Magnesium in PDB 8w9i: Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5

The structure of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5, PDB code: 8w9i was solved by Z.Luo, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.584, 102.622, 194.084, 90, 90, 90
R / Rfree (%)	21.4 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5 (pdb code 8w9i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5, PDB code: 8w9i:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5


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 Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:50.5 occ:1.00 O A:ALA308 2.4 36.3 1.0 O A:VAL313 2.4 36.3 1.0 O A:GLN310 2.6 38.7 1.0 C A:ALA308 3.6 35.3 1.0 C A:GLN310 3.6 38.0 1.0 C A:VAL313 3.6 34.7 1.0 CB A:SER315 3.9 38.0 1.0 C A:ASN309 4.1 37.4 1.0 N A:SER315 4.2 36.5 1.0 N A:GLN310 4.2 36.8 1.0 CA A:PRO311 4.2 39.6 1.0 N A:PRO311 4.3 39.5 1.0 CA A:ASN309 4.3 38.0 1.0 O A:PRO311 4.3 42.4 1.0 C A:ALA314 4.3 35.8 1.0 N A:ASN309 4.4 36.1 1.0 O A:ASN309 4.4 39.3 1.0 C A:PRO311 4.4 40.3 1.0 N A:VAL313 4.4 34.8 1.0 CA A:VAL313 4.5 34.1 1.0 CA A:GLN310 4.5 36.6 1.0 N A:ALA314 4.6 34.8 1.0 CA A:ALA308 4.6 34.0 1.0 CA A:SER315 4.6 38.3 1.0 CA A:ALA314 4.7 35.6 1.0 O A:ALA314 4.8 35.4 1.0 CB A:VAL313 4.8 33.2 1.0 OG A:SER315 5.0 37.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5


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 Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:55.8 occ:1.00 O B:GLN310 2.3 39.1 1.0 O B:ALA308 2.4 33.2 1.0 O B:VAL313 2.4 37.0 1.0 C B:GLN310 3.3 38.2 1.0 C B:ALA308 3.6 32.3 1.0 C B:VAL313 3.6 36.4 1.0 C B:ASN309 3.9 35.0 1.0 CB B:SER315 3.9 40.8 1.0 O B:PRO311 4.0 41.4 1.0 CA B:PRO311 4.0 40.5 1.0 N B:PRO311 4.0 39.0 1.0 N B:GLN310 4.0 36.3 1.0 O B:ASN309 4.1 35.3 1.0 C B:PRO311 4.1 41.8 1.0 N B:VAL313 4.2 38.0 1.0 O B:HOH723 4.3 36.9 1.0 CA B:ASN309 4.3 34.1 1.0 CA B:GLN310 4.3 37.1 1.0 N B:SER315 4.3 38.4 1.0 N B:ASN309 4.3 33.3 1.0 CA B:VAL313 4.4 37.0 1.0 C B:ALA314 4.5 36.8 1.0 CA B:ALA308 4.6 32.4 1.0 CB B:VAL313 4.6 36.9 1.0 N B:ALA314 4.6 35.7 1.0 CA B:SER315 4.7 40.0 1.0 OG B:SER315 4.8 43.2 1.0 CA B:ALA314 4.8 35.4 1.0 N B:LEU312 4.9 42.3 1.0 O B:ALA314 5.0 35.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5


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 Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:50.3 occ:1.00 OG B:SER335 2.6 32.0 1.0 OE2 B:GLU364 2.8 41.0 1.0 O B:PRO333 3.0 37.4 1.0 NZ B:LYS261 3.2 61.4 1.0 CD B:GLU364 3.4 41.3 1.0 O B:GLY332 3.5 33.7 1.0 N B:SER335 3.6 33.7 1.0 CB B:SER335 3.6 32.8 1.0 OE1 B:GLU364 3.6 41.2 1.0 C B:PRO333 3.7 36.4 1.0 C B:GLY334 3.8 35.3 1.0 CA B:GLY334 3.8 35.4 1.0 C B:GLY332 4.0 34.6 1.0 N B:GLY334 4.1 36.0 1.0 CD B:LYS261 4.2 59.9 1.0 CA B:SER335 4.2 33.0 1.0 CG B:LYS261 4.2 57.8 1.0 CE B:LYS261 4.3 60.8 1.0 CG B:GLU364 4.4 40.2 1.0 O B:GLY334 4.5 37.4 1.0 CA B:GLY332 4.5 34.0 1.0 N B:PRO333 4.6 35.8 1.0 N B:GLY332 4.6 33.7 1.0 N B:ASP365 4.6 39.3 1.0 NH2 B:ARG326 4.7 38.3 1.0 CA B:PRO333 4.8 35.9 1.0 OD1 B:ASP365 4.8 39.0 1.0

Z.Luo, H.Zhou. Structure-Guided Fluorine Scanning Accelerates the Discovery of Potent and Selective Inhibitors Against Bacterial Prolyl-Trna Synthetase To Be Published.