 10.3 1.0 O G:HOH457 4.6 19.6 1.0 CA G:ASP226 4.8 10.8 1.0

Calcium binding site 2 out of 4 in the L-Ficolin Complexed to Glucosamine-6-Sulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of L-Ficolin Complexed to Glucosamine-6-Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:16.1 occ:1.00 OD1 A:ASP226 2.3 13.1 1.0 O A:ASN228 2.3 15.1 1.0 O A:HOH417 2.3 15.9 1.0 O A:GLY230 2.3 17.2 1.0 O A:HOH405 2.3 14.6 1.0 OD2 A:ASP224 2.4 16.6 1.0 OD1 A:ASP224 2.4 16.7 1.0 CG A:ASP224 2.8 17.2 1.0 CG A:ASP226 3.1 14.2 1.0 C A:ASN228 3.4 18.9 1.0 OD2 A:ASP226 3.4 13.2 1.0 C A:GLY230 3.5 16.6 1.0 N A:ASN228 4.0 18.4 1.0 O A:HOH435 4.1 22.5 1.0 CA A:ASN228 4.2 19.2 1.0 O A:ASP226 4.2 17.8 1.0 O A:HOH441 4.3 23.4 1.0 CB A:ASP224 4.3 16.1 1.0 C A:THR229 4.3 20.5 1.0 O A:HOH476 4.3 20.8 1.0 CB A:ASN228 4.3 20.4 1.0 N A:GLY230 4.4 18.6 1.0 N A:THR229 4.4 18.6 1.0 C A:ASP226 4.4 16.2 1.0 O A:THR229 4.4 18.9 1.0 CB A:ASP226 4.4 14.0 1.0 N A:ASN231 4.5 15.1 1.0 CA A:GLY230 4.5 17.1 1.0 CA A:ASN231 4.5 13.1 1.0 N A:ASP226 4.6 15.6 1.0 CA A:THR229 4.7 22.7 1.0 CA A:ASP226 4.7 15.4 1.0

Calcium binding site 3 out of 4 in the L-Ficolin Complexed to Glucosamine-6-Sulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of L-Ficolin Complexed to Glucosamine-6-Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:29.1 occ:1.00 O A:HOH426 2.3 23.4 1.0 O A:HOH425 2.3 24.4 1.0 O A:ASP222 2.4 16.1 1.0 O A:HOH427 2.4 22.3 1.0 C A:ASP222 3.6 15.4 1.0 O A:HOH440 4.2 18.0 1.0 CB A:ASP222 4.3 15.7 1.0 CA A:ASP222 4.4 15.6 1.0 N A:GLN223 4.5 16.3 1.0 CA A:GLN223 4.5 15.5 1.0 O A:HOH424 4.7 12.8 1.0 OD2 A:ASP222 4.8 16.3 1.0 CB A:GLN223 4.8 16.6 1.0 CG A:ASP222 4.9 15.8 1.0

Calcium binding site 4 out of 4 in the L-Ficolin Complexed to Glucosamine-6-Sulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of L-Ficolin Complexed to Glucosamine-6-Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:28.3 occ:1.00 O B:HOH437 2.3 20.8 1.0 O B:GLY230 2.3 32.8 1.0 OD1 B:ASP226 2.3 26.5 1.0 O B:HOH444 2.3 31.3 1.0 O B:ASN228 2.3 34.1 1.0 OD2 B:ASP224 2.3 35.6 1.0 OD1 B:ASP224 2.4 33.1 1.0 CG B:ASP224 2.7 33.1 1.0 CG B:ASP226 3.1 27.2 1.0 OD2 B:ASP226 3.4 27.1 1.0 C B:ASN228 3.4 38.5 1.0 C B:GLY230 3.5 34.4 1.0 N B:ASN228 4.0 37.8 1.0 CA B:ASN228 4.1 38.2 1.0 CB B:ASP224 4.2 30.5 1.0 O B:ASP226 4.3 28.3 1.0 C B:THR229 4.3 42.2 1.0 O B:THR229 4.3 36.8 1.0 CB B:ASN228 4.3 39.5 1.0 N B:ASN231 4.4 33.6 1.0 N B:THR229 4.4 39.0 1.0 N B:GLY230 4.4 36.0 1.0 CA B:ASN231 4.4 31.6 1.0 CB B:ASP226 4.4 26.0 1.0 C B:ASP226 4.5 29.5 1.0 CA B:GLY230 4.5 36.9 1.0 N B:ASP226 4.6 25.2 1.0 CA B:ASP226 4.7 27.0 1.0 CA B:THR229 4.7 40.7 1.0

E.Laffly, M.Lacroix, L.Martin, E.Vassal-Stermann, N.Thielens, C.Gaboriaud. Human Ficolin-2 Recognition Versatility Extended: An Update on Its Binding to Sulphated/Phosphated Carbohydrates. Febs Lett. 2014.
ISSN: ISSN 0014-5793