Calcium in PDB 4c9f: Structure of Sign-R1 in Complex with Sulfodextran

The structure of Structure of Sign-R1 in Complex with Sulfodextran, PDB code: 4c9f was solved by N.Silva-Martin, S.G.Bartual, A.Rodriguez, E.Ramirez, P.Chacon, R.M.Anthony, C.G.Park, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.025, 97.959, 73.846, 90.00, 120.86, 90.00
R / Rfree (%)	19.107 / 23.265

The binding sites of Calcium atom in the Structure of Sign-R1 in Complex with Sulfodextran (pdb code 4c9f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Sign-R1 in Complex with Sulfodextran, PDB code: 4c9f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Sign-R1 in Complex with Sulfodextran


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Sign-R1 in Complex with Sulfodextran within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:56.2 occ:1.00 OD1 A:ASP304 2.1 33.0 1.0 OD1 A:ASN287 2.5 35.6 1.0 OE1 A:GLU285 2.6 29.7 1.0 OE1 A:GLU292 2.7 34.6 1.0 O A:ASP304 2.7 32.6 1.0 O5A A:GQ21324 3.1 0.4 1.0 OE2 A:GLU285 3.1 27.6 1.0 CD A:GLU285 3.2 30.6 1.0 C1A A:GQ21324 3.3 87.6 1.0 CG A:ASP304 3.3 35.2 1.0 CG A:ASN287 3.4 30.0 1.0 C A:ASP304 3.7 32.3 1.0 C2A A:GQ21324 3.7 83.2 1.0 ND2 A:ASN287 3.8 30.6 1.0 CD A:GLU292 3.8 31.2 1.0 N A:ASP304 3.8 32.8 1.0 CA A:ASP304 4.0 32.2 1.0 N A:ASN287 4.1 33.1 1.0 OD2 A:ASP304 4.1 38.8 1.0 O A:ASN287 4.2 36.4 1.0 CB A:ASP304 4.2 33.9 1.0 OE2 A:GLU292 4.3 32.4 1.0 C5A A:GQ21324 4.5 0.2 1.0 CB A:ASN287 4.5 31.9 1.0 C A:ASN287 4.5 34.2 1.0 O2A A:GQ21324 4.5 70.8 1.0 O1A A:GQ21324 4.6 84.4 1.0 CA A:ASN287 4.6 33.1 1.0 CG A:GLU285 4.7 31.1 1.0 CB A:ASN303 4.7 29.6 1.0 N A:SER305 4.8 30.2 1.0 C A:ASN303 4.8 32.6 1.0 CB A:GLU292 4.9 31.2 1.0 ND2 A:ASN288 4.9 42.7 1.0 C3A A:GQ21324 4.9 0.5 1.0 CG A:GLU292 5.0 29.4 1.0 CA A:ASN303 5.0 31.1 1.0

Calcium binding site 2 out of 4 in the Structure of Sign-R1 in Complex with Sulfodextran


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Sign-R1 in Complex with Sulfodextran within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:50.2 occ:1.00 OE1 B:GLU292 2.4 35.6 1.0 OD1 B:ASN287 2.4 37.4 1.0 OD1 B:ASP304 2.4 29.5 1.0 O4A B:GQ21329 2.5 56.7 1.0 OE1 B:GLU285 2.6 26.7 1.0 O B:ASP304 2.6 32.1 1.0 CG B:ASN287 3.3 32.4 1.0 CG B:ASP304 3.4 30.9 1.0 C4A B:GQ21329 3.4 64.0 1.0 C B:ASP304 3.5 27.8 1.0 CD B:GLU285 3.5 27.6 1.0 CD B:GLU292 3.5 35.1 1.0 OE2 B:GLU285 3.6 26.8 1.0 N B:ASP304 3.6 29.6 1.0 ND2 B:ASN287 3.8 29.8 1.0 CA B:ASP304 3.8 28.9 1.0 N B:ASN287 4.0 29.6 1.0 OE2 B:GLU292 4.0 34.3 1.0 O B:ASN287 4.1 29.7 1.0 C6A B:GQ21329 4.2 72.6 1.0 CB B:ASP304 4.2 31.6 1.0 C5A B:GQ21329 4.2 74.2 1.0 OD2 B:ASP304 4.3 31.1 1.0 C B:ASN287 4.4 32.6 1.0 C3A B:GQ21329 4.5 68.1 1.0 ND2 B:ASN288 4.5 46.6 1.0 CB B:GLU292 4.5 38.1 1.0 CB B:ASN287 4.5 31.2 1.0 N B:SER305 4.6 26.6 1.0 CA B:ASN287 4.6 30.4 1.0 CG B:GLU292 4.6 37.0 1.0 O3A B:GQ21329 4.7 65.2 1.0 C B:ASN303 4.7 28.8 1.0 CB B:ASN303 4.9 25.6 1.0 CG B:GLU285 4.9 27.8 1.0 C B:PRO286 4.9 30.0 1.0 CA B:PRO286 4.9 30.4 1.0

Calcium binding site 3 out of 4 in the Structure of Sign-R1 in Complex with Sulfodextran


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Sign-R1 in Complex with Sulfodextran within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:54.4 occ:1.00 OD1 C:ASP304 2.3 27.1 1.0 OD1 C:ASN287 2.4 33.3 1.0 O C:ASP304 2.5 30.4 1.0 OE1 C:GLU285 2.5 29.8 1.0 OE1 C:GLU292 2.6 35.0 1.0 OE2 C:GLU285 3.1 25.7 1.0 CD C:GLU285 3.2 27.4 1.0 O5A C:GQ41325 3.3 92.9 1.0 C1A C:GQ41325 3.4 79.3 1.0 CG C:ASP304 3.4 31.8 1.0 CG C:ASN287 3.5 29.1 1.0 C C:ASP304 3.5 28.2 1.0 N C:ASP304 3.6 29.1 1.0 CD C:GLU292 3.7 33.0 1.0 CA C:ASP304 3.9 29.3 1.0 ND2 C:ASN287 4.0 26.2 1.0 N C:ASN287 4.1 32.2 1.0 CB C:ASP304 4.2 32.1 1.0 CB C:ASN303 4.3 27.3 1.0 OD2 C:ASP304 4.3 31.3 1.0 OE2 C:GLU292 4.4 37.2 1.0 O1A C:GQ41325 4.4 74.9 1.0 C2A C:GQ41325 4.4 88.3 1.0 C C:ASN303 4.5 28.8 1.0 O C:ASN287 4.5 34.5 1.0 CA C:ASN303 4.6 28.7 1.0 CB C:GLU292 4.6 33.0 1.0 N C:SER305 4.6 27.7 1.0 C5A C:GQ41325 4.7 1.0 1.0 CG C:GLU285 4.7 28.9 1.0 CB C:ASN287 4.7 30.8 1.0 C C:ASN287 4.7 35.7 1.0 CA C:ASN287 4.8 31.8 1.0 ND2 C:ASN288 4.8 41.1 1.0 CG C:GLU292 4.8 33.1 1.0 CG C:ASN303 4.9 27.2 1.0

Calcium binding site 4 out of 4 in the Structure of Sign-R1 in Complex with Sulfodextran


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Sign-R1 in Complex with Sulfodextran within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:53.1 occ:1.00 OD1 D:ASN287 2.4 29.7 1.0 OD1 D:ASP304 2.4 31.1 1.0 OE1 D:GLU292 2.5 29.6 1.0 OE1 D:GLU285 2.5 30.5 1.0 O D:ASP304 2.7 33.7 1.0 OE2 D:GLU285 3.3 24.9 1.0 CD D:GLU285 3.3 29.4 1.0 CG D:ASN287 3.4 28.8 1.0 CG D:ASP304 3.6 34.9 1.0 C D:ASP304 3.7 29.9 1.0 CD D:GLU292 3.7 30.8 1.0 N D:ASP304 3.8 29.4 1.0 ND2 D:ASN287 3.9 26.9 1.0 ND2 D:ASN288 4.1 49.5 1.0 CA D:ASP304 4.1 30.8 1.0 N D:ASN287 4.2 29.8 1.0 OE2 D:GLU292 4.3 31.4 1.0 CB D:ASN303 4.4 26.0 1.0 O D:ASN287 4.4 34.2 1.0 CB D:ASP304 4.5 32.1 1.0 OD2 D:ASP304 4.6 35.0 1.0 CB D:ASN287 4.7 30.3 1.0 C D:ASN287 4.7 31.9 1.0 CG D:GLU285 4.7 30.5 1.0 N D:SER305 4.7 30.1 1.0 C D:ASN303 4.8 28.6 1.0 CA D:ASN287 4.8 30.5 1.0 CG D:GLU292 4.8 34.5 1.0 CB D:GLU292 4.9 35.8 1.0 CA D:ASN303 4.9 27.7 1.0 CG D:ASN303 4.9 25.6 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