Magnesium in PDB 3gyg: Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis

The structure of Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis, PDB code: 3gyg was solved by B.Nocek, A.Stein, R.Wu, R.Jedrzejczak, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.077, 111.732, 135.173, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis (pdb code 3gyg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis, PDB code: 3gyg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:45.5 occ:1.00 O A:ASP27 2.0 22.4 1.0 OD2 A:ASP25 2.0 25.2 1.0 O A:HOH485 2.0 17.2 1.0 OD2 A:ASP232 2.1 30.6 1.0 CG A:ASP25 3.1 24.0 1.0 C A:ASP27 3.1 22.4 1.0 CG A:ASP232 3.2 29.5 1.0 OD1 A:ASP25 3.6 24.4 1.0 OD1 A:ASP232 3.6 29.4 1.0 CA A:ASP27 3.8 22.9 1.0 N A:ASP27 3.9 22.6 1.0 OD2 A:ASP236 3.9 30.6 1.0 CB A:ASP27 4.0 23.2 1.0 OG A:SER233 4.2 29.7 1.0 N A:GLU28 4.2 22.1 1.0 OG1 A:THR29 4.2 21.7 1.0 CB A:GLU28 4.3 22.7 1.0 CB A:ASP25 4.4 23.7 1.0 CB A:ASP232 4.5 28.6 1.0 CA A:GLU28 4.6 22.4 1.0 C A:GLU28 4.6 22.2 1.0 C A:PHE26 4.7 22.4 1.0 N A:THR29 4.8 21.6 1.0 CG A:ASP236 4.9 30.3 1.0 N A:ASP232 5.0 28.1 1.0 OD1 A:ASP236 5.0 32.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:42.3 occ:1.00 O B:ASP27 1.9 19.6 1.0 OD2 B:ASP25 2.0 18.9 1.0 OD2 B:ASP232 2.1 22.4 1.0 O B:HOH472 2.2 11.4 1.0 CG B:ASP232 3.1 22.7 1.0 CG B:ASP25 3.1 21.1 1.0 C B:ASP27 3.1 20.0 1.0 OD1 B:ASP232 3.3 23.6 1.0 OD1 B:ASP25 3.6 23.3 1.0 CA B:ASP27 4.0 20.2 1.0 CB B:ASP27 4.1 20.6 1.0 OD2 B:ASP236 4.2 25.5 1.0 OG1 B:THR29 4.2 18.0 1.0 N B:GLU28 4.2 19.6 1.0 N B:ASP27 4.2 19.7 1.0 CB B:GLU28 4.2 20.6 1.0 OG B:SER233 4.3 24.7 1.0 CB B:ASP25 4.4 20.9 1.0 CB B:ASP232 4.4 22.8 1.0 CA B:GLU28 4.5 20.2 1.0 C B:GLU28 4.5 19.8 1.0 N B:THR29 4.5 19.6 1.0 N B:ASP232 4.8 22.4 1.0 C B:PHE26 4.8 19.1 1.0 OD1 B:ASP236 4.9 28.0 1.0 CB B:THR29 4.9 19.1 1.0 O B:GLU28 4.9 19.7 1.0 CG B:ASP236 5.0 26.1 1.0 CA B:ASP232 5.0 22.8 1.0 CB B:SER233 5.0 23.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:49.7 occ:1.00 O C:HOH486 2.0 27.0 1.0 OD1 C:ASP232 2.1 29.1 1.0 OD2 C:ASP25 2.2 25.5 1.0 O C:ASP27 2.6 23.2 1.0 CG C:ASP232 3.0 29.4 1.0 CG C:ASP25 3.2 23.3 1.0 OD2 C:ASP232 3.4 29.7 1.0 OD2 C:ASP236 3.5 36.1 1.0 OD1 C:ASP25 3.7 24.2 1.0 C C:ASP27 3.8 23.5 1.0 OG C:SER233 4.0 29.7 1.0 OG1 C:THR29 4.3 24.1 1.0 CB C:ASP232 4.3 29.0 1.0 N C:SER233 4.3 29.9 1.0 CB C:ASP25 4.4 23.2 1.0 CG C:ASP236 4.4 36.1 1.0 N C:ASP232 4.5 28.1 1.0 OD1 C:ASP236 4.6 37.0 1.0 CB C:SER233 4.6 29.9 1.0 CA C:ASP27 4.6 23.7 1.0 CB C:ASP27 4.7 23.9 1.0 CB C:GLU28 4.8 23.8 1.0 N C:GLU28 4.8 23.3 1.0 N C:ASP27 4.8 22.9 1.0 CA C:ASP232 4.8 29.1 1.0 C C:GLU28 5.0 23.5 1.0 N C:THR29 5.0 23.2 1.0 C C:ASP232 5.0 29.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:49.0 occ:1.00 OD2 D:ASP25 1.8 22.7 1.0 O D:HOH487 2.3 21.6 1.0 O D:ASP27 2.3 19.2 1.0 OD2 D:ASP232 2.3 26.6 1.0 CG D:ASP25 2.9 20.2 1.0 CG D:ASP232 3.1 26.0 1.0 OD1 D:ASP232 3.1 26.8 1.0 OD1 D:ASP25 3.3 20.5 1.0 C D:ASP27 3.5 19.2 1.0 OD2 D:ASP236 3.9 23.0 1.0 CB D:ASP25 4.2 19.4 1.0 CB D:SER233 4.3 24.8 1.0 OG1 D:THR29 4.3 17.6 1.0 CA D:ASP27 4.4 19.5 1.0 N D:ASP27 4.4 19.0 1.0 OD2 D:ASP27 4.4 26.2 1.0 N D:GLU28 4.5 19.1 1.0 CB D:GLU28 4.5 19.4 1.0 CB D:ASP232 4.5 25.0 1.0 C D:GLU28 4.7 18.9 1.0 CA D:GLU28 4.7 19.2 1.0 N D:ASP232 4.8 24.8 1.0 CG D:ASP236 4.8 24.6 1.0 N D:SER233 4.9 24.9 1.0 OD1 D:ASP236 4.9 26.9 1.0 N D:THR29 4.9 18.6 1.0

B.Nocek, A.Stein, R.Wu, R.Jedrzejczak, A.Joachimiak. Crystal Structure of Yhjk (Haloacid Dehalogenase-Like Hydrolase Protein) From Bacillus Subtilis To Be Published.