Calcium in PDB 4nyt: L-Ficolin Complexed to Phosphocholine

The structure of L-Ficolin Complexed to Phosphocholine, PDB code: 4nyt was solved by E.Laffly, C.Gaboriaud, L.Martin, N.Thielens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.130, 96.130, 139.880, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.3

The binding sites of Calcium atom in the L-Ficolin Complexed to Phosphocholine (pdb code 4nyt). 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 Phosphocholine, PDB code: 4nyt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the L-Ficolin Complexed to Phosphocholine


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 Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca306 b:20.5 occ:1.00 O C:GLY230 2.1 22.0 0.0 OD1 C:ASP226 2.2 19.6 1.0 O C:HOH412 2.2 18.8 1.0 O C:ASN228 2.2 22.2 1.0 OD2 C:ASP224 2.3 23.8 1.0 O C:HOH411 2.4 15.7 1.0 OD1 C:ASP224 2.5 23.1 1.0 CG C:ASP224 2.7 23.1 1.0 CG C:ASP226 3.1 19.2 1.0 C C:GLY230 3.2 22.4 1.0 C C:ASN228 3.4 23.8 1.0 OD2 C:ASP226 3.4 19.0 1.0 O C:ASP226 4.1 21.5 1.0 CA C:GLY230 4.1 24.1 1.0 CA C:ASN228 4.2 23.9 1.0 N C:ASN228 4.2 23.3 1.0 N C:ASN231 4.2 22.5 1.0 CB C:ASP224 4.2 22.1 1.0 N C:GLY230 4.3 24.4 1.0 C C:THR229 4.3 25.2 1.0 CB C:ASN228 4.3 23.8 1.0 N C:THR229 4.3 25.3 1.0 C C:ASP226 4.4 21.0 1.0 CB C:ASP226 4.5 18.9 1.0 O C:HOH430 4.5 23.9 1.0 CA C:ASN231 4.5 21.7 1.0 N C:ASP226 4.5 19.5 1.0 CA C:THR229 4.6 26.5 1.0 O C:THR229 4.6 25.9 0.0 CA C:ASP226 4.7 19.5 1.0

Calcium binding site 2 out of 4 in the L-Ficolin Complexed to Phosphocholine


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 Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:38.1 occ:1.00 O A:HOH425 2.0 25.9 1.0 O A:GLY230 2.1 37.3 0.0 OD2 A:ASP224 2.3 41.7 1.0 OD1 A:ASP226 2.3 41.6 1.0 O A:ASN228 2.4 45.6 1.0 OD1 A:ASP224 2.6 44.9 1.0 CG A:ASP224 2.8 42.0 1.0 CG A:ASP226 3.1 39.5 1.0 C A:GLY230 3.3 36.1 1.0 OD2 A:ASP226 3.3 36.4 1.0 C A:ASN228 3.4 46.5 1.0 N A:ASN228 3.9 47.9 1.0 O A:ASP226 3.9 47.4 1.0 CA A:ASN228 4.0 46.9 1.0 CA A:GLY230 4.1 38.3 1.0 C A:THR229 4.2 44.5 1.0 N A:GLY230 4.2 41.1 1.0 CB A:ASN228 4.2 45.2 1.0 N A:ASN231 4.3 33.6 1.0 O A:THR229 4.3 45.7 0.0 CB A:ASP224 4.4 41.0 1.0 C A:ASP226 4.4 45.7 1.0 N A:THR229 4.4 47.3 1.0 CB A:ASP226 4.5 39.3 1.0 CA A:ASN231 4.6 31.8 1.0 N A:ASP226 4.7 43.9 1.0 CA A:ASP226 4.7 43.2 1.0 CA A:THR229 4.7 48.4 1.0

Calcium binding site 3 out of 4 in the L-Ficolin Complexed to Phosphocholine


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 Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:46.6 occ:1.00 O A:HOH428 2.2 23.6 1.0 O A:ASP222 2.3 39.7 1.0 C A:ASP222 3.5 37.5 1.0 CA A:ASP222 4.3 34.7 1.0 CB A:ASP222 4.4 35.4 1.0 N A:GLN223 4.5 38.0 1.0 CA A:GLN223 4.6 41.1 1.0 O A:HOH424 4.8 45.2 1.0 OD2 A:ASP222 4.9 37.8 1.0 CG A:ASP222 5.0 35.2 1.0

Calcium binding site 4 out of 4 in the L-Ficolin Complexed to Phosphocholine


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 Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:67.8 occ:1.00 OD2 B:ASP224 2.1 0.9 1.0 O B:ASN228 2.5 0.8 1.0 O B:GLY230 2.6 0.2 0.0 OD1 B:ASP226 2.8 0.1 1.0 CG B:ASP224 2.9 0.5 1.0 OD1 B:ASP224 3.0 0.0 1.0 O B:ASP226 3.1 0.9 1.0 C B:ASN228 3.6 0.4 1.0 C B:GLY230 3.7 0.2 1.0 CG B:ASP226 3.9 0.7 1.0 N B:ASN228 4.1 0.5 1.0 C B:ASP226 4.2 0.2 1.0 CB B:ASP224 4.3 0.4 1.0 CA B:ASN228 4.3 0.9 1.0 C B:THR229 4.5 0.5 1.0 CA B:GLY230 4.5 0.3 1.0 N B:GLY230 4.5 1.0 1.0 O B:THR229 4.5 0.1 0.0 OD2 B:ASP226 4.6 0.4 1.0 CB B:ASN228 4.6 0.6 1.0 N B:THR229 4.7 0.2 1.0 N B:ASN231 4.7 0.3 1.0 C B:LEU227 4.8 0.7 1.0 CA B:ASN231 4.9 0.0 1.0 CB B:ASP226 4.9 1.0 1.0 O B:ASP224 4.9 0.6 1.0 CA B:ASP226 5.0 0.1 1.0 CA B:THR229 5.0 0.4 1.0

E.Vassal-Stermann, M.Lacroix, E.Gout, E.Laffly, C.M.Pedersen, L.Martin, A.Amoroso, R.R.Schmidt, U.Zahringer, C.Gaboriaud, A.-M.Di Guilmi, N.M.Thielens. Human L-Ficolin Recognizes Phosphocholine Moieties of Pneumococcal Teichoic Acid J.Immunol. 2014.
ISSN: ISSN 0022-1767
DOI: 10.4049/JIMMUNOL.1400127