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

Protein crystallography data

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

Calcium Binding Sites:

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 5b1x

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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 5b1x

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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 5b1x

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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 5b1x

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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 5b1x

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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 5b1x

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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 5b1x

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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 5b1x

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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

Reference:

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
Page generated: Sun Jul 14 16:39:49 2024

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