Calcium in PDB 8q28: Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803

The structure of Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803, PDB code: 8q28 was solved by B.S.Rajagopal, G.R.Hemsworth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.88 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.004, 75.443, 69.751, 90, 107.62, 90
R / Rfree (%)	15.7 / 20.2

The structure of Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803 (pdb code 8q28). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803, PDB code: 8q28:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:21.2 occ:1.00 OE2 A:GLU12 2.3 23.3 1.0 O A:HOH483 2.4 19.0 1.0 O A:GLY10 2.4 19.6 1.0 O A:THR53 2.4 22.7 1.0 O A:ASN56 2.4 17.8 1.0 OD1 A:ASP225 2.5 20.0 1.0 OD2 A:ASP225 2.6 22.6 1.0 CG A:ASP225 2.9 20.0 1.0 H A:ASN56 3.3 23.8 1.0 C A:GLY10 3.4 18.7 1.0 HG2 A:GLU12 3.5 24.7 1.0 CD A:GLU12 3.5 28.8 1.0 C A:ASN56 3.6 21.1 1.0 C A:THR53 3.6 25.1 1.0 HB1 A:ALA51 3.7 21.1 1.0 H A:THR53 3.7 24.5 1.0 HA2 A:GLY10 3.7 19.9 1.0 HA3 A:GLY10 3.7 19.9 1.0 HB A:THR53 3.9 25.0 1.0 CA A:GLY10 3.9 20.1 1.0 N A:ASN56 4.0 23.7 1.0 CG A:GLU12 4.0 23.2 1.0 HB2 A:ASN56 4.0 23.2 1.0 HA3 A:GLY54 4.1 21.9 1.0 HA A:SER57 4.1 19.8 1.0 HB2 A:PHE11 4.2 18.9 1.0 CA A:ASN56 4.3 23.7 1.0 HD2 A:PHE11 4.4 19.1 1.0 N A:THR53 4.4 23.4 1.0 CB A:ASP225 4.4 17.6 1.0 H A:ASP226 4.4 16.9 1.0 HG3 A:GLU12 4.4 24.7 1.0 OD1 A:ASP226 4.4 18.9 1.0 CA A:THR53 4.5 26.1 1.0 H A:PHE52 4.5 24.2 1.0 CB A:ALA51 4.6 20.8 1.0 OE1 A:GLU12 4.6 26.4 1.0 N A:GLY54 4.6 21.7 1.0 O A:HOH560 4.6 33.6 1.0 N A:PHE11 4.6 18.3 1.0 N A:SER57 4.6 19.2 1.0 CB A:THR53 4.6 22.9 1.0 CA A:GLY54 4.6 21.7 1.0 CB A:ASN56 4.7 23.7 1.0 HB2 A:ASP225 4.7 18.1 1.0 HB2 A:ALA51 4.7 21.1 1.0 C A:GLY54 4.7 22.4 1.0 H A:ASN55 4.7 25.2 1.0 HA A:ASP225 4.8 16.9 1.0 N A:ASN55 4.8 27.4 1.0 CA A:SER57 4.8 19.9 1.0 HB3 A:ASP225 4.9 18.1 1.0 H A:GLU12 5.0 24.5 1.0 N A:GLU12 5.0 24.7 1.0

Calcium binding site 2 out of 2 in the Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Se-Met Labelled TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:17.6 occ:1.00 OE2 B:GLU12 2.4 17.6 1.0 O B:HOH461 2.4 15.0 1.0 O B:ASN56 2.4 16.4 1.0 O B:THR53 2.4 19.6 1.0 O B:GLY10 2.5 18.4 1.0 OD1 B:ASP225 2.5 16.1 1.0 OD2 B:ASP225 2.6 17.8 1.0 CG B:ASP225 2.9 16.2 1.0 H B:ASN56 3.2 16.6 1.0 CD B:GLU12 3.4 21.3 1.0 C B:GLY10 3.5 17.6 1.0 HG2 B:GLU12 3.5 20.3 1.0 C B:ASN56 3.6 15.7 1.0 C B:THR53 3.6 21.3 1.0 H B:THR53 3.6 18.8 1.0 HA3 B:GLY10 3.6 18.0 1.0 HB1 B:ALA51 3.7 19.6 1.0 HA2 B:GLY10 3.7 17.9 1.0 CA B:GLY10 3.8 18.3 1.0 HB B:THR53 3.9 21.6 1.0 N B:ASN56 3.9 16.2 1.0 CG B:GLU12 4.0 20.8 1.0 HB2 B:ASN56 4.0 18.1 1.0 HA3 B:GLY54 4.0 19.2 1.0 HA B:SER57 4.2 14.5 1.0 CA B:ASN56 4.2 16.4 1.0 HB2 B:PHE11 4.3 16.4 1.0 N B:THR53 4.3 18.3 1.0 OD1 B:ASP226 4.3 17.6 1.0 CB B:ASP225 4.3 16.0 1.0 H B:ASP226 4.4 14.9 1.0 HD2 B:PHE11 4.4 16.2 1.0 HG3 B:GLU12 4.4 20.3 1.0 CA B:THR53 4.4 19.7 1.0 N B:GLY54 4.5 18.1 1.0 OE1 B:GLU12 4.5 22.0 1.0 H B:PHE52 4.5 17.5 1.0 CA B:GLY54 4.6 19.4 1.0 CB B:THR53 4.6 20.8 1.0 H B:ASN55 4.6 20.9 1.0 CB B:ALA51 4.6 20.6 1.0 N B:SER57 4.6 16.6 1.0 HB2 B:ASP225 4.6 15.7 1.0 CB B:ASN56 4.6 17.6 1.0 O B:HOH622 4.6 23.5 1.0 N B:PHE11 4.7 18.9 1.0 HB2 B:ALA51 4.7 19.6 1.0 C B:GLY54 4.7 20.0 1.0 N B:ASN55 4.8 20.7 1.0 HB3 B:ASP225 4.9 15.7 1.0 HA B:ASP225 4.9 14.6 1.0 H B:GLU12 4.9 18.7 1.0 N B:GLU12 4.9 19.5 1.0 CA B:SER57 4.9 14.1 1.0 HA B:GLU12 5.0 18.6 1.0 HB3 B:ASN56 5.0 18.1 1.0

B.S.Rajagopal, N.Yates, J.Smith, A.Paradisi, C.Tetard-Jones, W.G.T.Willats, S.Marcus, P.J.Knox, M.Firdaus-Raih, B.Henrissat, G.J.Davies, P.H.Walton, A.Parkin, G.R.Hemsworth. Structural Dissection of Two Redox Proteins From the Shipworm Symbiont Teredinibacter Turnerae Iucrj 2024.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252524001386