Calcium in PDB 6kzr: Crystal Structure of Mouse DCAR2 Crd Domain

The structure of Crystal Structure of Mouse DCAR2 Crd Domain, PDB code: 6kzr was solved by Z.Omahdi, Y.Horikawa, K.Toyonaga, T.Teramoto, Y.Kakuta, S.Yamasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.97 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.979, 72.435, 101.106, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.1

The binding sites of Calcium atom in the Crystal Structure of Mouse DCAR2 Crd Domain (pdb code 6kzr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Mouse DCAR2 Crd Domain, PDB code: 6kzr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Mouse DCAR2 Crd Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Mouse DCAR2 Crd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:24.8 occ:1.00 OD1 A:ASP191 2.3 24.1 1.0 O A:ASP191 2.3 20.9 1.0 OD1 A:ASN190 2.3 25.0 1.0 OG A:SER170 2.3 24.3 1.0 OE1 A:GLU174 2.4 24.6 1.0 OE1 A:GLU168 2.5 28.7 1.0 O1 A:GOL301 2.6 29.0 1.0 O2 A:GOL301 2.6 27.7 1.0 C2 A:GOL301 3.3 31.1 1.0 CG A:ASP191 3.3 23.2 1.0 CD A:GLU168 3.3 29.0 1.0 CD A:GLU174 3.4 25.3 1.0 CG A:ASN190 3.4 27.2 1.0 C A:ASP191 3.4 24.2 1.0 CB A:SER170 3.5 23.7 1.0 C1 A:GOL301 3.5 30.6 1.0 OE2 A:GLU168 3.6 28.7 1.0 N A:ASP191 3.7 24.6 1.0 OE2 A:GLU174 3.7 27.8 1.0 ND2 A:ASN190 3.9 27.9 1.0 CA A:ASP191 3.9 24.4 1.0 OD2 A:ASP191 4.1 23.6 1.0 N A:SER170 4.1 22.5 1.0 CB A:ASP191 4.2 23.0 1.0 O A:HOH440 4.3 31.8 1.0 CA A:SER170 4.4 24.4 1.0 C A:ASN190 4.5 25.2 1.0 N A:ILE192 4.6 24.2 1.0 CG A:GLU168 4.6 30.5 1.0 CG A:GLU174 4.7 24.6 1.0 CB A:ASN190 4.7 27.3 1.0 O A:HOH464 4.7 39.9 1.0 C3 A:GOL301 4.7 34.3 1.0 CA A:ASN190 4.8 25.6 1.0 CB A:GLU174 4.8 25.4 1.0 N A:SER171 4.9 24.3 1.0 CG2 A:ILE192 5.0 41.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Mouse DCAR2 Crd Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Mouse DCAR2 Crd Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:41.1 occ:1.00 O B:ASP191 2.3 39.6 1.0 OD1 B:ASN190 2.3 38.6 1.0 OD1 B:ASP191 2.3 39.8 1.0 OE1 B:GLU174 2.3 39.9 1.0 OG B:SER170 2.4 44.5 1.0 OE1 B:GLU168 2.5 51.7 1.0 O2 B:GOL302 2.5 45.4 1.0 O3 B:GOL302 2.6 39.7 1.0 CD B:GLU168 3.2 46.4 1.0 CD B:GLU174 3.3 42.8 1.0 CG B:ASP191 3.4 37.3 1.0 C3 B:GOL302 3.4 41.3 1.0 C2 B:GOL302 3.4 44.1 1.0 CG B:ASN190 3.4 37.9 1.0 C B:ASP191 3.4 36.5 1.0 OE2 B:GLU168 3.4 45.5 1.0 CB B:SER170 3.5 45.0 1.0 N B:ASP191 3.6 34.5 1.0 OE2 B:GLU174 3.8 40.2 1.0 CA B:ASP191 3.9 35.8 1.0 ND2 B:ASN190 3.9 42.7 1.0 N B:SER170 4.0 41.5 1.0 OD2 B:ASP191 4.2 36.0 1.0 CB B:ASP191 4.2 34.8 1.0 CA B:SER170 4.3 45.3 1.0 C B:ASN190 4.4 35.3 1.0 CG B:GLU168 4.5 45.0 1.0 CG B:GLU174 4.6 46.9 1.0 N B:ILE192 4.6 40.5 1.0 O B:HOH427 4.6 60.8 1.0 CB B:ASN190 4.7 34.4 1.0 CB B:GLU174 4.7 45.9 1.0 CA B:ASN190 4.7 36.1 1.0 C1 B:GOL302 4.7 45.7 1.0 N B:SER171 4.9 51.3 1.0 CG2 B:ILE192 4.9 44.4 1.0

Z.Omahdi, Y.Horikawa, M.Nagae, K.Toyonaga, A.Imamura, K.Takato, T.Teramoto, H.Ishida, Y.Kakuta, S.Yamasaki. Structural Insight Into the Recognition of Pathogen-Derived Phosphoglycolipids By C-Type Lectin Receptor Dcar. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32139512
DOI: 10.1074/JBC.RA120.012491