Calcium in PDB 6lfj: Crystal Structure of Mouse DCAR2 Crd Domain Complex with IPM2

The structure of Crystal Structure of Mouse DCAR2 Crd Domain Complex with IPM2, PDB code: 6lfj was solved by Z.Omahdi, Y.Horikawa, K.Toyonaga, Y.Kakuta, S.Yamasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.689, 72.564, 100.469, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.8

The binding sites of Calcium atom in the Crystal Structure of Mouse DCAR2 Crd Domain Complex with IPM2 (pdb code 6lfj). 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 Complex with IPM2, PDB code: 6lfj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Mouse DCAR2 Crd Domain Complex with IPM2


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 Complex with IPM2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:22.0 occ:1.00 OD1 A:ASP191 2.3 23.5 1.0 OG A:SER170 2.4 21.5 1.0 OD1 A:ASN190 2.4 23.9 1.0 O A:ASP191 2.4 22.3 1.0 OE1 A:GLU174 2.5 22.9 1.0 O3 A:MAN305 2.5 26.5 1.0 OE1 A:GLU168 2.5 22.6 1.0 O4 A:MAN305 2.6 22.9 1.0 CG A:ASP191 3.3 21.6 1.0 C3 A:MAN305 3.3 24.6 1.0 C4 A:MAN305 3.3 26.0 1.0 CD A:GLU168 3.4 24.0 1.0 CD A:GLU174 3.4 27.3 1.0 CB A:SER170 3.5 22.9 1.0 CG A:ASN190 3.5 23.1 1.0 C A:ASP191 3.5 23.1 1.0 N A:ASP191 3.7 21.0 1.0 OE2 A:GLU168 3.8 23.6 1.0 OE2 A:GLU174 3.8 27.2 1.0 CA A:ASP191 4.0 17.6 1.0 ND2 A:ASN190 4.0 26.6 1.0 OD2 A:ASP191 4.0 24.9 1.0 N A:SER170 4.0 23.5 1.0 CB A:ASP191 4.2 17.2 1.0 CA A:SER170 4.3 24.4 1.0 O A:HOH418 4.3 27.2 1.0 C A:ASN190 4.5 23.7 1.0 CG A:GLU168 4.7 23.7 1.0 N A:ILE192 4.7 20.4 1.0 C2 A:MAN305 4.7 32.8 1.0 CG A:GLU174 4.7 22.5 1.0 CB A:ASN190 4.7 22.4 1.0 C5 A:MAN305 4.7 37.6 1.0 CA A:ASN190 4.8 22.0 1.0 CB A:GLU174 4.8 19.4 1.0 N A:SER171 4.9 21.2 1.0 O A:HOH531 5.0 45.5 1.0 O2 A:MAN305 5.0 33.5 1.0 C A:SER170 5.0 25.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Mouse DCAR2 Crd Domain Complex with IPM2


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 Complex with IPM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:35.6 occ:1.00 OD1 B:ASP191 2.3 39.2 1.0 O3 B:MAN303 2.4 38.7 1.0 OD1 B:ASN190 2.4 32.6 1.0 O B:ASP191 2.4 36.8 1.0 OG B:SER170 2.4 40.0 1.0 OE1 B:GLU174 2.5 37.4 1.0 OE1 B:GLU168 2.6 39.6 1.0 O4 B:MAN303 2.6 44.6 1.0 C3 B:MAN303 3.3 39.0 1.0 CG B:ASP191 3.4 37.4 1.0 C4 B:MAN303 3.4 43.6 1.0 CD B:GLU174 3.4 38.6 1.0 CD B:GLU168 3.4 43.5 1.0 CG B:ASN190 3.5 36.1 1.0 C B:ASP191 3.5 32.3 1.0 CB B:SER170 3.5 39.6 1.0 OE2 B:GLU168 3.7 39.3 1.0 N B:ASP191 3.7 29.6 1.0 OE2 B:GLU174 3.7 41.1 1.0 CA B:ASP191 4.0 31.1 1.0 ND2 B:ASN190 4.0 35.1 1.0 N B:SER170 4.1 39.5 1.0 OD2 B:ASP191 4.1 40.1 1.0 CB B:ASP191 4.2 31.8 1.0 CA B:SER170 4.4 42.0 1.0 C B:ASN190 4.5 29.8 1.0 N B:ILE192 4.6 30.9 1.0 CG B:GLU174 4.6 36.3 1.0 C2 B:MAN303 4.7 46.6 1.0 CB B:ASN190 4.7 27.1 1.0 OG B:SER171 4.7 60.0 1.0 CA B:ASN190 4.7 29.1 1.0 CG B:GLU168 4.7 39.1 1.0 CB B:GLU174 4.8 37.3 1.0 C5 B:MAN303 4.8 51.6 1.0 N B:SER171 4.9 51.8 1.0 O2 B:MAN303 5.0 48.0 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