Zinc in PDB 4fw3: Crystal Structure of the Lpxc in Complex with N-[(2S)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor

The structure of Crystal Structure of the Lpxc in Complex with N-[(2S)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor, PDB code: 4fw3 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)	42.73 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.599, 170.903, 89.853, 90.00, 90.01, 90.00
R / Rfree (%)	19.7 / 24.7

The binding sites of Zinc atom in the Crystal Structure of the Lpxc in Complex with N-[(2S)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor (pdb code 4fw3). 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)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor, PDB code: 4fw3:
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)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) 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)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.9 occ:1.00 OD1 A:ASP241 2.0 33.0 1.0 NE2 A:HIS78 2.1 25.3 1.0 NE2 A:HIS237 2.1 24.1 1.0 H13 A:L52302 2.1 41.0 0.0 O2 A:L52302 2.2 41.7 1.0 O3 A:L52302 2.3 41.0 1.0 CG A:ASP241 2.6 31.3 1.0 OD2 A:ASP241 2.6 34.1 1.0 CD2 A:HIS78 3.0 25.2 1.0 CE1 A:HIS237 3.0 24.3 1.0 C19 A:L52302 3.0 42.9 1.0 CE1 A:HIS78 3.1 25.5 1.0 N2 A:L52302 3.1 41.7 1.0 CD2 A:HIS237 3.1 23.9 1.0 H12 A:L52302 3.9 41.8 0.0 OG1 A:THR190 4.0 36.5 1.0 CB A:ASP241 4.1 23.7 1.0 ND1 A:HIS237 4.1 24.9 1.0 CG A:HIS78 4.1 23.8 1.0 CG A:HIS237 4.2 22.6 1.0 ND1 A:HIS78 4.2 26.1 1.0 CG A:GLU77 4.3 26.9 1.0 CB A:THR190 4.4 39.5 1.0 OE2 A:GLU77 4.4 32.5 1.0 C18 A:L52302 4.5 45.1 1.0 H15 A:L52302 4.5 45.6 0.0 O A:HIS237 4.7 21.2 1.0 CA A:ASP241 4.8 21.9 1.0 H14 A:L52302 4.8 45.6 0.0 NE2 A:HIS264 4.8 26.4 1.0 CE1 A:HIS264 4.8 25.5 1.0 CD A:GLU77 4.9 40.8 1.0 C20 A:L52302 4.9 45.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) 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)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:19.2 occ:1.00 H13 B:L52301 1.7 32.6 0.0 O2 B:L52301 2.0 31.2 1.0 OD1 B:ASP241 2.0 24.2 1.0 NE2 B:HIS237 2.1 20.3 1.0 NE2 B:HIS78 2.1 19.9 1.0 O3 B:L52301 2.2 32.6 1.0 CG B:ASP241 2.7 23.4 1.0 C19 B:L52301 2.7 32.3 1.0 OD2 B:ASP241 2.8 25.2 1.0 N2 B:L52301 2.9 32.2 1.0 CE1 B:HIS237 3.0 20.0 1.0 CD2 B:HIS78 3.0 20.2 1.0 CD2 B:HIS237 3.1 20.7 1.0 CE1 B:HIS78 3.1 19.6 1.0 H12 B:L52301 3.8 32.2 0.0 OG1 B:THR190 3.9 26.5 1.0 ND1 B:HIS237 4.1 21.0 1.0 CG B:HIS237 4.1 19.7 1.0 CG B:HIS78 4.2 18.8 1.0 CB B:ASP241 4.2 17.9 1.0 C18 B:L52301 4.2 33.6 1.0 CB B:THR190 4.2 27.0 1.0 ND1 B:HIS78 4.2 20.4 1.0 OE2 B:GLU77 4.3 18.8 1.0 CG B:GLU77 4.3 24.8 1.0 H2 B:L52301 4.4 34.4 0.0 H15 B:L52301 4.4 34.6 0.0 H14 B:L52301 4.6 34.6 0.0 O B:HIS237 4.7 19.1 1.0 C20 B:L52301 4.7 34.6 1.0 CE1 B:HIS264 4.8 23.6 1.0 NE2 B:HIS264 4.8 23.7 1.0 H1 B:L52301 4.8 33.6 0.0 CA B:ASP241 4.8 16.6 1.0 N1 B:L52301 4.8 34.4 1.0 CD B:GLU77 4.9 34.2 1.0 CA B:THR190 4.9 20.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) 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)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:20.2 occ:1.00 NE2 C:HIS237 2.0 19.1 1.0 OD1 C:ASP241 2.1 25.2 1.0 NE2 C:HIS78 2.1 19.5 1.0 H13 C:L52301 2.2 31.9 0.0 O2 C:L52301 2.2 31.3 1.0 O3 C:L52301 2.5 31.9 1.0 OD2 C:ASP241 2.7 29.1 1.0 CG C:ASP241 2.7 25.0 1.0 CE1 C:HIS237 2.9 18.8 1.0 CD2 C:HIS78 3.0 19.7 1.0 C19 C:L52301 3.1 32.5 1.0 CD2 C:HIS237 3.1 19.7 1.0 CE1 C:HIS78 3.2 19.3 1.0 N2 C:L52301 3.3 32.0 1.0 OG1 C:THR190 3.8 25.4 1.0 ND1 C:HIS237 4.1 19.8 1.0 H12 C:L52301 4.1 32.0 0.0 CG C:HIS237 4.1 18.6 1.0 CB C:ASP241 4.2 18.8 1.0 CG C:HIS78 4.2 18.3 1.0 CB C:THR190 4.2 25.9 1.0 ND1 C:HIS78 4.3 20.1 1.0 CG C:GLU77 4.3 25.0 1.0 OE2 C:GLU77 4.4 28.8 1.0 C18 C:L52301 4.5 33.9 1.0 H15 C:L52301 4.6 34.7 0.0 O C:HIS237 4.7 18.5 1.0 H14 C:L52301 4.7 34.7 0.0 CE1 C:HIS264 4.8 22.9 1.0 NE2 C:HIS264 4.8 23.1 1.0 CA C:ASP241 4.9 17.2 1.0 CA C:THR190 4.9 20.0 1.0 CD C:GLU77 4.9 39.0 1.0 C20 C:L52301 4.9 34.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(2S)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) 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)-3-Amino-1- (Hydroxyamino)-1-Oxopropan-2-Yl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl) Benzamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:22.6 occ:1.00 OD1 D:ASP241 2.0 29.9 1.0 NE2 D:HIS78 2.1 27.7 1.0 H13 D:L52302 2.1 36.4 0.0 NE2 D:HIS237 2.1 22.2 1.0 O2 D:L52302 2.1 36.4 1.0 O3 D:L52302 2.2 36.4 1.0 OD2 D:ASP241 2.6 35.9 1.0 CG D:ASP241 2.6 30.2 1.0 C19 D:L52302 2.9 37.5 1.0 CE1 D:HIS237 2.9 22.0 1.0 N2 D:L52302 2.9 37.0 1.0 CD2 D:HIS78 3.0 27.1 1.0 CE1 D:HIS78 3.2 27.4 1.0 CD2 D:HIS237 3.2 22.4 1.0 H12 D:L52302 3.8 37.0 0.0 OG1 D:THR190 4.1 33.5 1.0 ND1 D:HIS237 4.1 23.0 1.0 CB D:ASP241 4.1 23.7 1.0 CG D:HIS78 4.2 25.1 1.0 CG D:HIS237 4.2 21.3 1.0 ND1 D:HIS78 4.3 27.4 1.0 CB D:THR190 4.3 33.9 1.0 C18 D:L52302 4.4 38.9 1.0 CG D:GLU77 4.4 29.1 1.0 H17 D:L52302 4.4 38.0 0.0 OE2 D:GLU77 4.4 28.8 1.0 H15 D:L52302 4.5 38.1 0.0 CE1 D:HIS264 4.8 25.2 1.0 NE2 D:HIS264 4.8 26.0 1.0 CA D:ASP241 4.8 21.8 1.0 O D:HIS237 4.8 21.5 1.0 C20 D:L52302 4.9 38.1 1.0 CD D:GLU77 5.0 42.4 1.0 H1 D:L52302 5.0 38.9 0.0

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