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

The structure of Transglutaminase 3 Zymogen in Complex with Dh Patient-Derived Fab DH63-B02, PDB code: 8oxv 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)	41.81 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.659, 94.04, 91.143, 90, 93.46, 90
R / Rfree (%)	18.5 / 22.9

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

Calcium binding site 1 out of 3 in the Transglutaminase 3 Zymogen 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 Zymogen in Complex with Dh Patient-Derived Fab DH63-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:20.1 occ:1.00 O A:ALA222 2.3 20.2 1.0 OD1 A:ASP229 2.4 19.7 1.0 O A:ASN227 2.4 20.0 1.0 OD1 A:ASN225 2.4 19.8 1.0 O A:ASN225 2.4 19.2 1.0 O A:HOH918 2.4 22.9 1.0 OD2 A:ASP229 2.5 21.1 1.0 CG A:ASP229 2.7 20.1 1.0 C A:ALA222 3.3 20.0 1.0 C A:ASN225 3.4 18.8 1.0 CG A:ASN225 3.4 18.6 1.0 HA A:MET223 3.5 17.5 1.0 C A:ASN227 3.5 22.2 1.0 HB2 A:ASP228 3.7 23.6 1.0 N A:ASN227 3.8 22.6 1.0 H A:ASN225 3.8 18.5 1.0 H A:ASP229 3.8 22.6 1.0 H A:ASN227 3.9 22.4 1.0 HB2 A:ASN227 3.9 23.5 1.0 C A:SER226 3.9 22.4 1.0 HA A:ALA222 4.0 20.2 1.0 HB1 A:ALA222 4.0 20.5 1.0 HA3 A:GLY231 4.1 21.4 1.0 HD22 A:ASN225 4.1 18.5 1.0 H A:GLY231 4.1 22.0 1.0 CA A:ASN227 4.1 22.9 1.0 CB A:ASP229 4.2 22.1 1.0 CA A:ASN225 4.2 18.6 1.0 ND2 A:ASN225 4.2 18.4 1.0 CA A:ALA222 4.2 19.9 1.0 CA A:MET223 4.2 17.1 1.0 N A:SER226 4.2 18.6 1.0 N A:MET223 4.2 17.6 1.0 N A:ASN225 4.3 18.6 1.0 O A:SER226 4.3 25.0 1.0 CB A:ASN225 4.3 18.9 1.0 N A:ASP229 4.3 22.5 1.0 O A:PHE365 4.4 23.3 1.0 HB3 A:ASP229 4.4 21.9 1.0 OD2 A:ASP228 4.5 24.8 1.0 HA A:SER226 4.5 20.0 1.0 CA A:SER226 4.5 19.7 1.0 HB2 A:PHE365 4.5 23.2 1.0 CB A:ASP228 4.5 23.7 1.0 CB A:ASN227 4.5 23.1 1.0 C A:MET223 4.6 17.1 1.0 CB A:ALA222 4.6 20.5 1.0 N A:ASP228 4.6 21.2 1.0 HB2 A:ASN225 4.7 18.8 1.0 HB2 A:ASP229 4.8 21.7 1.0 O A:MET223 4.8 16.3 1.0 N A:GLY231 4.8 21.7 1.0 CA A:ASP229 4.8 22.4 1.0 CA A:GLY231 4.9 21.6 1.0 HB3 A:ALA222 4.9 20.4 1.0 CG A:ASP228 4.9 25.9 1.0 HD21 A:ASN225 4.9 18.4 1.0 H A:SER226 5.0 18.9 1.0 CA A:ASP228 5.0 22.3 1.0

Calcium binding site 2 out of 3 in the Transglutaminase 3 Zymogen 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 Zymogen in Complex with Dh Patient-Derived Fab DH63-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:37.8 occ:1.00 O A:HOH1029 2.2 29.4 1.0 OE2 A:GLU449 2.3 44.6 1.0 O A:HOH1149 2.4 44.1 1.0 OE1 A:GLU444 2.4 43.4 1.0 O A:SER416 2.4 38.2 1.0 OE2 A:GLU444 2.4 42.7 1.0 OD1 A:ASN394 2.5 37.2 1.0 CD A:GLU444 2.7 48.4 1.0 HA A:HIS417 3.0 46.1 1.0 HH11 A:ARG450 3.2 57.7 1.0 HD22 A:ASN394 3.2 40.0 1.0 CG A:ASN394 3.4 37.5 1.0 CD A:GLU449 3.4 50.5 1.0 C A:SER416 3.5 37.0 1.0 HZ1 A:LYS441 3.7 37.7 1.0 ND2 A:ASN394 3.7 40.9 1.0 CA A:HIS417 3.9 48.0 1.0 NH1 A:ARG450 3.9 59.5 1.0 HH12 A:ARG450 4.0 57.5 1.0 HE2 A:LYS441 4.1 38.5 1.0 N A:HIS417 4.1 41.8 1.0 HG3 A:GLU449 4.1 46.3 1.0 OE1 A:GLU449 4.1 48.1 1.0 HA A:ASN394 4.1 34.4 1.0 HZ3 A:LYS441 4.2 37.4 1.0 CG A:GLU444 4.2 48.7 1.0 CG A:GLU449 4.3 45.8 1.0 NZ A:LYS441 4.3 36.9 1.0 O A:ASN394 4.4 36.6 1.0 HG2 A:GLU449 4.4 46.2 1.0 HG3 A:GLU444 4.5 47.9 1.0 HD21 A:ASN394 4.5 39.8 1.0 O A:HOH1003 4.6 32.0 1.0 HG A:SER416 4.6 42.6 0.0 OD1 A:ASP396 4.6 39.7 1.0 C A:HIS417 4.7 39.6 1.0 CE A:LYS441 4.7 39.1 1.0 HG2 A:GLU444 4.7 47.9 1.0 CB A:ASN394 4.7 34.5 1.0 CA A:SER416 4.7 38.3 1.0 O A:ILE419 4.7 35.1 1.0 HA A:SER416 4.8 38.6 1.0 HA A:GLU444 4.8 49.2 1.0 CA A:ASN394 4.8 35.9 1.0 HE A:ARG450 4.9 54.2 1.0 HB3 A:HIS417 4.9 56.6 1.0 HB2 A:SER416 4.9 40.8 1.0 CB A:HIS417 4.9 56.0 1.0 C A:ASN394 4.9 33.3 1.0 H A:HIS417 5.0 41.8 1.0 HD3 A:LYS441 5.0 38.5 1.0

Calcium binding site 3 out of 3 in the Transglutaminase 3 Zymogen 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 Zymogen in Complex with Dh Patient-Derived Fab DH63-B02 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:35.2 occ:1.00 O A:SER308 2.3 34.6 1.0 OD1 A:ASP304 2.3 39.7 1.0 OD2 A:ASP325 2.4 40.3 1.0 OD1 A:ASN306 2.4 43.5 1.0 OD1 A:ASP302 2.4 38.9 1.0 O A:HOH1009 2.5 43.0 1.0 HD22 A:ASN306 3.3 39.8 1.0 CG A:ASN306 3.4 41.0 1.0 CG A:ASP325 3.4 39.6 1.0 CG A:ASP302 3.5 37.4 1.0 H A:SER308 3.5 34.8 1.0 CG A:ASP304 3.5 45.6 1.0 O A:HOH852 3.5 51.8 1.0 C A:SER308 3.6 33.9 1.0 HA A:VAL309 3.6 33.7 1.0 H A:ASP304 3.6 43.6 1.0 ND2 A:ASN306 3.7 39.3 1.0 HA A:ASP302 3.8 36.8 1.0 H A:THR303 3.8 39.7 1.0 H A:ASN306 3.8 41.0 1.0 HG12 A:VAL309 3.9 36.9 1.0 OD1 A:ASP325 3.9 41.7 1.0 OD2 A:ASP304 4.1 51.3 1.0 HB3 A:SER308 4.2 37.7 1.0 OD2 A:ASP302 4.2 35.4 1.0 N A:SER308 4.2 34.2 1.0 O A:HOH959 4.3 41.9 1.0 CB A:ASP302 4.3 37.5 1.0 N A:ASP304 4.4 43.7 1.0 CA A:SER308 4.4 36.2 1.0 CA A:VAL309 4.4 33.4 1.0 CA A:ASP302 4.4 36.0 1.0 HB2 A:ASP302 4.5 37.0 1.0 N A:VAL309 4.5 30.8 1.0 N A:THR303 4.5 40.6 1.0 HD21 A:ASN306 4.6 40.1 1.0 O A:HOH877 4.6 37.5 1.0 N A:ASN306 4.6 40.4 1.0 CG1 A:VAL309 4.7 37.9 1.0 HG11 A:VAL309 4.7 36.8 1.0 HG1 A:THR303 4.7 40.2 0.0 CB A:ASP325 4.7 39.1 1.0 CB A:ASP304 4.7 44.4 1.0 CB A:ASN306 4.7 41.4 1.0 HB3 A:ASP325 4.8 38.9 1.0 H A:ARG305 4.8 49.6 1.0 H A:LEU307 4.8 39.8 1.0 CB A:SER308 4.8 38.3 1.0 C A:ASP304 4.8 47.8 1.0 CA A:ASP304 4.9 44.2 1.0 HB2 A:ASP325 4.9 39.3 1.0 C A:ASP302 4.9 39.0 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