Calcium in PDB 3zhg: Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain

The structure of Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain, PDB code: 3zhg 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)	27.627 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.720, 92.770, 77.060, 90.00, 121.66, 90.00
R / Rfree (%)	20.45 / 24.43

The binding sites of Calcium atom in the Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain (pdb code 3zhg). 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 Native Mouse Sign-R1 Crd Domain, PDB code: 3zhg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain


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 Native Mouse Sign-R1 Crd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1323 b:37.0 occ:1.00 O A:HOH2116 2.2 30.0 1.0 OE1 A:GLU292 2.3 33.3 1.0 OD1 A:ASP304 2.4 31.1 1.0 OD1 A:ASN287 2.5 35.6 1.0 OE1 A:GLU285 2.5 27.4 1.0 O A:ASP304 2.6 25.3 1.0 O A:HOH2117 2.8 41.6 1.0 OE2 A:GLU285 3.0 32.5 1.0 CD A:GLU285 3.1 30.1 1.0 CD A:GLU292 3.5 30.8 1.0 CG A:ASN287 3.6 35.3 1.0 CG A:ASP304 3.6 29.8 1.0 C A:ASP304 3.6 27.6 1.0 N A:ASP304 3.8 24.4 1.0 O A:HOH2126 3.9 44.8 1.0 OE2 A:GLU292 4.1 30.2 1.0 ND2 A:ASN287 4.1 30.0 1.0 ND2 A:ASN288 4.2 33.5 1.0 CA A:ASP304 4.2 25.7 1.0 N A:ASN287 4.4 31.0 1.0 OD2 A:ASP304 4.4 28.2 1.0 CB A:ASP304 4.5 23.4 1.0 CB A:ASN303 4.5 26.1 1.0 O A:ASN287 4.5 31.0 1.0 CG A:GLU292 4.6 30.3 1.0 CB A:GLU292 4.6 30.2 1.0 CG A:GLU285 4.6 26.0 1.0 N A:SER305 4.7 26.2 1.0 C A:ASN287 4.8 35.5 1.0 C A:ASN303 4.8 28.5 1.0 CB A:ASN287 4.8 31.9 1.0 CA A:ASN287 4.9 32.4 1.0 CA A:ASN303 4.9 23.5 1.0

Calcium binding site 2 out of 4 in the Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain


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 Native Mouse Sign-R1 Crd Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1323 b:51.2 occ:1.00 OD1 B:ASP304 2.3 39.8 1.0 OE1 B:GLU292 2.4 50.0 1.0 OD1 B:ASN287 2.4 51.4 1.0 O B:ASP304 2.5 44.2 1.0 OE1 B:GLU285 2.6 42.6 1.0 OE2 B:GLU285 3.2 47.0 1.0 CD B:GLU285 3.2 48.1 1.0 O B:HOH2062 3.3 48.7 1.0 CD B:GLU292 3.5 46.5 1.0 CG B:ASP304 3.5 46.5 1.0 C B:ASP304 3.5 43.1 1.0 CG B:ASN287 3.5 49.7 1.0 N B:ASP304 3.8 39.9 1.0 OE2 B:GLU292 4.0 48.2 1.0 CA B:ASP304 4.1 40.9 1.0 ND2 B:ASN287 4.1 50.0 1.0 N B:ASN287 4.2 49.0 1.0 O B:ASN287 4.3 50.6 1.0 OD2 B:ASP304 4.4 44.5 1.0 CB B:ASP304 4.4 43.6 1.0 OD1 B:ASN288 4.5 52.4 1.0 CB B:GLU292 4.5 42.9 1.0 CB B:ASN303 4.6 38.6 1.0 CG B:GLU292 4.6 44.7 1.0 C B:ASN287 4.6 52.1 1.0 N B:SER305 4.6 43.9 1.0 CB B:ASN287 4.7 46.7 1.0 C B:ASN303 4.7 43.2 1.0 CG B:GLU285 4.7 44.4 1.0 CA B:ASN287 4.7 45.1 1.0 CA B:ASN303 4.9 43.2 1.0

Calcium binding site 3 out of 4 in the Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain


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 Native Mouse Sign-R1 Crd Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1323 b:37.0 occ:1.00 OE1 C:GLU292 2.3 31.7 1.0 OD1 C:ASP304 2.4 30.2 1.0 OD1 C:ASN287 2.5 36.0 1.0 OE1 C:GLU285 2.5 29.3 1.0 O C:ASP304 2.6 24.7 1.0 O C:HOH2104 2.9 45.7 1.0 OE2 C:GLU285 3.0 28.9 1.0 CD C:GLU285 3.1 29.6 1.0 CD C:GLU292 3.5 31.7 1.0 CG C:ASN287 3.6 36.5 1.0 C C:ASP304 3.6 26.9 1.0 CG C:ASP304 3.6 30.5 1.0 N C:ASP304 3.8 25.6 1.0 OE2 C:GLU292 4.0 32.1 1.0 ND2 C:ASN287 4.1 35.1 1.0 O C:HOH2108 4.1 48.6 1.0 CA C:ASP304 4.2 28.3 1.0 OD1 C:ASN288 4.3 37.9 1.0 N C:ASN287 4.4 28.2 1.0 O C:ASN287 4.4 30.3 1.0 OD2 C:ASP304 4.5 27.3 1.0 CB C:ASN303 4.5 25.1 1.0 CB C:ASP304 4.5 24.9 1.0 CG C:GLU285 4.6 24.9 1.0 CG C:GLU292 4.7 30.6 1.0 CB C:GLU292 4.7 31.1 1.0 N C:SER305 4.7 25.7 1.0 C C:ASN287 4.7 34.6 1.0 C C:ASN303 4.8 28.5 1.0 CB C:ASN287 4.8 30.7 1.0 CA C:ASN303 4.9 23.2 1.0 CA C:ASN287 4.9 32.0 1.0 CG C:ASN303 5.0 29.5 1.0

Calcium binding site 4 out of 4 in the Crystallographic Structure of the Native Mouse Sign-R1 Crd Domain


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 Native Mouse Sign-R1 Crd Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1323 b:52.3 occ:1.00 OD1 D:ASP304 2.3 39.8 1.0 OE1 D:GLU292 2.4 50.3 1.0 OD1 D:ASN287 2.5 51.8 1.0 O D:ASP304 2.5 43.2 1.0 OE1 D:GLU285 2.5 41.2 1.0 O D:HOH2060 2.6 48.6 1.0 OE2 D:GLU285 3.0 45.6 1.0 CD D:GLU285 3.1 45.8 1.0 CD D:GLU292 3.5 48.9 1.0 CG D:ASP304 3.5 44.9 1.0 CG D:ASN287 3.6 50.5 1.0 C D:ASP304 3.6 40.8 1.0 N D:ASP304 3.9 40.1 1.0 OE2 D:GLU292 4.0 50.9 1.0 ND2 D:ASN287 4.1 49.9 1.0 CA D:ASP304 4.2 38.5 1.0 OD2 D:ASP304 4.4 45.0 1.0 N D:ASN287 4.4 54.2 1.0 ND2 D:ASN288 4.4 53.4 1.0 CB D:ASP304 4.5 43.0 1.0 O D:ASN287 4.5 53.4 1.0 O D:HOH2064 4.6 48.7 1.0 CB D:ASN303 4.6 36.8 1.0 CB D:GLU292 4.6 42.6 1.0 CG D:GLU285 4.6 44.3 1.0 N D:SER305 4.6 42.8 1.0 CG D:GLU292 4.7 44.1 1.0 C D:ASN287 4.7 52.2 1.0 CB D:ASN287 4.8 47.1 1.0 C D:ASN303 4.8 42.8 1.0 CA D:ASN287 4.9 50.1 1.0 CA D:SER305 4.9 40.5 1.0 CA D:ASN303 5.0 41.8 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