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Calcium in PDB 4gko: Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23

Protein crystallography data

The structure of Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23, PDB code: 4gko was solved by D.Yuan, B.J.Sutton, B.Dhaliwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.50 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.830, 110.130, 367.410, 90.00, 90.00, 90.00
R / Rfree (%) 27.3 / 31.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 (pdb code 4gko). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23, PDB code: 4gko:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4gko

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Calcium binding site 1 out of 6 in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23


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 the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:0.9
occ:1.00
 OE2 G:GLU249 2.2 0.0 1.0
OE1 G:GLU257 2.4 0.6 1.0
OG1 G:THR251 2.4 0.6 1.0
O G:ASP270 2.6 0.6 1.0
OD1 G:ASP270 2.7 0.8 1.0
CD G:GLU249 3.2 0.9 1.0
CD G:GLU257 3.2 1.0 1.0
OE1 G:GLU249 3.2 0.5 1.0
OE2 G:GLU257 3.3 0.6 1.0
CB G:THR251 3.6 1.0 1.0
CG G:ASP270 3.8 0.7 1.0
CG2 G:THR251 3.8 0.6 1.0
C G:ASP270 3.8 0.5 1.0
OD2 G:ASP270 4.4 0.5 1.0
N G:ASP270 4.5 0.3 1.0
OD1 G:ASN269 4.6 0.1 1.0
CA G:ASP270 4.6 0.7 1.0
CG G:GLU257 4.6 0.5 1.0
CG G:GLU249 4.6 0.2 1.0
CB G:ASP270 4.8 1.0 1.0
CA G:THR251 4.8 0.0 1.0
N G:THR251 4.8 0.8 1.0
N G:ALA271 4.8 1.0 1.0

Calcium binding site 2 out of 6 in 4gko

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Calcium binding site 2 out of 6 in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23


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 the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:0.6
occ:1.00
 OE2 H:GLU249 1.9 1.0 1.0
OG1 H:THR251 2.4 0.5 1.0
CD H:GLU249 3.0 0.7 1.0
OD1 H:ASP270 3.1 0.5 1.0
OE1 H:GLU257 3.2 0.6 1.0
CG2 H:THR251 3.3 0.5 1.0
OE1 H:GLU249 3.3 0.2 1.0
CB H:THR251 3.4 0.7 1.0
O H:ASP270 3.5 0.6 1.0
OE2 H:GLU257 3.9 0.1 1.0
CD H:GLU257 3.9 1.0 1.0
CG H:ASP270 4.2 0.9 1.0
CG H:GLU249 4.3 0.6 1.0
OD1 H:ASN269 4.6 0.8 1.0
C H:ASP270 4.6 0.1 1.0
CA H:THR251 4.6 0.7 1.0
OD2 H:ASP270 4.7 0.2 1.0
N H:THR251 4.7 0.0 1.0
N H:ASP270 4.9 1.0 1.0

Calcium binding site 3 out of 6 in 4gko

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Calcium binding site 3 out of 6 in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23


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 the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca301

b:0.9
occ:1.00
 O I:ASP270 2.3 0.1 1.0
OE2 I:GLU249 2.4 0.4 1.0
OD1 I:ASP270 3.0 0.4 1.0
OE1 I:GLU257 3.1 0.8 1.0
OE2 I:GLU257 3.3 0.8 1.0
OD1 I:ASN269 3.3 0.8 1.0
CD I:GLU249 3.3 0.1 1.0
C I:ASP270 3.5 0.1 1.0
CD I:GLU257 3.5 0.7 1.0
OG1 I:THR251 3.5 0.0 1.0
OE1 I:GLU249 3.7 0.9 1.0
CG I:ASN269 4.1 0.7 1.0
CG I:ASP270 4.1 0.4 1.0
N I:ASP270 4.1 0.3 1.0
CB I:ASN269 4.2 0.9 1.0
CA I:ASP270 4.4 0.8 1.0
N I:ALA271 4.5 0.6 1.0
CG I:GLU249 4.6 0.7 1.0
C I:ASN269 4.6 0.6 1.0
CA I:ALA271 4.7 0.6 1.0
CB I:THR251 4.7 0.1 1.0
CG2 I:THR251 4.8 0.0 1.0
CB I:ASP270 4.9 0.8 1.0
CG I:GLU257 4.9 0.7 1.0
OD2 I:ASP270 4.9 0.6 1.0
CA I:ASN269 5.0 0.5 1.0

Calcium binding site 4 out of 6 in 4gko

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Calcium binding site 4 out of 6 in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23


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 the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca301

b:1.0
occ:1.00
 OE2 J:GLU249 1.9 0.1 1.0
OG1 J:THR251 2.9 0.5 1.0
O J:ASP270 2.9 0.5 1.0
OD1 J:ASP270 3.0 0.1 1.0
CD J:GLU249 3.0 0.8 1.0
OE1 J:GLU257 3.3 0.3 1.0
OE2 J:GLU257 3.4 0.5 1.0
OE1 J:GLU249 3.5 0.4 1.0
CG2 J:THR251 3.7 0.7 1.0
CD J:GLU257 3.7 0.1 1.0
CB J:THR251 3.8 0.8 1.0
C J:ASP270 4.1 0.2 1.0
CG J:ASP270 4.2 1.0 1.0
OD1 J:ASN269 4.2 0.4 1.0
CG J:GLU249 4.4 0.9 1.0
N J:ASP270 4.7 0.3 1.0
OD2 J:ASP270 4.8 0.8 1.0
CB J:ASN269 4.8 0.2 1.0
CA J:ASP270 4.9 0.8 1.0
CG J:ASN269 4.9 0.9 1.0

Calcium binding site 5 out of 6 in 4gko

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Calcium binding site 5 out of 6 in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23


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 the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca301

b:0.6
occ:1.00
 OE2 K:GLU249 1.6 0.6 1.0
OG1 K:THR251 2.5 0.1 1.0
CD K:GLU249 2.6 0.7 1.0
OD1 K:ASP270 2.9 0.4 1.0
OE1 K:GLU249 3.1 0.0 1.0
O K:ASP270 3.1 0.0 1.0
OE1 K:GLU257 3.2 0.1 1.0
CG2 K:THR251 3.5 0.2 1.0
CB K:THR251 3.5 0.4 1.0
OE2 K:GLU257 3.9 0.6 1.0
CD K:GLU257 3.9 0.5 1.0
CG K:GLU249 4.0 0.8 1.0
CG K:ASP270 4.1 1.0 1.0
C K:ASP270 4.3 0.8 1.0
OD1 K:ASN269 4.3 0.2 1.0
N K:ASP270 4.5 0.9 1.0
N K:THR251 4.6 0.7 1.0
OD2 K:ASP270 4.7 0.9 1.0
CB K:ASN269 4.7 0.5 1.0
CA K:THR251 4.7 0.8 1.0
CA K:ASP270 4.9 0.8 1.0
CG K:ASN269 4.9 0.1 1.0

Calcium binding site 6 out of 6 in 4gko

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Calcium binding site 6 out of 6 in the Crystal Structure of the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23


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 the CALCIUM2+-Bound Human Ige-Fc(Epsilon)3-4 Bound to Its B Cell Receptor DERCD23 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca301

b:0.1
occ:1.00
 OE2 L:GLU249 2.4 0.5 1.0
OG1 L:THR251 2.4 0.5 1.0
OE1 L:GLU257 2.7 0.6 1.0
OD1 L:ASP270 3.0 0.2 1.0
OE2 L:GLU257 3.1 0.3 1.0
O L:ASP270 3.1 0.4 1.0
CD L:GLU257 3.3 0.3 1.0
CD L:GLU249 3.4 0.9 1.0
CB L:THR251 3.4 0.4 1.0
CG2 L:THR251 3.5 0.3 1.0
OE1 L:GLU249 3.6 0.9 1.0
CG L:ASP270 4.0 0.1 1.0
C L:ASP270 4.4 0.8 1.0
OD2 L:ASP270 4.5 0.1 1.0
CA L:THR251 4.7 0.0 1.0
CG L:GLU249 4.8 0.6 1.0
OD1 L:ASN269 4.8 0.9 1.0
CG L:GLU257 4.8 0.1 1.0
N L:THR251 4.9 0.5 1.0
N L:ASP270 5.0 0.1 1.0

Reference:

D.Yuan, A.H.Keeble, R.G.Hibbert, S.Fabiane, H.J.Gould, J.M.Mcdonnell, A.J.Beavil, B.J.Sutton, B.Dhaliwal. CA2+-Dependent Structural Changes in the B-Cell Receptor CD23 Increase Its Affinity For Human Immunoglobulin E. J.Biol.Chem. V. 288 21667 2013.
ISSN: ISSN 0021-9258
PubMed: 23775083
DOI: 10.1074/JBC.M113.480657
Page generated: Tue Jul 8 22:19:00 2025

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