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Calcium in PDB 5ks9: BEL502-DQ8-Glia-ALPHA1 Complex

Protein crystallography data

The structure of BEL502-DQ8-Glia-ALPHA1 Complex, PDB code: 5ks9 was solved by J.Petersen, J.Rossjohn, H.H.Reid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.90 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.560, 56.870, 232.050, 90.00, 92.77, 90.00
R / Rfree (%) 19.9 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the BEL502-DQ8-Glia-ALPHA1 Complex (pdb code 5ks9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the BEL502-DQ8-Glia-ALPHA1 Complex, PDB code: 5ks9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5ks9

Go back to Calcium Binding Sites List in 5ks9
Calcium binding site 1 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:75.2
occ:1.00
OE1 A:GLN44 2.5 62.2 1.0
O A:HOH450 2.8 34.7 1.0
O A:GLU134 3.7 29.7 1.0
CD A:GLN44 3.7 64.3 1.0
O B:HOH1143 4.2 44.3 1.0
CA A:THR135 4.2 22.7 1.0
C A:GLU134 4.2 29.7 1.0
N A:THR135 4.5 24.4 1.0
NE2 A:GLN44 4.5 50.9 1.0
OE1 A:GLU30 4.5 46.3 1.0
CG2 A:THR135 4.7 25.1 1.0
CG A:GLN44 4.8 46.8 1.0
CB A:THR135 4.9 24.4 1.0

Calcium binding site 2 out of 4 in 5ks9

Go back to Calcium Binding Sites List in 5ks9
Calcium binding site 2 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:66.0
occ:1.00
OE1 C:GLN44 2.8 42.9 1.0
O C:GLU134 3.4 29.6 1.0
CD C:GLN44 3.8 45.8 1.0
C C:GLU134 4.1 29.9 1.0
CA C:THR135 4.1 22.2 1.0
N C:THR135 4.4 24.8 1.0
NE2 C:GLN44 4.5 31.5 1.0
O C:HOH431 4.5 46.3 1.0
O D:HOH1157 4.6 47.9 1.0
OE1 C:GLU30 4.8 34.8 1.0
CG2 C:THR135 4.8 29.6 1.0
CG C:GLN44 4.8 35.6 1.0
CB C:THR135 4.9 27.9 1.0

Calcium binding site 3 out of 4 in 5ks9

Go back to Calcium Binding Sites List in 5ks9
Calcium binding site 3 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:66.5
occ:1.00
OE1 E:GLN164 2.2 83.1 1.0
OD1 E:ASP174 2.4 54.0 1.0
CD E:GLN164 3.2 89.5 1.0
CG E:ASP174 3.4 51.2 1.0
O E:HOH464 3.6 25.5 1.0
CG E:GLN164 3.7 71.5 1.0
OD2 E:ASP174 4.0 57.5 1.0
O E:HOH472 4.0 33.7 1.0
O E:VAL162 4.1 55.7 1.0
CA E:ASP174 4.3 33.5 1.0
NE2 E:GLN164 4.3 83.3 1.0
CB E:ASP174 4.4 35.4 1.0
N E:GLN164 4.7 59.7 1.0
N E:ASP174 4.7 32.8 1.0
O E:THR173 4.7 35.7 1.0
C E:SER163 4.8 61.5 1.0
C E:THR173 4.9 34.9 1.0
CB E:GLN164 4.9 61.6 1.0
CA E:GLN164 5.0 59.8 1.0

Calcium binding site 4 out of 4 in 5ks9

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Calcium binding site 4 out of 4 in the BEL502-DQ8-Glia-ALPHA1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of BEL502-DQ8-Glia-ALPHA1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:0.3
occ:1.00
OD1 G:ASP174 2.1 58.0 1.0
NE2 G:GLN164 2.5 77.3 1.0
O G:HOH408 2.6 41.0 1.0
OE1 G:GLN164 2.9 80.2 1.0
CD G:GLN164 3.0 86.6 1.0
CG G:ASP174 3.2 56.3 1.0
OD2 G:ASP174 3.6 63.9 1.0
O G:HOH439 4.3 33.3 1.0
CG G:GLN164 4.3 73.3 1.0
CB G:ASP174 4.4 40.6 1.0
N G:ASP174 4.6 37.3 1.0
CA G:ASP174 4.8 38.3 1.0
O H:HOH350 4.8 27.5 1.0
O G:ILE172 5.0 33.2 1.0

Reference:

J.Petersen, Y.Kooy-Winkelaar, K.L.Loh, M.Tran, J.Van Bergen, F.Koning, J.Rossjohn, H.H.Reid. Diverse T Cell Receptor Gene Usage in Hla-DQ8-Associated Celiac Disease Converges Into A Consensus Binding Solution. Structure V. 24 1643 2016.
ISSN: ISSN 0969-2126
PubMed: 27568928
DOI: 10.1016/J.STR.2016.07.010
Page generated: Mon Jul 15 07:02:09 2024

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