Calcium in PDB 8oxw: Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-B02

The structure of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-B02, PDB code: 8oxw 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)	45.32 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.505, 93.488, 90.644, 90, 92.63, 90
R / Rfree (%)	17.2 / 21

The structure of Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-B02 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Transglutaminase 3 in Complex with Dh Patient-Derived Fab DH63-B02 (pdb code 8oxw). 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 Dh Patient-Derived Fab DH63-B02, PDB code: 8oxw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Transglutaminase 3 in Complex with 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 Dh Patient-Derived Fab DH63-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca711 b:22.6 occ:1.00 O A:ASN225 2.3 22.3 1.0 O A:ALA222 2.3 22.8 1.0 O A:ASN227 2.4 22.5 1.0 OD1 A:ASN225 2.4 20.8 1.0 OD1 A:ASP229 2.4 22.8 1.0 O A:HOH981 2.5 25.0 1.0 OD2 A:ASP229 2.5 22.0 1.0 CG A:ASP229 2.7 22.0 1.0 C A:ASN225 3.3 22.2 1.0 C A:ALA222 3.4 23.1 1.0 CG A:ASN225 3.4 18.1 1.0 C A:ASN227 3.5 27.9 1.0 HA A:MET223 3.5 20.0 1.0 H A:ASN225 3.8 21.7 1.0 H A:ASP229 3.8 22.5 1.0 N A:ASN227 3.8 25.4 1.0 HB2 A:ASP228 3.8 27.1 1.0 HB2 A:ASN227 3.9 26.1 1.0 HB1 A:ALA222 3.9 23.4 1.0 C A:SER226 3.9 22.8 1.0 H A:ASN227 3.9 24.9 1.0 H A:GLY231 4.0 22.7 1.0 HA A:ALA222 4.0 23.0 1.0 CA A:ASN225 4.1 22.1 1.0 HA3 A:GLY231 4.1 21.7 1.0 HD22 A:ASN225 4.1 19.4 1.0 CA A:ASN227 4.1 26.7 1.0 CB A:ASP229 4.2 20.7 1.0 ND2 A:ASN225 4.2 19.8 1.0 CA A:ALA222 4.2 23.2 1.0 N A:ASN225 4.2 22.1 1.0 N A:SER226 4.2 20.9 1.0 CA A:MET223 4.2 18.9 1.0 N A:MET223 4.2 20.2 1.0 O A:SER226 4.3 23.6 1.0 CB A:ASN225 4.3 22.6 1.0 N A:ASP229 4.3 21.7 1.0 OD2 A:ASP228 4.4 29.8 1.0 HB3 A:ASP229 4.4 21.4 1.0 CA A:SER226 4.5 21.9 1.0 O A:PHE365 4.5 24.2 1.0 CB A:ASN227 4.5 25.6 1.0 CB A:ALA222 4.5 23.3 1.0 HB2 A:PHE365 4.5 26.0 1.0 HA A:SER226 4.5 21.9 1.0 N A:ASP228 4.6 23.2 1.0 C A:MET223 4.6 20.8 1.0 CB A:ASP228 4.6 26.4 1.0 HB2 A:ASN225 4.7 21.4 1.0 N A:GLY231 4.7 22.7 1.0 HB2 A:ASP229 4.8 21.2 1.0 CA A:ASP229 4.8 21.6 1.0 O A:MET223 4.8 20.1 1.0 HB3 A:ALA222 4.9 23.3 1.0 CA A:GLY231 4.9 20.6 1.0 CG A:ASP228 4.9 33.2 1.0 HD21 A:ASN225 4.9 19.3 1.0 CA A:ASP228 5.0 24.4 1.0 H A:SER226 5.0 21.4 1.0 HG11 A:VAL364 5.0 33.4 1.0

Calcium binding site 2 out of 3 in the Transglutaminase 3 in Complex with 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 Dh Patient-Derived Fab DH63-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca712 b:35.2 occ:1.00 O A:HOH1057 2.1 28.6 1.0 OE2 A:GLU449 2.3 41.5 1.0 OD1 A:ASN394 2.4 35.5 1.0 O A:SER416 2.4 32.6 1.0 OE2 A:GLU444 2.4 35.9 1.0 OE1 A:GLU444 2.5 43.0 1.0 O A:HOH1092 2.6 38.5 1.0 CD A:GLU444 2.8 44.0 1.0 HH22 A:ARG450 3.2 42.8 1.0 CD A:GLU449 3.4 45.9 1.0 CG A:ASN394 3.4 38.7 1.0 HA A:HIS417 3.4 44.2 1.0 HD22 A:ASN394 3.4 38.8 1.0 HZ1 A:LYS441 3.5 36.8 1.0 C A:SER416 3.6 33.0 1.0 ND2 A:ASN394 3.8 38.5 1.0 NH2 A:ARG450 3.9 41.1 1.0 HG3 A:GLU449 4.0 40.4 1.0 HA A:ASN394 4.1 35.2 1.0 HH21 A:ARG450 4.1 42.8 1.0 OE1 A:GLU449 4.2 43.0 1.0 CG A:GLU449 4.2 39.5 1.0 CA A:HIS417 4.2 44.6 1.0 CG A:GLU444 4.3 43.4 1.0 N A:HIS417 4.3 39.0 1.0 HG2 A:GLU449 4.3 40.3 1.0 NZ A:LYS441 4.3 35.6 1.0 O A:HOH896 4.4 33.2 1.0 HZ3 A:LYS441 4.4 36.5 1.0 O A:ASN394 4.4 33.3 1.0 HE2 A:LYS441 4.5 38.9 1.0 HA A:SER416 4.5 35.1 1.0 HG3 A:GLU444 4.6 42.9 1.0 CA A:SER416 4.6 34.7 1.0 HB2 A:SER416 4.6 38.6 1.0 HG A:SER416 4.6 42.0 0.0 OD1 A:ASP396 4.6 36.9 1.0 HD21 A:ASN394 4.7 38.6 1.0 CB A:ASN394 4.7 37.7 1.0 HG2 A:GLU444 4.7 42.9 1.0 CA A:ASN394 4.7 35.7 1.0 O A:ILE419 4.8 30.1 1.0 HA A:GLU444 4.8 41.7 1.0 C A:HIS417 4.8 39.9 1.0 HD3 A:LYS441 4.8 40.8 1.0 HE A:ARG450 4.9 47.9 1.0 C A:ASN394 4.9 37.5 1.0 CE A:LYS441 4.9 39.4 1.0 CB A:SER416 5.0 38.9 1.0 HZ2 A:LYS441 5.0 36.6 1.0

Calcium binding site 3 out of 3 in the Transglutaminase 3 in Complex with 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 Dh Patient-Derived Fab DH63-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca713 b:37.0 occ:1.00 O A:SER308 2.3 38.5 1.0 OD1 A:ASP304 2.3 30.1 1.0 OD1 A:ASN306 2.3 46.8 1.0 OD2 A:ASP325 2.4 43.7 1.0 OD1 A:ASP302 2.4 41.3 1.0 O A:HOH965 2.4 45.8 1.0 O A:HOH813 3.1 53.8 1.0 HD22 A:ASN306 3.2 46.3 1.0 CG A:ASN306 3.3 51.5 1.0 CG A:ASP325 3.4 40.6 1.0 H A:SER308 3.4 35.4 1.0 CG A:ASP304 3.5 45.6 1.0 CG A:ASP302 3.5 39.7 1.0 HA A:VAL309 3.5 38.1 1.0 C A:SER308 3.5 35.3 1.0 ND2 A:ASN306 3.7 44.3 1.0 H A:ASP304 3.7 45.9 1.0 OD1 A:ASP325 3.7 42.0 1.0 H A:ASN306 3.8 45.6 1.0 HA A:ASP302 3.9 38.8 1.0 H A:THR303 3.9 41.1 1.0 HB3 A:SER308 4.0 39.6 1.0 OD2 A:ASP304 4.0 49.6 1.0 HG12 A:VAL309 4.0 39.3 1.0 N A:SER308 4.2 35.6 1.0 OD2 A:ASP302 4.2 35.8 1.0 CA A:VAL309 4.3 39.4 1.0 N A:VAL309 4.4 32.0 1.0 CA A:SER308 4.4 35.8 1.0 CB A:ASP302 4.4 40.7 1.0 N A:ASP304 4.5 45.7 1.0 HD21 A:ASN306 4.5 46.6 1.0 CA A:ASP302 4.5 38.9 1.0 HB2 A:ASP302 4.6 39.9 1.0 N A:ASN306 4.6 43.2 1.0 N A:THR303 4.6 43.7 1.0 CB A:SER308 4.7 40.1 1.0 CB A:ASP304 4.7 39.9 1.0 H A:LEU307 4.7 39.8 1.0 CB A:ASN306 4.7 47.1 1.0 HG1 A:THR303 4.7 44.5 0.0 CB A:ASP325 4.7 40.3 1.0 HG11 A:VAL309 4.7 39.4 1.0 CG1 A:VAL309 4.8 39.1 1.0 HB3 A:ASP325 4.8 39.9 1.0 C A:ASP304 4.8 52.0 1.0 CA A:ASP304 4.9 47.4 1.0 H A:ARG305 4.9 50.9 1.0 N A:LEU307 4.9 39.4 1.0 H A:ASP310 4.9 40.3 1.0 HB2 A:ASP325 5.0 40.2 1.0 N A:ARG305 5.0 49.5 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