Magnesium 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:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg302 b:19.0 occ:1.00 O A:HOH459 1.8 19.1 1.0 OE1 A:GLU242 1.8 22.4 1.0 O A:HOH475 2.1 19.6 1.0 O A:TRP154 2.1 21.4 1.0 O A:HOH498 2.1 19.9 1.0 O A:HOH439 2.2 19.7 1.0 HA A:HIS155 3.1 18.8 1.0 CD A:GLU242 3.1 23.5 1.0 C A:TRP154 3.3 25.2 1.0 HB2 A:GLU242 3.7 28.2 1.0 HG1 A:THR153 3.8 24.1 0.0 HD1 A:HIS155 3.9 21.1 0.0 OD2 A:ASP176 3.9 19.6 1.0 CA A:HIS155 4.0 17.2 1.0 HG3 A:GLU242 4.0 26.1 1.0 OE2 A:GLU242 4.0 23.0 1.0 N A:HIS155 4.0 20.9 1.0 CG A:GLU242 4.0 25.8 1.0 OD1 A:ASP176 4.2 19.8 1.0 ND1 A:HIS155 4.3 21.3 1.0 HB2 A:TRP154 4.3 21.2 1.0 H A:TRP154 4.3 25.0 1.0 CB A:GLU242 4.3 30.3 1.0 CA A:TRP154 4.4 23.4 1.0 HG22 A:THR153 4.4 21.0 1.0 OG1 A:THR153 4.5 23.9 1.0 CG A:ASP176 4.5 21.2 1.0 N A:TRP154 4.5 25.5 1.0 H A:CYS156 4.5 17.2 1.0 O A:LEU241 4.6 23.9 1.0 HB3 A:TRP154 4.7 21.1 1.0 O A:HOH406 4.7 35.5 1.0 CB A:TRP154 4.7 21.0 1.0 O A:GLU240 4.8 22.1 1.0 HE1 A:MSE85 4.8 21.7 1.0 HB3 A:GLU242 4.8 28.3 1.0 CG A:HIS155 4.8 20.5 1.0 H A:HIS155 4.9 20.9 1.0 C A:HIS155 4.9 18.4 1.0 HG2 A:GLU242 4.9 26.1 1.0 CB A:HIS155 5.0 20.8 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 A:Mg303 b:20.2 occ:1.00 O A:HOH484 2.0 24.3 1.0 OE2 A:GLU228 2.0 17.1 1.0 O A:HOH427 2.0 19.1 1.0 O A:HOH478 2.1 18.1 1.0 O A:HOH553 2.1 25.6 1.0 O A:HOH511 2.2 17.4 1.0 HZ2 A:LYS83 3.0 14.4 1.0 CD A:GLU228 3.0 19.0 1.0 OE1 A:GLU228 3.4 19.8 1.0 NZ A:LYS83 3.8 14.4 1.0 HZ3 A:LYS83 3.9 14.4 1.0 O A:HOH559 4.2 38.8 1.0 OE1 A:GLU240 4.2 19.6 1.0 HE3 A:LYS83 4.2 14.3 1.0 OE2 A:GLU240 4.2 19.2 1.0 CG A:GLU228 4.4 17.2 1.0 O A:SER235 4.4 19.0 1.0 HZ1 A:LYS83 4.4 14.4 1.0 HG3 A:GLU228 4.5 17.7 1.0 HD2 A:LYS83 4.5 14.0 1.0 CE A:LYS83 4.5 14.4 1.0 CD A:GLU240 4.6 17.7 1.0 HG21 A:ILE234 4.6 19.0 1.0 HG2 A:GLU228 4.7 17.8 1.0 OD2 A:ASP237 5.0 24.4 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg302 b:20.3 occ:1.00 O B:HOH488 2.0 17.2 1.0 O B:TRP154 2.1 17.1 1.0 O B:HOH522 2.1 17.5 1.0 O B:HOH572 2.1 20.7 1.0 OE1 B:GLU242 2.2 28.4 1.0 O B:HOH523 2.2 20.8 1.0 HA B:HIS155 3.0 15.7 1.0 C B:TRP154 3.3 17.0 1.0 CD B:GLU242 3.4 47.8 1.0 HD1 B:HIS155 3.8 17.6 0.0 CA B:HIS155 3.9 14.8 1.0 HG1 B:THR153 3.9 23.2 0.0 N B:HIS155 4.0 16.2 1.0 OD2 B:ASP176 4.0 17.9 1.0 OD1 B:ASP176 4.2 15.8 1.0 HB2 B:TRP154 4.2 16.8 1.0 OE2 B:GLU242 4.2 37.6 1.0 ND1 B:HIS155 4.3 17.4 1.0 HB2 B:GLU242 4.4 50.3 1.0 HG3 B:GLU242 4.4 49.3 1.0 CA B:TRP154 4.4 16.1 1.0 CG B:GLU242 4.4 49.2 1.0 H B:CYS156 4.5 15.1 1.0 CG B:ASP176 4.5 17.2 1.0 H B:TRP154 4.5 17.0 1.0 O B:GLU240 4.6 24.6 1.0 HB3 B:TRP154 4.6 16.8 1.0 HG22 B:THR153 4.6 22.3 1.0 N B:TRP154 4.6 16.6 1.0 OG1 B:THR153 4.6 23.8 1.0 CB B:TRP154 4.6 17.0 1.0 HE1 B:MSE85 4.7 18.3 1.0 C B:HIS155 4.8 15.8 1.0 H B:HIS155 4.9 16.1 1.0 CG B:HIS155 4.9 15.4 1.0 CB B:GLU242 4.9 51.4 1.0 CB B:HIS155 5.0 17.1 1.0 N B:CYS156 5.0 15.1 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg303 b:18.9 occ:1.00 O B:HOH502 2.0 17.3 1.0 O B:HOH433 2.1 17.2 1.0 O B:HOH493 2.1 21.2 1.0 O B:HOH565 2.1 21.8 1.0 OE2 B:GLU228 2.1 16.8 1.0 O B:HOH571 2.2 16.3 1.0 CD B:GLU228 3.1 16.3 1.0 HZ2 B:LYS83 3.2 14.3 1.0 OE1 B:GLU228 3.4 17.0 1.0 NZ B:LYS83 4.0 14.2 1.0 HZ3 B:LYS83 4.0 14.3 1.0 OE2 B:GLU240 4.1 17.3 1.0 OE1 B:GLU240 4.2 14.8 1.0 HE3 B:LYS83 4.2 14.5 1.0 HG21 B:ILE234 4.3 17.4 1.0 OD2 B:ASP237 4.4 22.2 1.0 O B:SER235 4.4 19.2 1.0 CG B:GLU228 4.5 14.2 1.0 O B:HOH583 4.5 17.0 1.0 HD2 B:LYS83 4.5 14.6 1.0 CD B:GLU240 4.5 18.3 1.0 HG3 B:GLU228 4.6 14.7 1.0 CE B:LYS83 4.6 14.7 1.0 HZ1 B:LYS83 4.6 14.3 1.0 HB3 B:ASP237 4.7 19.8 1.0 HG2 B:GLU228 4.8 14.7 1.0 HG23 B:ILE234 5.0 17.4 1.0 CG2 B:ILE234 5.0 17.6 1.0 H B:ASP237 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