Calcium in PDB 8oxx: Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02

The structure of Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02, PDB code: 8oxx 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)	52.80 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.271, 65.005, 90.908, 90, 96.85, 90
R / Rfree (%)	15.4 / 22.2

The binding sites of Calcium atom in the Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02 (pdb code 8oxx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02, PDB code: 8oxx:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02


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-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:29.0 occ:1.00 O A:HOH693 2.3 24.3 1.0 OD1 A:ASP229 2.4 32.4 1.0 OD1 A:ASN225 2.4 32.5 1.0 O A:ASN227 2.4 32.5 1.0 O A:ALA222 2.4 34.1 1.0 O A:ASN225 2.4 32.4 1.0 OD2 A:ASP229 2.4 39.2 1.0 CG A:ASP229 2.7 34.5 1.0 CG A:ASN225 3.3 36.0 1.0 C A:ASN225 3.4 32.7 1.0 C A:ALA222 3.4 33.3 1.0 C A:ASN227 3.5 38.8 1.0 HA A:MET223 3.5 31.9 1.0 HB1 A:ALA222 3.8 34.8 1.0 HB2 A:ASP228 3.8 49.5 1.0 N A:ASN227 3.8 32.0 1.0 H A:ASP229 3.9 44.2 1.0 HB2 A:ASN227 3.9 36.0 1.0 H A:ASN225 3.9 31.4 1.0 HD22 A:ASN225 3.9 34.2 1.0 HA A:ALA222 3.9 34.1 1.0 H A:ASN227 4.0 32.4 1.0 C A:SER226 4.0 30.4 1.0 ND2 A:ASN225 4.0 33.3 1.0 H A:GLY231 4.0 39.9 1.0 HA3 A:GLY231 4.1 38.4 1.0 CA A:ASN227 4.1 36.2 1.0 CB A:ASP229 4.1 37.1 1.0 CA A:ALA222 4.1 34.5 1.0 CA A:ASN225 4.2 33.9 1.0 O A:SER226 4.3 31.3 1.0 CB A:ASN225 4.3 34.2 1.0 N A:SER226 4.3 30.6 1.0 CA A:MET223 4.3 32.5 1.0 N A:MET223 4.3 31.9 1.0 N A:ASN225 4.3 30.9 1.0 N A:ASP229 4.4 46.5 1.0 HB3 A:ASP229 4.4 37.0 1.0 CB A:ALA222 4.4 34.6 1.0 HB2 A:PHE365 4.5 43.5 1.0 O A:PHE365 4.5 37.1 1.0 CB A:ASN227 4.5 35.2 1.0 CA A:SER226 4.6 30.6 1.0 CB A:ASP228 4.6 50.4 1.0 OD2 A:ASP228 4.6 50.0 1.0 HA A:SER226 4.6 30.1 1.0 N A:ASP228 4.6 44.5 1.0 C A:MET223 4.7 29.1 1.0 HB2 A:ASN225 4.7 34.7 1.0 HB2 A:ASP229 4.7 36.7 1.0 N A:GLY231 4.8 38.7 1.0 HD21 A:ASN225 4.8 33.9 1.0 CA A:ASP229 4.8 38.8 1.0 CG A:ASP228 4.9 53.0 1.0 HB3 A:ALA222 4.9 34.5 1.0 CA A:GLY231 4.9 40.2 1.0 CA A:ASP228 5.0 46.5 1.0

Calcium binding site 2 out of 3 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02


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-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:51.4 occ:1.00 O A:HOH667 2.2 31.5 1.0 O A:HOH647 2.3 49.2 1.0 OE2 A:GLU449 2.4 53.9 1.0 OD1 A:ASN394 2.4 67.6 1.0 OE2 A:GLU444 2.4 63.6 1.0 O A:SER416 2.4 59.2 1.0 OE1 A:GLU444 2.5 68.6 1.0 CD A:GLU444 2.8 62.9 1.0 HA A:HIS417 3.3 61.3 1.0 CD A:GLU449 3.5 61.5 1.0 CG A:ASN394 3.5 65.5 1.0 C A:SER416 3.5 62.1 1.0 HH22 A:ARG450 3.6 80.8 1.0 HZ2 A:LYS441 3.7 46.9 1.0 HD22 A:ASN394 3.7 66.6 1.0 HH21 A:ARG450 3.8 80.7 1.0 NH2 A:ARG450 4.0 82.9 1.0 ND2 A:ASN394 4.0 66.6 1.0 HA A:ASN394 4.1 57.1 1.0 CA A:HIS417 4.2 62.0 1.0 OE1 A:GLU449 4.2 68.9 1.0 HB2 A:SER416 4.2 68.2 1.0 HD2 A:LYS441 4.2 49.4 1.0 CG A:GLU444 4.3 62.3 1.0 N A:HIS417 4.3 58.0 1.0 HG3 A:GLU449 4.3 65.4 1.0 HB3 A:HIS417 4.3 69.5 1.0 CG A:GLU449 4.4 65.3 1.0 HA A:SER416 4.4 63.8 1.0 HA A:GLU444 4.4 67.3 1.0 CA A:SER416 4.5 63.9 1.0 HG2 A:GLU449 4.5 65.5 1.0 O A:HOH660 4.5 36.3 1.0 NZ A:LYS441 4.5 46.5 1.0 OD1 A:ASP396 4.6 61.5 1.0 O A:ASN394 4.6 54.0 1.0 O A:ALA395 4.6 58.9 1.0 HG3 A:GLU444 4.6 61.9 1.0 HG A:SER416 4.6 75.2 0.0 CB A:ASN394 4.7 59.3 1.0 HG2 A:GLU444 4.7 62.0 1.0 CB A:SER416 4.8 66.4 1.0 CA A:ASN394 4.8 57.0 1.0 HZ1 A:LYS441 4.8 46.5 1.0 CB A:HIS417 4.8 69.7 1.0 HD21 A:ASN394 4.9 66.2 1.0 C A:ASN394 4.9 58.2 1.0 CZ A:ARG450 5.0 78.0 1.0

Calcium binding site 3 out of 3 in the Transglutaminase 3 in Complex with Inhibitor Z-Don and Dh Patient- Derived Fab DH63-B02


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-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:55.5 occ:1.00 O A:SER308 2.4 55.5 1.0 OD2 A:ASP310 2.4 79.8 1.0 OD1 A:ASN306 2.4 64.5 1.0 OD2 A:ASP325 2.4 53.8 1.0 OD1 A:ASP302 2.4 65.3 1.0 OD1 A:ASP304 2.4 82.9 1.0 HD22 A:ASN306 2.8 74.9 1.0 CG A:ASN306 3.1 70.8 1.0 ND2 A:ASN306 3.2 77.0 1.0 CG A:ASP302 3.2 58.1 1.0 CG A:ASP325 3.3 52.5 1.0 CG A:ASP304 3.3 81.5 1.0 CG A:ASP310 3.4 72.9 1.0 OD1 A:ASP325 3.4 59.0 1.0 OD2 A:ASP304 3.5 89.9 1.0 C A:SER308 3.5 54.5 1.0 HA A:VAL309 3.7 58.0 1.0 OD2 A:ASP302 3.7 50.9 1.0 H A:SER308 3.7 59.9 1.0 H A:ASP310 3.7 62.9 1.0 HG A:SER308 3.8 72.5 0.0 H A:THR303 3.9 63.5 1.0 HD21 A:ASN306 4.0 75.5 1.0 OD1 A:ASP310 4.0 59.8 1.0 H A:ASN306 4.0 69.4 1.0 HB2 A:ASP310 4.3 71.0 1.0 HA A:ASP302 4.3 57.3 1.0 N A:ASP310 4.3 64.0 1.0 H A:ASP304 4.3 66.4 1.0 CB A:ASP302 4.4 61.7 1.0 N A:SER308 4.4 58.4 1.0 N A:VAL309 4.4 57.8 1.0 CB A:ASP310 4.4 71.5 1.0 CA A:VAL309 4.4 58.0 1.0 CA A:SER308 4.4 59.5 1.0 OG A:SER308 4.4 71.6 1.0 HB2 A:ASP302 4.4 59.6 1.0 CB A:ASN306 4.5 67.2 1.0 N A:THR303 4.7 64.6 1.0 CB A:ASP304 4.7 76.8 1.0 CB A:ASP325 4.7 54.2 1.0 N A:ASN306 4.7 67.8 1.0 N A:ASP304 4.8 67.4 1.0 HB3 A:ASN306 4.8 68.6 1.0 CA A:ASP302 4.8 57.0 1.0 CB A:SER308 4.8 65.5 1.0 HB2 A:SER308 4.8 65.5 1.0 C A:VAL309 4.8 58.0 1.0 HB3 A:ASP325 4.9 53.2 1.0 HG1 A:THR303 4.9 67.2 0.0 C A:ASP304 4.9 67.6 1.0

J.E.Heggelund, S.Das, J.Stamnaes, R.Iversen, L.M.Sollid. Autoantibody Binding and Unique Enzyme-Substrate Intermediate Conformation of Human Transglutaminase 3. Nat Commun V. 14 6216 2023.
ISSN: ESSN 2041-1723
PubMed: 37798283
DOI: 10.1038/S41467-023-42004-Z