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Calcium in PDB 5b1w: Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Ligand-Free Form

Protein crystallography data

The structure of Crystal Structure of Human Dendritic Cell Inhibitory Receptor (Dcir) C-Type Lectin Domain in Ligand-Free Form, PDB code: 5b1w 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) 47.02 / 3.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 102.489, 105.832, 65.387, 90.00, 90.00, 90.00
R / Rfree (%) 25.3 / 28.5

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 Ligand-Free Form (pdb code 5b1w). 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 Ligand-Free Form, PDB code: 5b1w:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:17.2
occ:1.00
 O A:VAL143 2.3 17.1 1.0
OE2 A:GLU149 2.4 16.9 1.0
OE2 A:GLU231 2.4 17.9 1.0
OD1 A:ASN145 2.4 16.8 1.0
OE1 A:GLU231 2.5 17.9 1.0
OE1 A:GLU149 2.5 16.9 1.0
CD A:GLU231 2.8 17.9 1.0
CD A:GLU149 2.8 16.9 1.0
C A:VAL143 3.6 17.1 1.0
CG A:ASN145 3.6 16.8 1.0
OH A:TYR118 4.1 17.8 1.0
CG A:GLU231 4.3 17.9 1.0
CG A:GLU149 4.3 16.9 1.0
CA A:VAL143 4.4 17.1 1.0
N A:ASN145 4.4 16.8 1.0
ND2 A:ASN145 4.4 16.8 1.0
CB A:VAL143 4.4 17.1 1.0
ND2 A:ASN116 4.5 18.5 1.0
N A:ILE144 4.5 16.7 1.0
N A:VAL143 4.5 17.1 1.0
CB A:ASN145 4.6 16.8 1.0
CA A:ILE144 4.6 16.7 1.0
CE1 A:TYR118 4.8 17.8 1.0
CD1 A:LEU142 4.9 17.0 1.0
C A:ILE144 4.9 16.7 1.0
CG1 A:VAL143 4.9 17.1 1.0
CZ A:TYR118 5.0 17.8 1.0

Calcium binding site 2 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:16.4
occ:1.00
 OE2 A:GLU201 2.4 17.0 1.0
OD1 A:ASN218 2.4 16.3 1.0
O A:HOH2101 2.4 14.4 1.0
OE1 A:GLU195 2.4 16.9 1.0
OD1 A:ASP219 2.4 16.8 1.0
OG A:SER197 2.4 16.9 1.0
OE2 A:GLU195 2.5 16.9 1.0
O A:ASP219 2.5 16.8 1.0
CD A:GLU195 2.7 16.9 1.0
CG A:ASP219 3.3 16.8 1.0
CD A:GLU201 3.4 17.0 1.0
CG A:ASN218 3.5 16.3 1.0
C A:ASP219 3.6 16.8 1.0
CB A:SER197 3.7 16.9 1.0
OE1 A:GLU201 3.8 17.0 1.0
N A:ASP219 3.8 16.8 1.0
OD2 A:ASP219 3.9 16.8 1.0
ND2 A:ASN218 4.0 16.3 1.0
CA A:ASP219 4.1 16.8 1.0
CG A:GLU195 4.2 16.9 1.0
N A:SER197 4.2 16.9 1.0
CB A:ASP219 4.3 16.8 1.0
CA A:SER197 4.5 16.9 1.0
CG A:GLU201 4.6 17.0 1.0
CB A:GLU201 4.7 17.0 1.0
C A:ASN218 4.7 16.3 1.0
CB A:ASN218 4.8 16.3 1.0
N A:VAL220 4.8 16.7 1.0
CB A:GLU195 4.9 16.9 1.0
N A:ASP198 4.9 17.2 1.0
CA A:ASN218 5.0 16.3 1.0

Calcium binding site 3 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2001

b:16.1
occ:1.00
 OE2 B:GLU149 2.3 17.0 1.0
OE2 B:GLU231 2.3 18.1 1.0
O B:VAL143 2.4 16.9 1.0
OD1 B:ASN145 2.4 16.8 1.0
OE1 B:GLU231 2.5 18.1 1.0
OE1 B:GLU149 2.6 17.0 1.0
CD B:GLU231 2.8 18.1 1.0
CD B:GLU149 2.8 17.0 1.0
CG B:ASN145 3.6 16.8 1.0
C B:VAL143 3.6 16.9 1.0
OH B:TYR118 4.1 18.0 1.0
CG B:GLU231 4.3 18.1 1.0
CG B:GLU149 4.3 17.0 1.0
CB B:VAL143 4.3 16.9 1.0
CA B:VAL143 4.4 16.9 1.0
N B:ASN145 4.5 16.8 1.0
ND2 B:ASN145 4.5 16.8 1.0
CB B:ASN145 4.5 16.8 1.0
N B:VAL143 4.5 16.9 1.0
N B:ILE144 4.6 16.7 1.0
CA B:ILE144 4.8 16.7 1.0
CG1 B:VAL143 4.8 16.9 1.0
ND2 B:ASN116 4.8 18.5 1.0
CD1 B:LEU142 4.9 17.3 1.0
CE1 B:TYR118 4.9 18.0 1.0
C B:ILE144 5.0 16.7 1.0
CZ B:TYR118 5.0 18.0 1.0

Calcium binding site 4 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:17.4
occ:1.00
 ND2 B:ASN218 2.3 16.8 1.0
OD1 B:ASP219 2.3 17.2 1.0
OG B:SER197 2.4 17.2 1.0
O B:HOH2101 2.5 14.4 1.0
OE1 B:GLU195 2.5 17.0 1.0
OE2 B:GLU195 2.5 17.0 1.0
O B:ASP219 2.5 17.2 1.0
OE2 B:GLU201 2.5 17.7 1.0
OD1 B:ASN218 2.5 16.8 1.0
CG B:ASN218 2.7 16.8 1.0
CD B:GLU195 2.8 17.0 1.0
CG B:ASP219 3.5 17.2 1.0
C B:ASP219 3.6 17.2 1.0
CD B:GLU201 3.6 17.7 1.0
N B:ASP219 3.6 17.2 1.0
CB B:SER197 3.8 17.2 1.0
OE1 B:GLU201 4.0 17.7 1.0
CB B:ASN218 4.1 16.8 1.0
CA B:ASP219 4.1 17.2 1.0
OD2 B:ASP219 4.2 17.2 1.0
CG B:GLU195 4.2 17.0 1.0
CB B:ASP219 4.4 17.2 1.0
C B:ASN218 4.4 16.8 1.0
CA B:ASN218 4.5 16.8 1.0
N B:SER197 4.5 17.2 1.0
NH2 B:ARG209 4.7 15.9 1.0
N B:VAL220 4.7 17.2 1.0
CA B:SER197 4.8 17.2 1.0
CG B:GLU201 4.9 17.7 1.0

Calcium binding site 5 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2001

b:18.6
occ:1.00
 OD1 C:ASN145 2.2 17.7 1.0
O C:VAL143 2.3 17.5 1.0
OE2 C:GLU231 2.3 19.3 1.0
OE2 C:GLU149 2.4 18.5 1.0
OE1 C:GLU231 2.4 19.3 1.0
OE1 C:GLU149 2.5 18.5 1.0
CD C:GLU231 2.7 19.3 1.0
CD C:GLU149 2.8 18.5 1.0
CG C:ASN145 3.4 17.7 1.0
C C:VAL143 3.5 17.5 1.0
CB C:VAL143 4.1 17.5 1.0
CA C:VAL143 4.2 17.5 1.0
CG C:GLU231 4.2 19.3 1.0
N C:VAL143 4.2 17.5 1.0
ND2 C:ASN145 4.3 17.7 1.0
CG C:GLU149 4.3 18.5 1.0
OH C:TYR118 4.3 19.7 1.0
N C:ASN145 4.3 17.7 1.0
CD1 C:LEU142 4.4 17.9 1.0
CB C:ASN145 4.5 17.7 1.0
N C:ILE144 4.5 17.3 1.0
CG1 C:VAL143 4.7 17.5 1.0
CA C:ILE144 4.7 17.3 1.0
CE1 C:TYR118 4.8 19.7 1.0
C C:ILE144 4.9 17.3 1.0
CB C:GLU231 5.0 19.3 1.0

Calcium binding site 6 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2002

b:17.2
occ:1.00
 OD1 C:ASP219 2.3 16.7 1.0
O C:HOH2101 2.4 15.1 1.0
OE2 C:GLU201 2.4 17.1 1.0
OD1 C:ASN218 2.4 16.8 1.0
OE1 C:GLU195 2.4 16.9 1.0
OE2 C:GLU195 2.4 16.9 1.0
OG C:SER197 2.4 17.0 1.0
O C:ASP219 2.5 16.7 1.0
CD C:GLU195 2.7 16.9 1.0
CD C:GLU201 3.4 17.1 1.0
CG C:ASN218 3.5 16.8 1.0
CG C:ASP219 3.6 16.7 1.0
C C:ASP219 3.6 16.7 1.0
OE1 C:GLU201 3.7 17.1 1.0
CB C:SER197 3.7 17.0 1.0
N C:ASP219 3.9 16.7 1.0
ND2 C:ASN218 4.0 16.8 1.0
CA C:ASP219 4.2 16.7 1.0
CG C:GLU195 4.2 16.9 1.0
N C:SER197 4.3 17.0 1.0
OD2 C:ASP219 4.3 16.7 1.0
CB C:ASP219 4.5 16.7 1.0
CA C:SER197 4.6 17.0 1.0
CG C:GLU201 4.6 17.1 1.0
N C:VAL220 4.7 16.9 1.0
C C:ASN218 4.7 16.8 1.0
CB C:GLU201 4.7 17.1 1.0
CB C:ASN218 4.8 16.8 1.0
CA C:ASN218 5.0 16.8 1.0
N C:ASP198 5.0 17.3 1.0

Calcium binding site 7 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2001

b:17.4
occ:1.00
 OE2 D:GLU231 2.3 18.9 1.0
OD1 D:ASN145 2.4 17.3 1.0
OE2 D:GLU149 2.4 18.2 1.0
O D:VAL143 2.5 17.5 1.0
OE1 D:GLU231 2.5 18.9 1.0
OE1 D:GLU149 2.6 18.2 1.0
CD D:GLU231 2.7 18.9 1.0
CD D:GLU149 2.8 18.2 1.0
CG D:ASN145 3.4 17.3 1.0
C D:VAL143 3.6 17.5 1.0
OH D:TYR118 4.2 19.1 1.0
CG D:GLU231 4.2 18.9 1.0
CB D:ASN145 4.3 17.3 1.0
N D:ASN145 4.3 17.3 1.0
CB D:VAL143 4.3 17.5 1.0
CG D:GLU149 4.3 18.2 1.0
ND2 D:ASN116 4.3 19.9 1.0
ND2 D:ASN145 4.3 17.3 1.0
CA D:VAL143 4.4 17.5 1.0
N D:VAL143 4.5 17.5 1.0
N D:ILE144 4.7 17.3 1.0
CG1 D:VAL143 4.7 17.5 1.0
CD1 D:LEU142 4.7 17.8 1.0
CA D:ILE144 4.8 17.3 1.0
C D:ILE144 4.9 17.3 1.0
CE1 D:TYR118 5.0 19.1 1.0
CA D:ASN145 5.0 17.3 1.0

Calcium binding site 8 out of 8 in 5b1w

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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 Ligand-Free Form


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 Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2002

b:16.7
occ:1.00
 O D:HOH2101 2.4 16.1 1.0
O D:ASP219 2.4 17.3 1.0
OD1 D:ASP219 2.4 17.3 1.0
OE2 D:GLU195 2.4 17.5 1.0
OE2 D:GLU201 2.4 17.7 1.0
OE1 D:GLU195 2.4 17.5 1.0
OG D:SER197 2.5 17.6 1.0
OD1 D:ASN218 2.5 17.1 1.0
OE1 D:GLU201 2.5 17.7 1.0
CD D:GLU201 2.7 17.7 1.0
CD D:GLU195 2.8 17.5 1.0
C D:ASP219 3.5 17.3 1.0
CG D:ASP219 3.5 17.3 1.0
CG D:ASN218 3.6 17.1 1.0
CB D:SER197 3.8 17.6 1.0
N D:ASP219 4.0 17.3 1.0
ND2 D:ASN218 4.0 17.1 1.0
CG D:GLU201 4.2 17.7 1.0
CA D:ASP219 4.2 17.3 1.0
OD2 D:ASP219 4.3 17.3 1.0
CG D:GLU195 4.3 17.5 1.0
N D:SER197 4.4 17.6 1.0
CB D:ASP219 4.5 17.3 1.0
CB D:GLU201 4.6 17.7 1.0
N D:VAL220 4.6 17.2 1.0
CA D:SER197 4.7 17.6 1.0
CG1 D:VAL220 4.8 17.2 1.0
C D:ASN218 4.8 17.1 1.0
CA D:VAL220 4.9 17.2 1.0
CB D:ASN218 4.9 17.1 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 16:39:34 2024

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