Atomistry » Calcium » PDB 5afp-5b4x » 5b1w
Atomistry »
  Calcium »
    PDB 5afp-5b4x »
      5b1w »

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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Go back to Calcium Binding Sites List in 5b1w
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy