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Calcium in PDB 8rmx: Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02

Enzymatic activity of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02

All present enzymatic activity of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02:
2.3.2.13;

Protein crystallography data

The structure of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02, PDB code: 8rmx was solved by J.E.Heggelund, L.M.Sollid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 132.00 / 2.80
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.031, 264.004, 148.7, 90, 106.29, 90
R / Rfree (%) 20.5 / 25

Calcium Binding Sites:

The binding sites of Calcium atom in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 (pdb code 8rmx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02, PDB code: 8rmx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8rmx

Go back to Calcium Binding Sites List in 8rmx
Calcium binding site 1 out of 6 in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:93.6
occ:1.00
 O A:ASN225 2.2 91.2 1.0
O A:HOH607 2.2 70.0 1.0
OD1 A:ASN225 2.2 89.0 1.0
O A:ASN227 2.2 95.4 1.0
OD1 A:ASP229 2.3 97.5 1.0
O A:ALA222 2.4 76.9 1.0
OD2 A:ASP229 2.7 88.6 1.0
CG A:ASP229 2.8 97.2 1.0
C A:ASN225 3.2 79.8 1.0
CG A:ASN225 3.3 85.8 1.0
C A:ASN227 3.4 92.0 1.0
C A:ALA222 3.5 88.9 1.0
N A:ASN227 3.6 79.7 1.0
C A:SER226 3.7 67.3 1.0
CA A:ASN227 4.0 97.2 1.0
CA A:ASN225 4.0 66.6 1.0
O A:SER226 4.0 85.8 1.0
N A:SER226 4.1 100.8 1.0
ND2 A:ASN225 4.1 80.8 1.0
N A:ASN225 4.2 74.3 1.0
CB A:ASN225 4.2 70.9 1.0
CB A:ASP229 4.2 96.7 1.0
CA A:MET223 4.3 89.8 1.0
CA A:SER226 4.3 91.5 1.0
CA A:ALA222 4.3 95.7 1.0
N A:MET223 4.3 81.8 1.0
N A:ASP229 4.3 85.5 1.0
CB A:ASN227 4.4 104.2 1.0
N A:ASP228 4.5 104.6 1.0
OD2 A:ASP228 4.6 111.1 1.0
O A:PHE365 4.6 77.0 1.0
CB A:ASP228 4.6 113.0 1.0
C A:MET223 4.6 85.3 1.0
N A:GLY231 4.7 86.0 1.0
CB A:ALA222 4.7 78.4 1.0
CA A:ASP229 4.8 88.4 1.0
CA A:GLY231 4.8 103.5 1.0
CA A:ASP228 4.9 113.8 1.0
O A:MET223 4.9 81.6 1.0
CG A:ASP228 5.0 109.3 1.0

Calcium binding site 2 out of 6 in 8rmx

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Calcium binding site 2 out of 6 in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:81.5
occ:1.00
 O A:SER416 2.2 124.6 1.0
OE2 A:GLU444 2.3 95.2 1.0
OD1 A:ASN394 2.5 89.1 1.0
OE1 A:GLU444 2.5 93.9 1.0
OE2 A:GLU449 2.5 88.8 1.0
CD A:GLU444 2.8 115.1 1.0
O A:HOH608 2.9 79.7 1.0
C A:SER416 3.3 112.2 1.0
CG A:ASN394 3.5 89.2 1.0
NH2 A:ARG450 3.5 125.6 1.0
CD A:GLU449 3.6 87.1 1.0
O A:ASN394 4.0 88.2 1.0
N A:HIS417 4.1 80.6 1.0
CA A:HIS417 4.1 80.7 1.0
ND2 A:ASN394 4.2 92.9 1.0
CA A:SER416 4.2 104.5 1.0
OE1 A:GLU449 4.3 94.8 1.0
CG A:GLU444 4.3 104.8 1.0
OD1 A:ASP396 4.4 102.7 1.0
CA A:ASN394 4.5 95.5 1.0
CB A:SER416 4.5 79.7 1.0
C A:ASN394 4.5 106.8 1.0
CG A:GLU449 4.5 112.8 1.0
CB A:ASN394 4.6 88.2 1.0
CZ A:ARG450 4.7 95.8 1.0
O A:ALA395 4.8 88.9 1.0
NZ A:LYS441 4.8 71.6 1.0
O A:ILE419 4.9 70.4 1.0
C A:HIS417 4.9 104.0 1.0

Calcium binding site 3 out of 6 in 8rmx

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Calcium binding site 3 out of 6 in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:91.5
occ:1.00
 OD2 A:ASP325 2.1 82.5 1.0
O A:SER308 2.2 90.4 1.0
OD1 A:ASP304 2.4 108.3 1.0
OD2 A:ASP310 2.4 83.2 1.0
OD1 A:ASN306 2.5 77.6 1.0
OD1 A:ASP302 2.5 87.8 1.0
CG A:ASP325 3.1 84.8 1.0
CG A:ASN306 3.3 80.1 1.0
ND2 A:ASN306 3.3 72.7 1.0
CG A:ASP304 3.4 92.8 1.0
C A:SER308 3.4 82.5 1.0
OD1 A:ASP325 3.5 95.9 1.0
CG A:ASP310 3.5 88.9 1.0
CG A:ASP302 3.7 89.1 1.0
OD2 A:ASP304 3.8 106.7 1.0
OD1 A:ASP310 4.2 89.2 1.0
N A:ASP310 4.2 90.6 1.0
N A:VAL309 4.3 77.7 1.0
CA A:VAL309 4.3 85.7 1.0
N A:SER308 4.4 59.4 1.0
OG A:SER308 4.4 91.0 1.0
CA A:SER308 4.4 79.7 1.0
CB A:ASP310 4.4 83.6 1.0
CB A:ASP325 4.4 79.7 1.0
OD2 A:ASP302 4.5 96.2 1.0
N A:ASP304 4.6 71.7 1.0
C A:VAL309 4.6 91.1 1.0
CB A:ASP302 4.6 90.7 1.0
CB A:ASP304 4.7 79.8 1.0
CB A:ASN306 4.7 90.1 1.0
CA A:ASP302 4.7 83.8 1.0
N A:THR303 4.7 91.9 1.0
CB A:SER308 4.8 82.9 1.0
N A:ASN306 4.8 95.8 1.0
CA A:ASP310 4.9 85.3 1.0
CA A:ASP304 5.0 75.1 1.0
C A:ASP304 5.0 83.8 1.0

Calcium binding site 4 out of 6 in 8rmx

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Calcium binding site 4 out of 6 in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:85.2
occ:1.00
 O D:ALA222 2.2 85.1 1.0
O D:ASN227 2.3 79.5 1.0
OD1 D:ASN225 2.3 96.1 1.0
OD1 D:ASP229 2.6 77.5 1.0
O D:ASN225 2.6 91.0 1.0
OD2 D:ASP229 2.6 91.7 1.0
CG D:ASP229 2.9 87.5 1.0
C D:ALA222 3.1 98.4 1.0
CG D:ASN225 3.3 89.1 1.0
C D:ASN227 3.5 95.6 1.0
C D:ASN225 3.5 93.2 1.0
CA D:ALA222 3.9 93.6 1.0
N D:ASN227 3.9 101.1 1.0
ND2 D:ASN225 4.0 102.2 1.0
N D:MET223 4.1 106.1 1.0
C D:SER226 4.2 91.2 1.0
O D:PHE365 4.2 97.4 1.0
CA D:ASN227 4.2 96.9 1.0
CB D:ALA222 4.2 88.7 1.0
CA D:MET223 4.2 99.0 1.0
CA D:ASN225 4.2 101.5 1.0
CB D:ASP229 4.3 84.8 1.0
OD2 D:ASP228 4.3 106.6 1.0
CB D:ASN225 4.3 101.7 1.0
N D:ASN225 4.3 88.8 1.0
CB D:ASP228 4.5 112.9 1.0
N D:ASP229 4.5 85.8 1.0
N D:SER226 4.5 88.3 1.0
O D:SER226 4.5 96.3 1.0
N D:ASP228 4.5 116.3 1.0
CB D:ASN227 4.6 91.5 1.0
C D:MET223 4.7 104.4 1.0
CA D:SER226 4.8 94.1 1.0
CG D:ASP228 4.8 110.3 1.0
CA D:ASP228 4.9 100.2 1.0
CA D:ASP229 5.0 96.7 1.0

Calcium binding site 5 out of 6 in 8rmx

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Calcium binding site 5 out of 6 in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:93.0
occ:1.00
 O D:SER416 2.2 84.8 1.0
OD1 D:ASN394 2.3 93.9 1.0
OE2 D:GLU444 2.4 100.1 1.0
OE2 D:GLU449 2.5 88.8 1.0
O D:HOH604 2.5 72.0 1.0
OE1 D:GLU444 2.7 109.7 1.0
CD D:GLU444 2.9 130.6 1.0
C D:SER416 3.3 96.4 1.0
CG D:ASN394 3.4 100.0 1.0
NH2 D:ARG450 3.6 136.9 1.0
CD D:GLU449 3.6 94.0 1.0
O D:ASN394 3.7 82.6 1.0
N D:HIS417 4.1 104.1 1.0
ND2 D:ASN394 4.1 115.7 1.0
CA D:SER416 4.2 105.3 1.0
CA D:HIS417 4.2 101.1 1.0
OE1 D:GLU449 4.3 100.1 1.0
OD1 D:ASP396 4.3 91.2 1.0
C D:ASN394 4.4 78.8 1.0
CA D:ASN394 4.4 85.8 1.0
CB D:SER416 4.4 98.6 1.0
CG D:GLU444 4.4 130.0 1.0
CB D:ASN394 4.5 102.0 1.0
CG D:GLU449 4.5 108.3 1.0
O D:ALA395 4.6 85.8 1.0
NZ D:LYS441 4.7 104.5 1.0
CZ D:ARG450 4.8 89.5 1.0
OG D:SER416 4.9 83.2 1.0
O D:ILE419 5.0 69.6 1.0

Calcium binding site 6 out of 6 in 8rmx

Go back to Calcium Binding Sites List in 8rmx
Calcium binding site 6 out of 6 in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:96.4
occ:1.00
 OD2 D:ASP325 2.2 81.4 1.0
O D:SER308 2.3 97.0 1.0
OD1 D:ASP304 2.3 131.5 1.0
OD1 D:ASN306 2.4 86.9 1.0
OD2 D:ASP310 2.5 77.1 1.0
OD1 D:ASP302 2.6 72.4 1.0
CG D:ASP325 3.1 107.0 1.0
CG D:ASN306 3.1 76.5 1.0
ND2 D:ASN306 3.2 83.9 1.0
CG D:ASP304 3.3 91.2 1.0
C D:SER308 3.4 80.4 1.0
OD1 D:ASP325 3.5 99.9 1.0
CG D:ASP310 3.6 81.7 1.0
OD2 D:ASP304 3.7 95.2 1.0
CG D:ASP302 3.7 93.2 1.0
N D:ASP310 4.2 77.9 1.0
OD1 D:ASP310 4.3 62.9 1.0
N D:VAL309 4.3 70.0 1.0
OG D:SER308 4.3 70.3 1.0
CA D:VAL309 4.3 82.4 1.0
N D:SER308 4.3 71.0 1.0
CA D:SER308 4.4 76.7 1.0
CB D:ASP325 4.5 111.7 1.0
OD2 D:ASP302 4.5 94.7 1.0
CB D:ASP310 4.5 78.5 1.0
N D:ASP304 4.5 86.3 1.0
CB D:ASN306 4.6 70.0 1.0
CB D:ASP304 4.6 76.8 1.0
C D:VAL309 4.7 85.1 1.0
CB D:ASP302 4.7 124.2 1.0
N D:THR303 4.7 98.3 1.0
CA D:ASP302 4.7 105.5 1.0
N D:ASN306 4.8 82.4 1.0
CB D:SER308 4.8 82.7 1.0
CA D:ASP304 4.9 84.6 1.0
C D:ASP304 4.9 80.1 1.0

Reference:

R.Iversen, J.E.Heggelund, S.Das, L.M.Sollid. Enzyme-Activating B-Cell Receptors Boost Antigen Presentation to Pathogenic T Cells in Gluten-Sensitive Autoimmunity Nat Commun 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-57564-5
Page generated: Thu Jul 10 06:54:35 2025

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