Calcium in PDB 4caj: Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid

The structure of Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid, PDB code: 4caj was solved by N.Silva-Martin, S.G.Bartual, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.948 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.200, 94.470, 76.140, 90.00, 121.42, 90.00
R / Rfree (%)	20.53 / 28.12

The structure of Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid (pdb code 4caj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid, PDB code: 4caj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1323 b:55.8 occ:1.00 OD1 A:ASN287 2.4 77.2 1.0 OE1 A:GLU292 2.5 50.0 1.0 O A:HOH2077 2.5 36.2 1.0 OD1 A:ASP304 2.7 42.3 1.0 OE2 A:GLU285 2.7 43.3 1.0 O A:ASP304 2.8 40.9 1.0 OE1 A:GLU285 3.1 40.9 1.0 CG A:ASN287 3.2 48.5 1.0 CD A:GLU285 3.3 41.7 1.0 ND2 A:ASN287 3.4 50.0 1.0 CD A:GLU292 3.4 53.5 1.0 OE2 A:GLU292 3.6 48.3 1.0 CG A:ASP304 3.9 56.9 1.0 C A:ASP304 3.9 47.6 1.0 OD1 A:ASN288 4.0 53.1 1.0 N A:ASP304 4.3 48.1 1.0 O A:HOH2079 4.5 50.0 1.0 CA A:ASP304 4.6 42.2 1.0 CB A:ASN287 4.6 52.2 1.0 CB A:ASN303 4.7 41.7 1.0 N A:ASN287 4.7 45.4 1.0 OD2 A:ASP304 4.7 43.2 1.0 CG A:GLU292 4.8 47.3 1.0 CG A:GLU285 4.8 41.1 1.0 CB A:ASP304 4.9 55.6 1.0 ND2 A:ASN303 5.0 40.5 1.0 CG A:ASN288 5.0 58.9 1.0 O A:HOH2076 5.0 52.7 1.0

Calcium binding site 2 out of 4 in the Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1325 b:75.5 occ:1.00 OD1 B:ASP304 2.1 42.5 1.0 OE1 B:GLU292 2.2 58.8 1.0 O B:ASP304 2.4 45.0 1.0 OD1 B:ASN287 2.4 77.2 1.0 OE1 B:GLU285 2.4 42.6 1.0 O1B B:SIA1329 2.9 80.2 1.0 O1A B:SIA1329 3.0 49.2 1.0 CD B:GLU285 3.2 43.8 1.0 OE2 B:GLU285 3.2 43.6 1.0 CG B:ASP304 3.2 51.0 1.0 CD B:GLU292 3.4 48.8 1.0 C B:ASP304 3.4 44.3 1.0 C1 B:SIA1329 3.4 82.9 1.0 CG B:ASN287 3.5 47.7 1.0 N B:ASP304 3.7 39.3 1.0 CA B:ASP304 3.9 46.8 1.0 OE2 B:GLU292 3.9 58.0 1.0 ND2 B:ASN287 4.0 49.3 1.0 OD2 B:ASP304 4.0 45.0 1.0 CB B:ASP304 4.2 49.4 1.0 N B:ASN287 4.3 46.0 1.0 CB B:GLU292 4.4 49.8 1.0 CB B:ASN303 4.5 39.2 1.0 CG B:GLU292 4.5 49.4 1.0 OD1 B:ASN288 4.5 59.0 1.0 N B:SER305 4.5 51.2 1.0 O B:ASN287 4.6 69.4 1.0 CG B:GLU285 4.7 53.5 1.0 C B:ASN303 4.7 53.8 1.0 CB B:ASN287 4.7 54.3 1.0 C B:ASN287 4.8 58.0 1.0 CA B:ASN303 4.8 38.1 1.0 CA B:ASN287 4.8 52.6 1.0 C2 B:SIA1329 4.9 0.4 1.0 CA B:SER305 4.9 51.5 1.0

Calcium binding site 3 out of 4 in the Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1323 b:76.5 occ:1.00 O1B C:SIA1328 2.2 53.1 1.0 OD1 C:ASP304 2.4 41.0 1.0 OE1 C:GLU292 2.4 52.1 1.0 OE1 C:GLU285 2.4 40.4 1.0 OD1 C:ASN287 2.5 73.7 1.0 O C:ASP304 2.7 40.3 1.0 O1A C:SIA1328 2.9 42.9 1.0 C1 C:SIA1328 2.9 54.1 1.0 OE2 C:GLU285 2.9 40.9 1.0 CD C:GLU285 3.0 40.4 1.0 O C:HOH2095 3.4 28.3 1.0 CD C:GLU292 3.4 50.1 1.0 CG C:ASN287 3.5 49.2 1.0 CG C:ASP304 3.6 57.8 1.0 OE2 C:GLU292 3.7 43.5 1.0 C C:ASP304 3.7 40.8 1.0 ND2 C:ASN287 3.8 44.8 1.0 N C:ASP304 3.9 52.6 1.0 CA C:ASP304 4.2 39.5 1.0 C2 C:SIA1328 4.3 79.3 1.0 CB C:ASN303 4.3 38.6 1.0 OD2 C:ASP304 4.4 41.7 1.0 N C:ASN287 4.5 42.6 1.0 CG C:GLU285 4.5 39.9 1.0 CB C:ASP304 4.5 52.2 1.0 OD1 C:ASN288 4.6 55.2 1.0 CG C:GLU292 4.7 43.4 1.0 C C:ASN303 4.8 58.5 1.0 CB C:ASN287 4.8 47.1 1.0 CG C:ASN303 4.8 38.8 1.0 N C:SER305 4.8 40.0 1.0 CA C:ASN303 4.8 42.9 1.0 O6 C:SIA1328 4.8 48.9 1.0 CB C:GLU292 4.9 46.6 1.0 ND2 C:ASN303 4.9 39.3 1.0

Calcium binding site 4 out of 4 in the Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystallographic Structure of the Mouse Sign-R1 Crd Domain in Complex with Sialic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1323 b:80.0 occ:1.00 OD1 D:ASP304 2.2 42.1 1.0 OD1 D:ASN287 2.3 77.8 1.0 OE1 D:GLU292 2.4 63.3 1.0 OE1 D:GLU285 2.4 48.6 1.0 O D:HOH2083 2.5 19.1 1.0 O D:ASP304 2.6 43.2 1.0 OE2 D:GLU285 3.0 42.5 1.0 CD D:GLU285 3.1 48.9 1.0 CG D:ASN287 3.4 46.1 1.0 CD D:GLU292 3.4 48.8 1.0 CG D:ASP304 3.4 54.5 1.0 C D:ASP304 3.6 48.3 1.0 O D:HOH2093 3.7 38.7 1.0 N D:ASP304 3.8 42.4 1.0 OE2 D:GLU292 3.9 56.2 1.0 ND2 D:ASN287 3.9 46.9 1.0 N D:ASN287 4.1 44.3 1.0 CA D:ASP304 4.1 47.8 1.0 OD1 D:ASN288 4.1 64.8 1.0 OD2 D:ASP304 4.3 47.4 1.0 O D:ASN287 4.3 65.6 1.0 CB D:ASP304 4.4 52.8 1.0 CG D:GLU285 4.6 54.4 1.0 CG D:GLU292 4.6 44.8 1.0 CB D:GLU292 4.6 45.4 1.0 CB D:ASN287 4.6 46.9 1.0 CB D:ASN303 4.6 39.2 1.0 C D:ASN287 4.6 63.1 1.0 CA D:ASN287 4.7 50.0 1.0 N D:SER305 4.7 51.5 1.0 C D:ASN303 4.8 50.3 1.0 CA D:ASN303 4.9 38.8 1.0

N.Silva-Martin, S.G.Bartual, A.Rodriguez, E.Ramirez, P.Chacon, R.M.Anthony, C.G.Park, J.A.Hermoso. Structural Basis For Selective Recognition of Endogenous and Microbial Polysaccharides By Macrophage Receptor Sign-R1 Structure 2014.
ISSN: ESSN 1878-4186
DOI: 10.1016/J.STR.2014.09.001