Calcium in PDB 2j3f: L-Ficolin Complexed to N-Acetyl-D-Galactosamine

The structure of L-Ficolin Complexed to N-Acetyl-D-Galactosamine, PDB code: 2j3f was solved by V.Garlatti, C.Gaboriaud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	96.825, 96.825, 141.898, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 27.7

The binding sites of Calcium atom in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine (pdb code 2j3f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine, PDB code: 2j3f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine


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 N-Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1289 b:58.0 occ:1.00 O A:ASN228 2.3 54.5 1.0 OD1 A:ASP224 2.4 57.9 1.0 OD1 A:ASP226 2.4 54.9 1.0 CG A:ASP226 3.0 52.7 1.0 O A:GLY230 3.1 52.7 1.0 CG A:ASP224 3.1 56.7 1.0 OD2 A:ASP226 3.2 51.9 1.0 C A:ASN228 3.3 52.8 1.0 OD2 A:ASP224 3.3 57.7 1.0 CA A:THR229 3.8 53.8 1.0 N A:GLY230 3.9 53.3 1.0 N A:THR229 3.9 53.7 1.0 C A:GLY230 4.2 53.3 1.0 C A:THR229 4.3 53.4 1.0 N A:ASP226 4.3 48.8 1.0 CB A:ASP226 4.3 50.9 1.0 N A:ASN228 4.4 51.9 1.0 CB A:ASP224 4.4 53.6 1.0 CA A:ASN228 4.4 52.4 1.0 CA A:ASP226 4.6 50.1 1.0 N A:ASN225 4.7 50.1 1.0 O A:ASP226 4.7 51.1 1.0 CA A:GLY230 4.7 52.9 1.0 C A:ASP226 4.8 50.9 1.0 C A:ASP224 5.0 51.3 1.0

Calcium binding site 2 out of 5 in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine


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 N-Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1290 b:30.5 occ:1.00 OD1 B:ASP226 2.3 36.1 1.0 OD1 B:ASP224 2.4 35.2 1.0 O B:ASN228 2.4 37.5 1.0 O B:GLY230 2.5 36.0 1.0 OD2 B:ASP224 2.6 36.0 1.0 O B:HOH2008 2.6 15.3 1.0 CG B:ASP224 2.8 35.6 1.0 CG B:ASP226 3.3 37.6 1.0 C B:ASN228 3.5 37.0 1.0 OD2 B:ASP226 3.6 38.1 1.0 C B:GLY230 3.6 36.3 1.0 N B:ASN228 4.1 37.2 1.0 O B:ASP226 4.1 37.6 1.0 CB B:ASP224 4.2 36.4 1.0 CA B:ASN228 4.2 36.9 1.0 C B:THR229 4.4 37.5 1.0 N B:GLY230 4.4 37.0 1.0 N B:ASP226 4.4 36.7 1.0 C B:ASP226 4.4 37.2 1.0 CB B:ASN228 4.5 37.2 1.0 N B:ASN231 4.5 36.5 1.0 CB B:ASP226 4.5 36.7 1.0 CA B:GLY230 4.5 36.4 1.0 CA B:ASN231 4.6 36.3 1.0 N B:THR229 4.6 37.0 1.0 O B:THR229 4.6 38.1 1.0 CA B:ASP226 4.6 37.0 1.0 CA B:THR229 4.8 37.1 1.0 C B:ASP224 5.0 36.5 1.0

Calcium binding site 3 out of 5 in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine


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 N-Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1290 b:37.3 occ:1.00 OD1 C:ASP226 2.3 37.0 1.0 O C:ASN228 2.3 36.8 1.0 O C:GLY230 2.4 36.8 1.0 OD2 C:ASP224 2.4 36.1 1.0 OD1 C:ASP224 2.6 36.0 1.0 CG C:ASP224 2.8 35.7 1.0 CG C:ASP226 3.1 37.9 1.0 OD2 C:ASP226 3.4 38.1 1.0 C C:ASN228 3.5 37.2 1.0 C C:GLY230 3.5 37.0 1.0 N C:ASN228 4.0 37.6 1.0 CA C:ASN228 4.2 37.4 1.0 CB C:ASP224 4.2 36.2 1.0 O C:ASP226 4.2 38.1 1.0 N C:GLY230 4.3 37.5 1.0 C C:THR229 4.3 37.7 1.0 N C:ASN231 4.4 36.7 1.0 CA C:GLY230 4.4 37.3 1.0 CB C:ASN228 4.4 37.7 1.0 CB C:ASP226 4.5 37.4 1.0 CA C:ASN231 4.5 36.7 1.0 C C:ASP226 4.5 37.5 1.0 N C:THR229 4.5 37.5 1.0 O C:THR229 4.5 38.4 1.0 N C:ASP226 4.5 37.0 1.0 CA C:THR229 4.7 37.9 1.0 CA C:ASP226 4.7 37.4 1.0

Calcium binding site 4 out of 5 in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine


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 N-Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1290 b:33.7 occ:1.00 O E:ASN228 2.3 37.1 1.0 O E:GLY230 2.3 36.0 1.0 OD1 E:ASP226 2.3 36.5 1.0 OD2 E:ASP224 2.4 35.5 1.0 OD1 E:ASP224 2.5 36.3 1.0 O E:HOH2008 2.7 21.8 1.0 CG E:ASP224 2.8 35.7 1.0 CG E:ASP226 3.3 37.6 1.0 C E:ASN228 3.5 37.0 1.0 C E:GLY230 3.5 36.5 1.0 OD2 E:ASP226 3.6 38.1 1.0 N E:ASN228 4.1 37.0 1.0 CA E:ASN228 4.2 36.9 1.0 CB E:ASP224 4.2 36.2 1.0 N E:GLY230 4.2 37.3 1.0 C E:THR229 4.2 37.4 1.0 O E:ASP226 4.3 37.9 1.0 N E:ASN231 4.4 36.6 1.0 CA E:GLY230 4.4 36.7 1.0 CB E:ASN228 4.4 37.2 1.0 CA E:ASN231 4.4 36.1 1.0 O E:THR229 4.5 38.2 1.0 N E:THR229 4.5 36.9 1.0 C E:ASP226 4.5 37.2 1.0 N E:ASP226 4.5 36.8 1.0 CB E:ASP226 4.6 36.8 1.0 CA E:THR229 4.7 37.1 1.0 CA E:ASP226 4.7 37.0 1.0

Calcium binding site 5 out of 5 in the L-Ficolin Complexed to N-Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of L-Ficolin Complexed to N-Acetyl-D-Galactosamine within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1290 b:37.2 occ:1.00 O F:GLY230 2.3 36.9 1.0 O F:ASN228 2.3 37.3 1.0 OD1 F:ASP226 2.3 37.0 1.0 OD2 F:ASP224 2.4 36.0 1.0 OD1 F:ASP224 2.4 36.5 1.0 CG F:ASP224 2.7 35.8 1.0 CG F:ASP226 3.1 37.9 1.0 OD2 F:ASP226 3.3 37.5 1.0 C F:GLY230 3.4 37.2 1.0 C F:ASN228 3.5 37.5 1.0 N F:ASN228 4.1 37.8 1.0 CB F:ASP224 4.2 36.2 1.0 CA F:ASN228 4.2 37.7 1.0 N F:GLY230 4.2 37.5 1.0 C F:THR229 4.3 37.6 1.0 O F:ASP226 4.3 38.1 1.0 N F:ASN231 4.3 36.9 1.0 CA F:GLY230 4.4 37.1 1.0 CA F:ASN231 4.4 36.4 1.0 CB F:ASN228 4.4 37.5 1.0 CB F:ASP226 4.5 37.4 1.0 O F:THR229 4.5 38.0 1.0 N F:THR229 4.5 37.5 1.0 N F:ASP226 4.5 37.0 1.0 C F:ASP226 4.5 37.6 1.0 CA F:THR229 4.7 37.8 1.0 CA F:ASP226 4.7 37.4 1.0

V.Garlatti, N.Belloy, L.Martin, M.Lacroix, M.Matsushita, Y.Endo, T.Fujita, J.C.Fontecilla-Camps, G.J.Arlaud, N.M.Thielens, C.Gaboriaud. Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins. Embo J. V. 26 623 2007.
ISSN: ISSN 0261-4189
PubMed: 17215869
DOI: 10.1038/SJ.EMBOJ.7601500