Atomistry » Calcium » PDB 8qyd-8s38 » 8rmy
Atomistry »
  Calcium »
    PDB 8qyd-8s38 »
      8rmy »

Calcium in PDB 8rmy: Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02

Enzymatic activity of Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02

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

Protein crystallography data

The structure of Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02, PDB code: 8rmy 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) 69.20 / 2.90
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.184, 260.191, 139.024, 90, 95.1, 90
R / Rfree (%) 19.5 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 (pdb code 8rmy). 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02, PDB code: 8rmy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8rmy

Go back to Calcium Binding Sites List in 8rmy
Calcium binding site 1 out of 6 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:89.9
occ:1.00
 OD1 A:ASN225 2.2 103.6 1.0
O A:ASN225 2.3 92.0 1.0
O A:ASN227 2.3 122.1 1.0
O A:ALA222 2.4 91.0 1.0
OD1 A:ASP229 2.4 93.2 1.0
O A:HOH604 2.6 61.8 1.0
OD2 A:ASP229 2.7 90.5 1.0
CG A:ASP229 2.9 91.3 1.0
CG A:ASN225 3.2 91.7 1.0
C A:ASN225 3.2 102.1 1.0
C A:ASN227 3.4 106.4 1.0
C A:ALA222 3.4 90.2 1.0
N A:ASN227 3.6 88.4 1.0
C A:SER226 3.8 90.9 1.0
ND2 A:ASN225 3.9 111.9 1.0
CA A:ASN227 4.0 103.8 1.0
CA A:ASN225 4.0 98.8 1.0
O A:SER226 4.1 90.1 1.0
N A:SER226 4.1 108.1 1.0
CB A:ASN225 4.2 95.0 1.0
N A:ASN225 4.2 76.8 1.0
CA A:ALA222 4.2 85.8 1.0
CB A:ASP229 4.3 118.4 1.0
N A:MET223 4.3 71.6 1.0
CA A:MET223 4.3 78.6 1.0
CB A:ASN227 4.4 88.9 1.0
O A:PHE365 4.4 88.1 1.0
CA A:SER226 4.5 97.7 1.0
N A:ASP229 4.5 72.6 1.0
N A:ASP228 4.6 101.8 1.0
OD2 A:ASP228 4.6 156.3 1.0
CB A:ALA222 4.6 71.1 1.0
C A:MET223 4.7 76.6 1.0
CB A:ASP228 4.7 106.3 1.0
N A:GLY231 4.8 103.7 1.0
CG A:ASP228 4.9 115.8 1.0
CA A:ASP229 4.9 83.2 1.0
CA A:GLY231 4.9 105.9 1.0

Calcium binding site 2 out of 6 in 8rmy

Go back to Calcium Binding Sites List in 8rmy
Calcium binding site 2 out of 6 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:76.0
occ:1.00
 OD1 A:ASN394 2.2 76.2 1.0
O A:HOH606 2.2 72.9 1.0
O A:SER416 2.3 84.1 1.0
OE2 A:GLU449 2.4 73.8 1.0
OE2 A:GLU444 2.7 80.5 1.0
OE1 A:GLU444 2.8 75.2 1.0
CD A:GLU444 3.1 96.5 1.0
CG A:ASN394 3.3 112.7 1.0
C A:SER416 3.5 92.8 1.0
CD A:GLU449 3.6 100.3 1.0
NH2 A:ARG450 3.7 104.7 1.0
ND2 A:ASN394 3.9 112.1 1.0
O A:ASN394 4.1 98.7 1.0
OD1 A:ASP396 4.2 118.7 1.0
N A:HIS417 4.3 84.7 1.0
OE1 A:GLU449 4.3 100.0 1.0
O A:ALA395 4.3 129.9 1.0
CA A:HIS417 4.3 97.2 1.0
CA A:SER416 4.4 99.5 1.0
CA A:ASN394 4.4 85.3 1.0
CB A:ASN394 4.5 93.3 1.0
C A:ASN394 4.5 89.3 1.0
CG A:GLU449 4.6 102.7 1.0
NZ A:LYS441 4.7 74.5 1.0
CG A:GLU444 4.7 95.0 1.0
CB A:SER416 4.7 89.5 1.0
CZ A:ARG450 4.8 87.7 1.0

Calcium binding site 3 out of 6 in 8rmy

Go back to Calcium Binding Sites List in 8rmy
Calcium binding site 3 out of 6 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:84.3
occ:1.00
 OD2 A:ASP310 2.3 101.2 1.0
O A:SER308 2.3 102.6 1.0
OD2 A:ASP325 2.4 87.0 1.0
OD1 A:ASN306 2.4 73.8 1.0
OD1 A:ASP304 2.4 118.6 1.0
OD1 A:ASP302 2.5 108.0 1.0
CG A:ASN306 3.1 86.8 1.0
ND2 A:ASN306 3.1 87.3 1.0
CG A:ASP325 3.1 90.8 1.0
OD1 A:ASP325 3.2 94.4 1.0
CG A:ASP304 3.3 96.8 1.0
CG A:ASP302 3.4 87.4 1.0
CG A:ASP310 3.4 85.1 1.0
C A:SER308 3.5 76.5 1.0
OD2 A:ASP304 3.7 104.6 1.0
OD2 A:ASP302 3.8 70.6 1.0
OD1 A:ASP310 4.0 89.3 1.0
N A:SER308 4.3 76.1 1.0
OG A:SER308 4.3 88.3 1.0
N A:ASP310 4.3 108.8 1.0
CA A:SER308 4.3 86.8 1.0
N A:VAL309 4.4 71.1 1.0
CB A:ASP310 4.4 80.0 1.0
CA A:VAL309 4.5 83.5 1.0
CB A:ASP302 4.5 85.6 1.0
CB A:ASN306 4.5 85.1 1.0
CB A:ASP325 4.6 79.5 1.0
CB A:ASP304 4.6 91.1 1.0
N A:ASP304 4.7 92.6 1.0
CB A:SER308 4.7 79.7 1.0
N A:ASN306 4.8 81.1 1.0
N A:THR303 4.8 112.1 1.0
C A:VAL309 4.9 104.0 1.0
C A:ASP304 4.9 89.9 1.0
CA A:ASP302 4.9 87.4 1.0
CA A:ASP304 5.0 96.5 1.0

Calcium binding site 4 out of 6 in 8rmy

Go back to Calcium Binding Sites List in 8rmy
Calcium binding site 4 out of 6 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:96.8
occ:1.00
 OD1 D:ASN225 2.2 105.8 1.0
O D:ALA222 2.3 92.7 1.0
O D:ASN227 2.3 104.1 1.0
O D:ASN225 2.4 91.0 1.0
OD1 D:ASP229 2.6 81.1 1.0
OD2 D:ASP229 2.7 88.1 1.0
CG D:ASP229 2.9 85.7 1.0
CG D:ASN225 3.1 96.8 1.0
C D:ALA222 3.3 101.4 1.0
C D:ASN225 3.4 97.5 1.0
C D:ASN227 3.4 105.8 1.0
N D:ASN227 3.7 85.7 1.0
ND2 D:ASN225 3.8 103.5 1.0
C D:SER226 4.0 93.6 1.0
CA D:ASN227 4.0 84.1 1.0
CA D:ALA222 4.1 97.8 1.0
CA D:ASN225 4.1 88.7 1.0
CB D:ASN225 4.2 89.4 1.0
O D:PHE365 4.3 85.0 1.0
N D:ASN225 4.3 90.1 1.0
N D:SER226 4.3 88.1 1.0
O D:SER226 4.3 101.5 1.0
N D:MET223 4.3 95.2 1.0
OD2 D:ASP228 4.3 117.8 1.0
CB D:ASN227 4.3 91.3 1.0
CB D:ASP229 4.4 90.7 1.0
CA D:MET223 4.4 84.8 1.0
CB D:ALA222 4.5 93.2 1.0
CB D:ASP228 4.5 82.2 1.0
N D:ASP229 4.6 94.6 1.0
N D:ASP228 4.6 77.2 1.0
CA D:SER226 4.6 82.1 1.0
CG D:ASP228 4.7 106.7 1.0
C D:MET223 4.8 91.7 1.0
CA D:ASP228 5.0 85.9 1.0

Calcium binding site 5 out of 6 in 8rmy

Go back to Calcium Binding Sites List in 8rmy
Calcium binding site 5 out of 6 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:93.9
occ:1.00
 OD1 D:ASN394 2.2 87.8 1.0
O D:HOH607 2.3 108.2 1.0
O D:SER416 2.4 105.0 1.0
OE2 D:GLU449 2.5 76.2 1.0
OE2 D:GLU444 2.6 96.5 1.0
OE1 D:GLU444 2.8 90.8 1.0
CD D:GLU444 3.1 112.7 1.0
CG D:ASN394 3.3 83.5 1.0
C D:SER416 3.5 107.5 1.0
CD D:GLU449 3.6 95.3 1.0
NH2 D:ARG450 3.8 126.1 1.0
ND2 D:ASN394 4.0 98.2 1.0
OD1 D:ASP396 4.1 142.2 1.0
O D:ASN394 4.1 89.8 1.0
OE1 D:GLU449 4.3 94.4 1.0
O D:HOH604 4.3 76.3 1.0
CA D:HIS417 4.3 116.9 1.0
N D:HIS417 4.4 118.8 1.0
CA D:ASN394 4.4 87.1 1.0
CB D:ASN394 4.4 80.5 1.0
O D:ALA395 4.5 102.4 1.0
CA D:SER416 4.5 104.0 1.0
C D:ASN394 4.5 87.0 1.0
NZ D:LYS441 4.5 83.9 1.0
CG D:GLU449 4.6 114.1 1.0
CG D:GLU444 4.6 112.0 1.0
CB D:SER416 4.8 89.8 1.0
CZ D:ARG450 4.8 96.9 1.0
O D:ILE419 5.0 84.2 1.0

Calcium binding site 6 out of 6 in 8rmy

Go back to Calcium Binding Sites List in 8rmy
Calcium binding site 6 out of 6 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and 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 Inhibitor Z-Don and Dh Patient- Derived Fab DH63-A02 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:84.3
occ:1.00
 OD2 D:ASP325 2.2 72.4 1.0
OD1 D:ASP302 2.3 90.1 1.0
O D:SER308 2.4 112.9 1.0
OD1 D:ASP304 2.4 123.2 1.0
OD1 D:ASN306 2.5 71.7 1.0
OD2 D:ASP310 2.6 78.2 1.0
CG D:ASP325 2.9 83.8 1.0
OD1 D:ASP325 3.0 109.2 1.0
CG D:ASP302 3.2 85.0 1.0
CG D:ASP304 3.2 93.4 1.0
CG D:ASN306 3.3 71.3 1.0
ND2 D:ASN306 3.4 80.3 1.0
C D:SER308 3.5 84.2 1.0
OD2 D:ASP304 3.6 84.9 1.0
CG D:ASP310 3.7 82.3 1.0
OD2 D:ASP302 3.7 65.0 1.0
CB D:ASP302 4.3 103.2 1.0
CB D:ASP325 4.3 83.1 1.0
OD1 D:ASP310 4.4 64.6 1.0
N D:SER308 4.4 72.7 1.0
N D:VAL309 4.4 70.1 1.0
N D:ASP310 4.4 93.3 1.0
CA D:VAL309 4.5 76.1 1.0
CA D:SER308 4.5 85.7 1.0
CB D:ASP304 4.5 77.7 1.0
OG D:SER308 4.5 88.5 1.0
N D:THR303 4.5 111.8 1.0
N D:ASP304 4.6 88.0 1.0
CB D:ASP310 4.6 71.2 1.0
CA D:ASP302 4.7 100.8 1.0
CB D:ASN306 4.7 65.1 1.0
C D:ASP304 4.9 69.2 1.0
N D:ASN306 4.9 66.8 1.0
CA D:ASP304 4.9 76.3 1.0
C D:VAL309 4.9 88.1 1.0
CB D:SER308 5.0 98.1 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 06:54:55 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy