Magnesium in PDB 8q29: TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803

The structure of TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803, PDB code: 8q29 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)	49.55 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.081, 75.167, 69.074, 90, 107.42, 90
R / Rfree (%)	11.2 / 15.6

The structure of 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 TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803 (pdb code 8q29). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the TTX122A - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_3803, PDB code: 8q29:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 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 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:18.6 occ:1.00 O A:HOH423 2.0 19.0 1.0 O A:HOH486 2.0 20.9 1.0 OE1 A:GLU242 2.0 22.4 1.0 O A:TRP154 2.0 17.4 1.0 O A:HOH523 2.1 19.5 1.0 O A:HOH459 2.1 17.3 1.0 HA A:HIS155 3.2 15.1 1.0 CD A:GLU242 3.2 24.2 1.0 C A:TRP154 3.2 17.6 1.0 HB2 A:GLU242 3.6 24.4 1.0 HG1 A:THR153 3.7 22.8 0.0 HD1 A:HIS155 3.9 18.2 0.0 OD2 A:ASP176 4.0 20.0 1.0 HG3 A:GLU242 4.0 24.7 1.0 CA A:HIS155 4.0 14.6 1.0 N A:HIS155 4.0 15.9 1.0 O A:HOH567 4.0 35.6 1.0 CG A:GLU242 4.0 24.9 1.0 OE2 A:GLU242 4.1 25.3 1.0 O A:HOH566 4.1 47.8 1.0 HB2 A:TRP154 4.2 16.8 1.0 OD1 A:ASP176 4.2 16.8 1.0 CB A:GLU242 4.3 24.4 1.0 CA A:TRP154 4.3 18.4 1.0 ND1 A:HIS155 4.3 18.0 1.0 OG1 A:THR153 4.4 22.5 1.0 HG22 A:THR153 4.4 20.4 1.0 H A:TRP154 4.5 17.9 1.0 CG A:ASP176 4.5 18.2 1.0 N A:TRP154 4.5 18.0 1.0 O A:LEU241 4.6 20.8 1.0 H A:CYS156 4.6 14.4 1.0 O A:GLU240 4.6 18.2 1.0 CB A:TRP154 4.6 16.7 1.0 HB3 A:TRP154 4.6 16.5 1.0 HB3 A:GLU242 4.7 24.5 1.0 O A:HOH428 4.7 29.4 1.0 HE3 A:MET85 4.9 17.6 1.0 CG A:HIS155 4.9 17.0 1.0 H A:HIS155 4.9 15.8 1.0 HG2 A:GLU242 5.0 24.7 1.0 C A:HIS155 5.0 15.4 1.0

Magnesium binding site 2 out of 4 in the 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 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:17.7 occ:1.00 O A:HOH421 2.1 15.1 1.0 O A:HOH418 2.1 17.0 1.0 O A:HOH557 2.1 23.3 1.0 OE2 A:GLU228 2.1 16.2 1.0 O A:HOH505 2.1 22.6 1.0 O A:HOH456 2.1 17.1 1.0 HZ2 A:LYS83 3.0 15.3 1.0 CD A:GLU228 3.0 15.7 1.0 OE1 A:GLU228 3.3 19.4 1.0 NZ A:LYS83 3.8 15.1 1.0 HZ3 A:LYS83 3.9 15.3 1.0 OE2 A:GLU240 4.2 17.6 1.0 OE1 A:GLU240 4.2 17.1 1.0 HE3 A:LYS83 4.2 15.9 1.0 O A:SER235 4.4 16.1 1.0 CG A:GLU228 4.4 16.1 1.0 HZ1 A:LYS83 4.4 15.2 1.0 HD2 A:LYS83 4.5 15.4 1.0 HG3 A:GLU228 4.5 16.0 1.0 CE A:LYS83 4.6 16.2 1.0 CD A:GLU240 4.6 16.5 1.0 HG21 A:ILE234 4.7 14.3 1.0 HG2 A:GLU228 4.7 16.1 1.0 O A:HOH543 4.7 15.1 1.0 OD2 A:ASP237 4.7 24.9 1.0 HG21 A:THR8 4.7 37.1 0.5 HG21 A:THR8 5.0 30.7 0.5

Magnesium binding site 3 out of 4 in the 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 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:17.7 occ:1.00 HE2 B:HIS243 1.4 22.4 0.0 O B:HOH418 2.0 15.9 1.0 O B:TRP154 2.0 15.0 1.0 O B:HOH575 2.1 20.3 1.0 O B:HOH505 2.1 19.0 1.0 O B:HOH479 2.1 16.6 1.0 NE2 B:HIS243 2.2 21.1 1.0 CE1 B:HIS243 3.1 29.8 1.0 HA B:HIS155 3.1 13.2 1.0 HE1 B:HIS243 3.2 27.0 1.0 C B:TRP154 3.2 13.6 1.0 CD2 B:HIS243 3.3 25.4 1.0 HD2 B:HIS243 3.5 24.4 1.0 HG1 B:THR153 3.8 18.4 0.0 HD1 B:HIS155 3.8 14.5 0.0 CA B:HIS155 3.9 13.2 1.0 OD2 B:ASP176 4.0 18.1 1.0 N B:HIS155 4.0 12.4 1.0 HB2 B:TRP154 4.2 14.3 1.0 OD1 B:ASP176 4.2 14.6 1.0 O B:HOH606 4.2 36.9 1.0 ND1 B:HIS243 4.3 29.2 1.0 ND1 B:HIS155 4.3 14.4 1.0 CA B:TRP154 4.4 13.0 1.0 CG B:HIS243 4.4 30.2 1.0 HG22 B:THR153 4.5 17.4 1.0 O B:GLU240 4.5 18.8 1.0 H B:CYS156 4.5 12.5 1.0 OG1 B:THR153 4.5 18.2 1.0 CG B:ASP176 4.5 15.7 1.0 N B:TRP154 4.6 14.3 1.0 H B:TRP154 4.6 14.0 1.0 HB3 B:TRP154 4.6 14.2 1.0 CB B:TRP154 4.7 14.4 1.0 HE3 B:MET85 4.7 16.8 1.0 H B:HIS155 4.9 12.7 1.0 C B:HIS155 4.9 13.7 1.0 CG B:HIS155 4.9 13.9 1.0 CB B:HIS155 5.0 15.0 1.0

Magnesium binding site 4 out of 4 in the 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 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:17.1 occ:1.00 O B:HOH572 2.0 23.0 1.0 O B:HOH450 2.1 17.9 1.0 O B:HOH439 2.1 15.4 1.0 O B:HOH423 2.1 16.4 1.0 O B:HOH539 2.1 17.9 1.0 OE2 B:GLU228 2.1 14.6 1.0 CD B:GLU228 3.1 15.7 1.0 HZ2 B:LYS83 3.1 14.0 1.0 OE1 B:GLU228 3.3 18.3 1.0 NZ B:LYS83 3.9 13.7 1.0 HZ3 B:LYS83 4.0 13.9 1.0 OE2 B:GLU240 4.2 15.0 1.0 OE1 B:GLU240 4.2 15.2 1.0 HE3 B:LYS83 4.2 14.5 1.0 OD2 B:ASP237 4.3 23.1 1.0 O B:SER235 4.4 19.1 1.0 HB3 B:ASP237 4.4 16.5 1.0 HG21 B:ILE234 4.4 14.9 1.0 CG B:GLU228 4.5 14.9 1.0 O B:HOH574 4.5 18.4 1.0 HZ1 B:LYS83 4.5 13.9 1.0 CD B:GLU240 4.6 15.4 1.0 HD2 B:LYS83 4.6 13.7 1.0 HG3 B:GLU228 4.6 14.9 1.0 CE B:LYS83 4.6 15.0 1.0 HG2 B:GLU228 4.8 14.9 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