Zinc in PDB 4fw6: Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor

The structure of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor, PDB code: 4fw6 was solved by Y.N.Kang, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.64 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.477, 89.630, 169.997, 90.00, 90.08, 90.00
R / Rfree (%)	16.3 / 19.7

The structure of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor (pdb code 4fw6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor, PDB code: 4fw6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.2 occ:1.00 NE2 A:HIS78 2.0 16.4 1.0 OD1 A:ASP241 2.1 13.0 1.0 O2 A:L59302 2.1 16.9 1.0 NE2 A:HIS237 2.1 13.3 1.0 H14 A:L59302 2.1 19.3 0.0 O3 A:L59302 2.2 19.1 1.0 CG A:ASP241 2.7 15.8 1.0 OD2 A:ASP241 2.7 14.4 1.0 C17 A:L59302 2.8 18.7 1.0 N2 A:L59302 2.9 21.3 1.0 CE1 A:HIS78 3.0 16.2 1.0 CD2 A:HIS78 3.1 16.9 1.0 CE1 A:HIS237 3.1 13.7 1.0 CD2 A:HIS237 3.1 14.0 1.0 H13 A:L59302 3.8 21.8 0.0 H16 A:L59302 3.9 29.3 0.0 OG1 A:THR190 4.1 16.4 1.0 ND1 A:HIS78 4.2 17.9 1.0 CG A:HIS78 4.2 16.6 1.0 CB A:ASP241 4.2 12.8 1.0 ND1 A:HIS237 4.2 13.4 1.0 CG A:HIS237 4.2 13.4 1.0 CG A:GLU77 4.3 18.1 1.0 C16 A:L59302 4.3 21.2 1.0 CB A:THR190 4.3 17.9 1.0 OE2 A:GLU77 4.3 17.9 1.0 H3 A:L59302 4.6 17.2 0.0 C19 A:L59302 4.7 29.6 1.0 CE1 A:HIS264 4.7 16.7 1.0 O4 A:L59302 4.8 36.1 1.0 CA A:ASP241 4.8 10.7 1.0 NE2 A:HIS264 4.8 17.0 1.0 CD A:GLU77 4.9 19.3 1.0 CA A:THR190 4.9 12.2 1.0 O A:HIS237 4.9 12.4 1.0 H1 A:L59302 4.9 21.5 0.0 C18 A:L59302 4.9 29.9 1.0 H15 A:L59302 4.9 29.4 0.0 N1 A:L59302 4.9 17.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:13.8 occ:1.00 OD1 B:ASP241 2.1 11.7 1.0 NE2 B:HIS78 2.1 15.1 1.0 O2 B:L59302 2.1 15.1 1.0 NE2 B:HIS237 2.1 12.2 1.0 H14 B:L59302 2.1 19.6 0.0 O3 B:L59302 2.2 19.5 1.0 OD2 B:ASP241 2.7 12.4 1.0 CG B:ASP241 2.7 12.3 1.0 C17 B:L59302 2.8 18.3 1.0 N2 B:L59302 2.9 18.8 1.0 CD2 B:HIS78 3.1 15.2 1.0 CD2 B:HIS237 3.1 13.2 1.0 CE1 B:HIS78 3.1 16.1 1.0 CE1 B:HIS237 3.1 12.5 1.0 H13 B:L59302 3.8 19.2 0.0 H16 B:L59302 4.0 29.9 0.0 OG1 B:THR190 4.1 15.1 1.0 CB B:ASP241 4.2 12.6 1.0 CG B:HIS78 4.2 14.7 1.0 CG B:HIS237 4.2 12.4 1.0 ND1 B:HIS237 4.2 12.9 1.0 ND1 B:HIS78 4.2 17.1 1.0 CG B:GLU77 4.3 17.0 1.0 C16 B:L59302 4.3 20.5 1.0 CB B:THR190 4.3 16.7 1.0 OE2 B:GLU77 4.3 18.4 1.0 H3 B:L59302 4.5 16.1 0.0 C19 B:L59302 4.7 30.1 1.0 CE1 B:HIS264 4.8 15.2 1.0 CA B:ASP241 4.8 10.1 1.0 CD B:GLU77 4.9 18.3 1.0 O B:HIS237 4.9 10.9 1.0 CA B:THR190 4.9 11.4 1.0 H1 B:L59302 4.9 20.9 0.0 NE2 B:HIS264 4.9 15.9 1.0 O4 B:L59302 4.9 33.6 1.0 N1 B:L59302 4.9 16.0 1.0 C18 B:L59302 4.9 30.1 1.0 H15 B:L59302 4.9 30.1 0.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:18.2 occ:1.00 OD1 C:ASP241 2.1 15.3 1.0 O2 C:L59302 2.1 21.1 1.0 O3 C:L59302 2.1 23.0 1.0 NE2 C:HIS78 2.1 21.2 1.0 NE2 C:HIS237 2.1 15.2 1.0 H14 C:L59302 2.3 23.0 0.0 OD2 C:ASP241 2.6 21.0 1.0 CG C:ASP241 2.7 17.8 1.0 C17 C:L59302 2.8 24.3 1.0 N2 C:L59302 2.9 22.2 1.0 CD2 C:HIS237 3.1 16.7 1.0 CD2 C:HIS78 3.1 20.3 1.0 CE1 C:HIS237 3.1 15.8 1.0 CE1 C:HIS78 3.1 21.8 1.0 H13 C:L59302 3.7 23.0 0.0 H15 C:L59302 3.9 30.5 0.0 OG1 C:THR190 4.1 23.3 1.0 CB C:ASP241 4.2 14.5 1.0 CG C:GLU77 4.2 21.3 1.0 CG C:HIS237 4.2 16.4 1.0 CG C:HIS78 4.2 20.0 1.0 ND1 C:HIS237 4.2 16.9 1.0 ND1 C:HIS78 4.3 22.6 1.0 CB C:THR190 4.3 20.7 1.0 OE2 C:GLU77 4.3 19.6 1.0 C16 C:L59302 4.3 27.5 1.0 H3 C:L59302 4.6 28.3 0.0 C19 C:L59302 4.8 31.2 1.0 O4 C:L59302 4.8 32.5 1.0 CD C:GLU77 4.8 29.3 1.0 CA C:ASP241 4.8 13.3 1.0 CE1 C:HIS264 4.9 21.9 1.0 NE2 C:HIS264 4.9 22.6 1.0 CA C:THR190 4.9 16.2 1.0 H1 C:L59302 4.9 27.7 0.0 C18 C:L59302 4.9 31.8 1.0 O C:HIS237 4.9 16.3 1.0 N1 C:L59302 4.9 28.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]-4-(Phenylethynyl)Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:17.7 occ:1.00 OD1 D:ASP241 2.0 14.4 1.0 NE2 D:HIS78 2.1 19.6 1.0 O2 D:L59302 2.1 21.9 1.0 NE2 D:HIS237 2.1 15.3 1.0 O3 D:L59302 2.1 23.1 1.0 H14 D:L59302 2.3 23.0 0.0 OD2 D:ASP241 2.6 20.2 1.0 CG D:ASP241 2.7 15.5 1.0 C17 D:L59302 2.9 24.4 1.0 N2 D:L59302 2.9 22.2 1.0 CD2 D:HIS78 3.0 19.1 1.0 CD2 D:HIS237 3.1 16.5 1.0 CE1 D:HIS78 3.1 20.1 1.0 CE1 D:HIS237 3.1 15.8 1.0 H13 D:L59302 3.8 23.1 0.0 H16 D:L59302 3.9 31.1 0.0 OG1 D:THR190 4.1 25.1 1.0 CB D:ASP241 4.2 12.5 1.0 CG D:HIS78 4.2 18.9 1.0 CG D:HIS237 4.2 16.7 1.0 ND1 D:HIS237 4.2 16.9 1.0 ND1 D:HIS78 4.2 21.2 1.0 CG D:GLU77 4.3 19.9 1.0 OE2 D:GLU77 4.3 21.3 1.0 CB D:THR190 4.3 23.6 1.0 C16 D:L59302 4.3 27.2 1.0 H3 D:L59302 4.6 26.2 0.0 C19 D:L59302 4.7 32.0 1.0 CA D:ASP241 4.8 12.3 1.0 CD D:GLU77 4.8 29.8 1.0 CE1 D:HIS264 4.8 19.7 1.0 O4 D:L59302 4.8 34.9 1.0 O D:HIS237 4.9 16.6 1.0 CA D:THR190 4.9 16.6 1.0 NE2 D:HIS264 4.9 20.6 1.0 C18 D:L59302 4.9 32.2 1.0 N1 D:L59302 4.9 26.3 1.0 H1 D:L59302 4.9 27.4 0.0 H15 D:L59302 5.0 32.1 0.0 CD2 D:LEU240 5.0 19.4 1.0

Y.N.Kang, J.A.Stuckey. Crystal Structure of the Lpxc To Be Published.