Magnesium in PDB 8ffu: Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound

The structure of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound, PDB code: 8ffu was solved by P.Y.-T.Chen, B.S.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.80 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.062, 158.489, 73.6, 90, 90.02, 90
R / Rfree (%)	17.6 / 20.8

The binding sites of Magnesium atom in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound (pdb code 8ffu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound, PDB code: 8ffu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:27.2 occ:1.00 O A:HOH537 2.0 29.6 1.0 O A:VAL72 2.1 28.5 1.0 O A:ALA66 2.3 30.3 1.0 O A:ASP69 2.5 31.1 1.0 O A:HOH533 2.6 33.7 1.0 O A:HOH534 2.7 28.7 1.0 C A:ALA66 3.2 28.4 1.0 C A:VAL72 3.4 28.7 1.0 C A:ASP69 3.6 31.4 1.0 CB A:ALA66 4.0 28.9 1.0 CA A:ALA66 4.0 27.8 1.0 N A:SER67 4.0 28.0 1.0 CA A:LYS70 4.1 30.6 1.0 N A:VAL72 4.1 30.4 1.0 CA A:SER67 4.2 28.2 1.0 O A:LYS70 4.2 32.4 1.0 CA A:VAL72 4.2 28.9 1.0 C A:LYS70 4.2 29.3 1.0 N A:LYS70 4.3 31.0 1.0 N A:SER73 4.4 27.8 1.0 CB A:VAL72 4.5 28.1 1.0 N A:ASP69 4.6 29.8 1.0 C A:SER67 4.6 28.5 1.0 CA A:SER73 4.6 27.1 1.0 NZ A:LYS70 4.7 35.7 1.0 CA A:ASP69 4.7 29.7 1.0 O A:SER67 4.9 31.8 1.0 N A:SER71 5.0 29.9 1.0

Magnesium binding site 2 out of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:29.1 occ:1.00 O B:VAL72 2.2 30.2 1.0 O B:HOH525 2.2 27.9 1.0 O B:ALA66 2.5 30.1 1.0 O B:ASP69 2.6 33.4 1.0 O B:HOH535 2.8 29.4 1.0 C B:ALA66 3.4 30.3 1.0 C B:VAL72 3.4 30.9 1.0 C B:ASP69 3.7 34.5 1.0 CB B:ALA66 4.0 29.1 1.0 N B:VAL72 4.0 31.9 1.0 CA B:LYS70 4.1 32.7 1.0 O B:LYS70 4.1 32.9 1.0 CA B:ALA66 4.1 29.1 1.0 C B:LYS70 4.1 32.1 1.0 CA B:VAL72 4.2 31.2 1.0 N B:SER67 4.2 30.3 1.0 CA B:SER67 4.3 29.9 1.0 N B:LYS70 4.3 33.9 1.0 N B:SER73 4.4 29.3 1.0 CB B:VAL72 4.5 31.8 1.0 CA B:SER73 4.6 29.4 1.0 N B:ASP69 4.7 32.3 1.0 C B:SER67 4.7 30.8 1.0 CA B:ASP69 4.8 32.3 1.0 N B:SER71 4.9 30.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:28.4 occ:1.00 O C:HOH533 2.1 27.2 1.0 O C:ASP69 2.1 29.5 1.0 O C:ALA66 2.5 29.6 1.0 O C:VAL72 2.7 27.4 1.0 O C:HOH538 2.9 27.6 1.0 C C:ASP69 3.0 31.7 1.0 CA C:LYS70 3.5 32.3 1.0 C C:ALA66 3.5 27.1 1.0 N C:LYS70 3.6 33.3 1.0 C C:VAL72 3.8 27.9 1.0 C C:LYS70 3.9 30.6 1.0 N C:ASP69 4.1 30.9 1.0 O C:LYS70 4.1 33.0 1.0 CA C:ASP69 4.1 31.2 1.0 CA C:SER67 4.1 27.4 1.0 N C:VAL72 4.2 31.7 1.0 N C:SER67 4.3 28.2 1.0 C C:SER67 4.3 29.3 1.0 CA C:VAL72 4.5 30.1 1.0 CA C:ALA66 4.5 27.0 1.0 O C:SER67 4.5 31.9 1.0 CB C:ALA66 4.6 28.0 1.0 N C:SER71 4.7 27.9 1.0 CB C:VAL72 4.7 28.9 1.0 CB C:LYS70 4.8 33.3 1.0 N C:LEU68 4.9 30.1 1.0 N C:SER73 4.9 28.5 1.0

Magnesium binding site 4 out of 4 in the Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Gntc, A Plp-Dependent Enzyme Catalyzing L-Enduracididine Biosynthesis From (S)-4-Hydroxy-L-Arginine, with the Substrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:35.6 occ:1.00 O D:ALA66 2.3 33.6 1.0 O D:HOH546 2.6 36.5 1.0 O D:ASP69 2.6 35.1 1.0 O D:VAL72 2.7 33.8 1.0 C D:ALA66 3.2 32.2 1.0 C D:ASP69 3.5 36.5 1.0 CA D:LYS70 3.8 38.2 1.0 CA D:SER67 3.8 30.6 1.0 C D:VAL72 3.9 34.0 1.0 N D:SER67 3.9 31.5 1.0 N D:LYS70 4.0 38.6 1.0 C D:LYS70 4.2 36.0 1.0 CA D:ALA66 4.2 29.7 1.0 CB D:ALA66 4.2 32.3 1.0 O D:LYS70 4.2 36.9 1.0 C D:SER67 4.2 32.2 1.0 N D:ASP69 4.4 34.5 1.0 N D:VAL72 4.4 34.6 1.0 O D:SER67 4.5 34.8 1.0 CA D:VAL72 4.6 34.4 1.0 CA D:ASP69 4.6 35.7 1.0 CB D:VAL72 4.8 32.9 1.0 N D:LEU68 4.8 33.0 1.0 N D:SER73 4.9 32.2 1.0 N D:SER71 5.0 35.1 1.0

J.L.Cordoza, P.Y.Chen, L.R.Blaustein, S.T.Lima, M.F.Fiore, J.R.Chekan, B.S.Moore, S.M.K.Mckinnie. Mechanistic and Structural Insights Into A Divergent Plp-Dependent L-Enduracididine Cyclase From A Toxic Cyanobacterium. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993528
DOI: 10.1101/2023.03.21.533663