Calcium in PDB 2j3g: L-Ficolin

The structure of L-Ficolin, PDB code: 2j3g 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 / 2.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	98.890, 98.890, 141.975, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 25.9

The binding sites of Calcium atom in the L-Ficolin (pdb code 2j3g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the L-Ficolin, PDB code: 2j3g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the L-Ficolin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of L-Ficolin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1289 b:76.6 occ:1.00 O A:ASN228 2.3 70.1 1.0 O A:HOH2017 2.4 40.2 1.0 OD2 A:ASP226 2.7 72.5 1.0 OD1 A:ASP224 2.7 75.6 1.0 OD2 A:ASP224 3.1 74.3 1.0 O A:GLY230 3.1 71.8 1.0 O A:THR229 3.2 69.4 1.0 CG A:ASP224 3.3 74.7 1.0 C A:THR229 3.4 70.0 1.0 C A:ASN228 3.4 70.8 1.0 CG A:ASP226 3.5 72.1 1.0 C A:GLY230 3.6 71.3 1.0 OD1 A:ASP226 3.6 71.2 1.0 N A:GLY230 3.8 70.3 1.0 CA A:THR229 3.9 70.2 1.0 CA A:GLY230 4.0 70.9 1.0 N A:THR229 4.1 70.3 1.0 N A:ASN231 4.3 71.0 1.0 CA A:ASN228 4.5 71.4 1.0 CA A:ASN231 4.5 70.8 1.0 O A:ASP226 4.5 71.0 1.0 N A:ASN228 4.7 71.7 1.0 CB A:ASP224 4.7 73.8 1.0 C A:ASP226 4.9 71.6 1.0 CB A:ASP226 4.9 71.9 1.0 CB A:ASN228 4.9 71.5 1.0

Calcium binding site 2 out of 6 in the L-Ficolin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of L-Ficolin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1289 b:36.7 occ:1.00 OD2 B:ASP224 2.2 35.2 1.0 O B:ASN228 2.3 33.6 1.0 OD2 B:ASP226 2.3 31.9 1.0 O B:GLY230 2.4 33.0 1.0 CG B:ASP224 2.9 32.7 1.0 OD1 B:ASP224 3.0 34.7 1.0 CG B:ASP226 3.4 30.7 1.0 C B:ASN228 3.5 34.4 1.0 C B:GLY230 3.5 32.8 1.0 OD1 B:ASP226 3.7 29.7 1.0 C B:THR229 4.0 34.1 1.0 O B:THR229 4.1 35.8 1.0 N B:GLY230 4.2 33.2 1.0 N B:ASN228 4.2 34.1 1.0 CA B:ASN228 4.4 34.4 1.0 CB B:ASP224 4.4 32.0 1.0 N B:THR229 4.4 34.5 1.0 CA B:GLY230 4.4 32.7 1.0 CA B:THR229 4.4 34.4 1.0 O B:ASP226 4.5 31.7 1.0 N B:ASN231 4.5 32.2 1.0 CA B:ASN231 4.6 31.6 1.0 C B:ASP226 4.7 31.2 1.0 CB B:ASP226 4.7 30.2 1.0 CB B:ASN228 4.7 34.7 1.0 N B:ASP226 4.7 28.8 1.0 CA B:ASP226 4.9 29.9 1.0

Calcium binding site 3 out of 6 in the L-Ficolin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of L-Ficolin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1289 b:37.1 occ:1.00 OD1 C:ASP226 2.2 30.1 1.0 OD2 C:ASP224 2.3 34.9 1.0 O C:GLY230 2.4 33.0 1.0 O C:ASN228 2.5 33.6 1.0 O C:HOH2037 2.5 28.3 1.0 OD1 C:ASP224 2.7 34.1 1.0 CG C:ASP224 2.8 32.7 1.0 CG C:ASP226 3.2 31.0 1.0 OD2 C:ASP226 3.4 32.1 1.0 C C:GLY230 3.6 32.8 1.0 C C:ASN228 3.6 34.4 1.0 C C:THR229 4.1 34.1 1.0 N C:GLY230 4.3 33.2 1.0 O C:THR229 4.3 35.8 1.0 N C:ASN228 4.3 34.1 1.0 CB C:ASP224 4.3 32.2 1.0 O C:ASP226 4.4 31.7 1.0 CA C:ASN228 4.5 34.4 1.0 N C:ASN231 4.5 32.2 1.0 CA C:GLY230 4.5 32.7 1.0 CB C:ASP226 4.5 30.3 1.0 N C:THR229 4.5 34.5 1.0 CA C:ASN231 4.6 31.5 1.0 O C:HOH2026 4.6 39.5 1.0 CA C:THR229 4.6 34.5 1.0 N C:ASP226 4.6 28.8 1.0 C C:ASP226 4.6 31.2 1.0 CB C:ASN228 4.8 34.8 1.0 CA C:ASP226 4.8 29.9 1.0

Calcium binding site 4 out of 6 in the L-Ficolin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of L-Ficolin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1289 b:60.2 occ:1.00 O D:ASN228 2.2 57.6 1.0 O D:GLY230 2.3 57.1 1.0 OD2 D:ASP226 2.4 51.6 1.0 OD2 D:ASP224 2.4 54.4 1.0 OD1 D:ASP224 2.8 56.0 1.0 CG D:ASP224 2.9 54.5 1.0 C D:ASN228 3.4 57.6 1.0 CG D:ASP226 3.5 52.2 1.0 C D:GLY230 3.5 57.2 1.0 O D:THR229 3.5 59.6 1.0 C D:THR229 3.8 59.3 1.0 OD1 D:ASP226 3.9 52.2 1.0 N D:GLY230 4.1 59.2 1.0 O D:ASP226 4.1 55.2 1.0 N D:ASN228 4.3 57.1 1.0 CA D:GLY230 4.3 58.0 1.0 N D:THR229 4.3 58.8 1.0 CB D:ASP224 4.3 53.9 1.0 CA D:ASN228 4.4 57.0 1.0 CA D:THR229 4.4 59.2 1.0 N D:ASN231 4.5 56.2 1.0 C D:ASP226 4.6 54.8 1.0 CA D:ASN231 4.6 55.3 1.0 N D:ASP226 4.7 52.5 1.0 CB D:ASN228 4.7 56.5 1.0 CB D:ASP226 4.7 53.2 1.0 CA D:ASP226 4.9 53.6 1.0

Calcium binding site 5 out of 6 in the L-Ficolin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of L-Ficolin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1289 b:28.4 occ:1.00 O E:ASN228 2.3 33.6 1.0 OD2 E:ASP226 2.3 31.9 1.0 O E:GLY230 2.3 33.0 1.0 OD2 E:ASP224 2.4 35.2 1.0 O E:HOH2038 2.5 14.6 1.0 OD1 E:ASP224 2.7 34.7 1.0 CG E:ASP224 2.9 32.6 1.0 CG E:ASP226 3.3 30.7 1.0 C E:ASN228 3.5 34.4 1.0 C E:GLY230 3.6 32.8 1.0 OD1 E:ASP226 3.7 29.9 1.0 C E:THR229 4.1 34.1 1.0 N E:ASN228 4.2 34.1 1.0 O E:HOH2037 4.2 30.2 1.0 N E:GLY230 4.2 33.2 1.0 O E:THR229 4.2 35.8 1.0 CA E:ASN228 4.3 34.4 1.0 O E:ASP226 4.4 31.7 1.0 N E:THR229 4.4 34.5 1.0 CB E:ASP224 4.4 32.1 1.0 CA E:GLY230 4.4 32.8 1.0 N E:ASN231 4.5 32.2 1.0 CA E:THR229 4.5 34.4 1.0 CB E:ASN228 4.6 34.6 1.0 CA E:ASN231 4.6 31.6 1.0 C E:ASP226 4.6 31.2 1.0 CB E:ASP226 4.6 30.1 1.0 N E:ASP226 4.6 28.8 1.0 CA E:ASP226 4.8 29.9 1.0 OD1 E:ASN228 5.0 36.4 1.0

Calcium binding site 6 out of 6 in the L-Ficolin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of L-Ficolin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1289 b:44.7 occ:1.00 OD2 F:ASP226 2.2 32.2 1.0 OD2 F:ASP224 2.3 34.8 1.0 O F:GLY230 2.3 33.0 1.0 O F:ASN228 2.4 33.6 1.0 OD1 F:ASP224 2.7 34.2 1.0 CG F:ASP224 2.9 32.6 1.0 CG F:ASP226 3.1 31.0 1.0 OD1 F:ASP226 3.4 30.0 1.0 C F:ASN228 3.5 34.4 1.0 C F:GLY230 3.5 32.8 1.0 N F:ASN228 4.1 34.1 1.0 C F:THR229 4.2 34.1 1.0 N F:GLY230 4.2 33.2 1.0 CA F:ASN228 4.3 34.4 1.0 O F:ASP226 4.3 31.7 1.0 O F:THR229 4.3 35.8 1.0 CB F:ASP224 4.4 32.0 1.0 N F:ASN231 4.4 32.2 1.0 CB F:ASP226 4.5 30.2 1.0 CA F:GLY230 4.5 32.7 1.0 N F:THR229 4.5 34.5 1.0 C F:ASP226 4.5 31.2 1.0 N F:ASP226 4.5 28.8 1.0 CA F:ASN231 4.5 31.6 1.0 CA F:THR229 4.6 34.5 1.0 CB F:ASN228 4.6 34.8 1.0 CA F:ASP226 4.7 29.9 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