Calcium in PDB 5b1x: Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan

The structure of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan, PDB code: 5b1x was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.69 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.669, 104.845, 65.354, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 29

The binding sites of Calcium atom in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan (pdb code 5b1x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan, PDB code: 5b1x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


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 Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:12.1 occ:1.00 OD1 A:ASN145 2.4 12.4 1.0 OE2 A:GLU231 2.4 12.6 1.0 OE2 A:GLU149 2.4 12.2 1.0 O A:VAL143 2.5 12.7 1.0 OE1 A:GLU231 2.5 12.6 1.0 OE1 A:GLU149 2.6 12.2 1.0 CD A:GLU231 2.8 12.6 1.0 CD A:GLU149 2.8 12.2 1.0 C A:VAL143 3.6 12.7 1.0 CG A:ASN145 3.6 12.4 1.0 OH A:TYR118 4.1 12.2 1.0 N A:VAL143 4.3 12.7 1.0 CG A:GLU231 4.3 12.6 1.0 CA A:VAL143 4.3 12.7 1.0 CG A:GLU149 4.3 12.2 1.0 CB A:VAL143 4.3 12.7 1.0 N A:ASN145 4.5 12.4 1.0 CB A:ASN145 4.5 12.4 1.0 CD1 A:LEU142 4.5 12.6 1.0 ND2 A:ASN145 4.5 12.4 1.0 N A:ILE144 4.6 12.5 1.0 CE2 A:TYR118 4.8 12.2 1.0 ND2 A:ASN116 4.8 12.5 1.0 CA A:ILE144 4.8 12.5 1.0 CG1 A:VAL143 4.9 12.7 1.0 CZ A:TYR118 5.0 12.2 1.0 C A:ILE144 5.0 12.5 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


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 Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:13.4 occ:1.00 OD1 A:ASN218 2.3 12.8 1.0 OD1 A:ASP219 2.3 12.9 1.0 OG A:SER197 2.4 13.3 1.0 O4 A:MAN301 2.4 13.4 1.0 O A:ASP219 2.4 12.9 1.0 OE2 A:GLU201 2.4 13.1 1.0 OE1 A:GLU195 2.5 13.1 1.0 O3 A:MAN301 2.7 13.4 1.0 C4 A:MAN301 3.3 13.4 1.0 CG A:ASN218 3.3 12.8 1.0 CD A:GLU201 3.4 13.1 1.0 CG A:ASP219 3.4 12.9 1.0 C3 A:MAN301 3.5 13.4 1.0 C A:ASP219 3.6 12.9 1.0 CD A:GLU195 3.6 13.1 1.0 CB A:SER197 3.7 13.3 1.0 ND2 A:ASN218 3.8 12.8 1.0 OE1 A:GLU201 3.8 13.1 1.0 N A:ASP219 3.9 12.9 1.0 OE2 A:GLU195 4.0 13.1 1.0 OD2 A:ASP219 4.1 12.9 1.0 CA A:ASP219 4.2 12.9 1.0 N A:SER197 4.2 13.3 1.0 CB A:ASP219 4.4 12.9 1.0 CA A:SER197 4.5 13.3 1.0 CG A:GLU201 4.6 13.1 1.0 C A:ASN218 4.6 12.8 1.0 N A:VAL220 4.7 12.6 1.0 CB A:ASN218 4.7 12.8 1.0 C5 A:MAN301 4.7 13.4 1.0 CB A:GLU201 4.7 13.1 1.0 CG A:GLU195 4.9 13.1 1.0 CA A:ASN218 4.9 12.8 1.0 C2 A:MAN301 4.9 13.4 1.0 CA A:VAL220 5.0 12.6 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:11.7 occ:1.00 O B:VAL143 2.3 12.8 1.0 OE2 B:GLU231 2.3 12.9 1.0 OD1 B:ASN145 2.4 12.4 1.0 OE2 B:GLU149 2.4 12.1 1.0 OE1 B:GLU149 2.5 12.1 1.0 OE1 B:GLU231 2.6 12.9 1.0 CD B:GLU149 2.7 12.1 1.0 CD B:GLU231 2.8 12.9 1.0 C B:VAL143 3.5 12.8 1.0 CG B:ASN145 3.5 12.4 1.0 N B:ASN145 4.2 12.4 1.0 CB B:ASN145 4.2 12.4 1.0 OH B:TYR118 4.2 12.3 1.0 CG B:GLU149 4.2 12.1 1.0 CG B:GLU231 4.3 12.9 1.0 CA B:VAL143 4.3 12.8 1.0 CB B:VAL143 4.4 12.8 1.0 N B:VAL143 4.4 12.8 1.0 N B:ILE144 4.5 12.6 1.0 CA B:ILE144 4.6 12.6 1.0 ND2 B:ASN145 4.6 12.4 1.0 C B:ILE144 4.7 12.6 1.0 CD1 B:LEU142 4.8 12.7 1.0 CG1 B:VAL143 4.8 12.8 1.0 CA B:ASN145 4.8 12.4 1.0 CE1 B:TYR118 5.0 12.3 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:12.9 occ:1.00 OD1 B:ASP219 2.4 13.2 1.0 OD1 B:ASN218 2.4 12.9 1.0 OG B:SER197 2.4 13.2 1.0 OE2 B:GLU201 2.5 13.4 1.0 OE2 B:GLU195 2.5 13.0 1.0 O4 B:MAN301 2.5 13.5 1.0 O B:ASP219 2.5 13.2 1.0 O3 B:MAN301 2.6 13.5 1.0 CG B:ASP219 3.3 13.2 1.0 C4 B:MAN301 3.4 13.5 1.0 C3 B:MAN301 3.4 13.5 1.0 CD B:GLU195 3.5 13.0 1.0 CG B:ASN218 3.5 12.9 1.0 CD B:GLU201 3.5 13.4 1.0 C B:ASP219 3.6 13.2 1.0 CB B:SER197 3.7 13.2 1.0 OE1 B:GLU195 3.8 13.0 1.0 N B:ASP219 3.8 13.2 1.0 OD2 B:ASP219 3.9 13.2 1.0 ND2 B:ASN218 4.0 12.9 1.0 OE1 B:GLU201 4.1 13.4 1.0 CA B:ASP219 4.1 13.2 1.0 N B:SER197 4.2 13.2 1.0 CB B:ASP219 4.3 13.2 1.0 CA B:SER197 4.5 13.2 1.0 C B:ASN218 4.6 12.9 1.0 CG B:GLU201 4.7 13.4 1.0 C5 B:MAN301 4.7 13.5 1.0 N B:VAL220 4.8 13.2 1.0 CB B:ASN218 4.8 12.9 1.0 CB B:GLU201 4.8 13.4 1.0 CG B:GLU195 4.8 13.0 1.0 C2 B:MAN301 4.8 13.5 1.0 CA B:ASN218 4.9 12.9 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:12.8 occ:1.00 OE2 C:GLU231 2.2 13.8 1.0 OD1 C:ASN145 2.4 12.5 1.0 O C:VAL143 2.4 12.7 1.0 OE1 C:GLU149 2.5 13.1 1.0 OE2 C:GLU149 2.5 13.1 1.0 OE1 C:GLU231 2.6 13.8 1.0 CD C:GLU231 2.7 13.8 1.0 CD C:GLU149 2.8 13.1 1.0 CG C:ASN145 3.5 12.5 1.0 C C:VAL143 3.6 12.7 1.0 CG C:GLU231 4.2 13.8 1.0 N C:ASN145 4.2 12.5 1.0 O C:HOH406 4.2 13.2 1.0 CB C:VAL143 4.3 12.7 1.0 CB C:ASN145 4.3 12.5 1.0 CA C:VAL143 4.3 12.7 1.0 CG C:GLU149 4.3 13.1 1.0 N C:VAL143 4.5 12.7 1.0 ND2 C:ASN116 4.5 14.5 1.0 ND2 C:ASN145 4.5 12.5 1.0 N C:ILE144 4.6 12.5 1.0 OH C:TYR118 4.6 13.9 1.0 CD1 C:LEU142 4.7 12.7 1.0 CG1 C:VAL143 4.7 12.7 1.0 CA C:ILE144 4.8 12.5 1.0 C C:ILE144 4.9 12.5 1.0 CA C:ASN145 4.9 12.5 1.0 CE1 C:TYR118 5.0 13.9 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:11.9 occ:1.00 O3 C:MAN301 2.2 12.8 1.0 OE1 C:GLU201 2.2 12.7 1.0 OD1 C:ASP219 2.3 12.4 1.0 O C:ASP219 2.3 12.4 1.0 OG C:SER197 2.4 12.8 1.0 O4 C:MAN301 2.4 12.8 1.0 OD1 C:ASN218 2.4 12.3 1.0 OE1 C:GLU195 2.5 12.6 1.0 C3 C:MAN301 3.0 12.8 1.0 C4 C:MAN301 3.1 12.8 1.0 CG C:ASP219 3.3 12.4 1.0 CD C:GLU201 3.3 12.7 1.0 C C:ASP219 3.4 12.4 1.0 CD C:GLU195 3.4 12.6 1.0 CG C:ASN218 3.6 12.3 1.0 OE2 C:GLU201 3.7 12.7 1.0 OE2 C:GLU195 3.7 12.6 1.0 CB C:SER197 3.8 12.8 1.0 N C:ASP219 3.8 12.4 1.0 OD2 C:ASP219 4.0 12.4 1.0 CA C:ASP219 4.0 12.4 1.0 ND2 C:ASN218 4.1 12.3 1.0 CB C:ASP219 4.2 12.4 1.0 C2 C:MAN301 4.4 12.8 1.0 N C:SER197 4.5 12.8 1.0 N C:VAL220 4.5 12.3 1.0 C C:ASN218 4.5 12.3 1.0 CG C:GLU201 4.5 12.7 1.0 C5 C:MAN301 4.5 12.8 1.0 CB C:GLU201 4.6 12.7 1.0 CA C:SER197 4.7 12.8 1.0 CG1 C:VAL220 4.8 12.3 1.0 CG C:GLU195 4.8 12.6 1.0 CB C:ASN218 4.8 12.3 1.0 CA C:ASN218 4.9 12.3 1.0 CA C:VAL220 4.9 12.3 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:12.9 occ:1.00 OE2 D:GLU231 2.3 13.2 1.0 OD1 D:ASN145 2.3 12.1 1.0 OE1 D:GLU149 2.4 12.4 1.0 OE2 D:GLU149 2.4 12.4 1.0 O D:VAL143 2.4 12.2 1.0 OE1 D:GLU231 2.4 13.2 1.0 CD D:GLU231 2.7 13.2 1.0 CD D:GLU149 2.8 12.4 1.0 CG D:ASN145 3.5 12.1 1.0 C D:VAL143 3.6 12.2 1.0 CG D:GLU231 4.2 13.2 1.0 OH D:TYR118 4.2 13.1 1.0 CG D:GLU149 4.2 12.4 1.0 CB D:ASN145 4.2 12.1 1.0 N D:ASN145 4.2 12.1 1.0 CA D:VAL143 4.4 12.2 1.0 N D:VAL143 4.4 12.2 1.0 CB D:VAL143 4.4 12.2 1.0 ND2 D:ASN116 4.4 13.9 1.0 ND2 D:ASN145 4.5 12.1 1.0 CD1 D:LEU142 4.6 12.2 1.0 N D:ILE144 4.6 11.9 1.0 CE2 D:TYR118 4.8 13.1 1.0 CA D:ILE144 4.8 11.9 1.0 CG1 D:VAL143 4.9 12.2 1.0 CA D:ASN145 4.9 12.1 1.0 C D:ILE144 4.9 11.9 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Complex with Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca304 b:11.4 occ:1.00 OD1 D:ASP219 2.3 11.8 1.0 OG D:SER197 2.4 12.0 1.0 O3 D:MAN301 2.4 12.2 1.0 OD1 D:ASN218 2.4 11.8 1.0 OE2 D:GLU201 2.5 12.2 1.0 O4 D:MAN301 2.5 12.2 1.0 O D:ASP219 2.5 11.8 1.0 OE1 D:GLU195 2.5 12.0 1.0 C3 D:MAN301 3.2 12.2 1.0 C4 D:MAN301 3.3 12.2 1.0 CG D:ASP219 3.3 11.8 1.0 CG D:ASN218 3.5 11.8 1.0 C D:ASP219 3.5 11.8 1.0 CD D:GLU201 3.6 12.2 1.0 CD D:GLU195 3.6 12.0 1.0 CB D:SER197 3.7 12.0 1.0 N D:ASP219 3.8 11.8 1.0 OD2 D:ASP219 3.9 11.8 1.0 OE2 D:GLU195 4.0 12.0 1.0 CA D:ASP219 4.0 11.8 1.0 OE1 D:GLU201 4.1 12.2 1.0 ND2 D:ASN218 4.1 11.8 1.0 N D:SER197 4.1 12.0 1.0 CB D:ASP219 4.3 11.8 1.0 CA D:SER197 4.5 12.0 1.0 C D:ASN218 4.5 11.8 1.0 C2 D:MAN301 4.6 12.2 1.0 C5 D:MAN301 4.6 12.2 1.0 N D:VAL220 4.7 12.0 1.0 CB D:ASN218 4.7 11.8 1.0 CA D:ASN218 4.8 11.8 1.0 CG D:GLU201 4.8 12.2 1.0 CB D:GLU201 4.8 12.2 1.0 CG D:GLU195 4.9 12.0 1.0 N D:ASP198 5.0 12.3 1.0

M.Nagae, A.Ikeda, S.Hanashima, T.Kojima, N.Matsumoto, K.Yamamoto, Y.Yamaguchi. Crystal Structure of Human Dendritic Cell Inhibitory Receptor C-Type Lectin Domain Reveals the Binding Mode with N-Glycan Febs Lett. V. 590 1280 2016.
ISSN: ISSN 0014-5793
PubMed: 27015765
DOI: 10.1002/1873-3468.12162