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Zinc in PDB 4fw7: Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]Biphenyl-4-Carboxamide Inhibitor

Protein crystallography data

The structure of Crystal Structure of the Lpxc in Complex with N-[(2S,3R)-3-Hydroxy-1- (Hydroxyamino)-1-Oxobutan-2-Yl]Biphenyl-4-Carboxamide Inhibitor, PDB code: 4fw7 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) 38.22 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.583, 89.475, 169.067, 90.00, 90.02, 90.00
R / Rfree (%) 16.3 / 19.2

Zinc Binding Sites:

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]Biphenyl-4-Carboxamide Inhibitor (pdb code 4fw7). 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]Biphenyl-4-Carboxamide Inhibitor, PDB code: 4fw7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4fw7

Go back to Zinc Binding Sites List in 4fw7
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]Biphenyl-4-Carboxamide 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]Biphenyl-4-Carboxamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:12.8
occ:1.00
O2 A:L63302 2.0 16.8 1.0
NE2 A:HIS78 2.1 13.6 1.0
NE2 A:HIS237 2.1 10.9 1.0
OD1 A:ASP241 2.1 12.6 1.0
H14 A:L63302 2.2 18.1 1.0
O3 A:L63302 2.2 17.6 1.0
CG A:ASP241 2.8 12.8 1.0
OD2 A:ASP241 2.8 13.2 1.0
C15 A:L63302 2.8 18.9 1.0
N2 A:L63302 3.0 18.3 1.0
CD2 A:HIS237 3.0 12.1 1.0
CD2 A:HIS78 3.0 13.2 1.0
CE1 A:HIS237 3.0 11.8 1.0
CE1 A:HIS78 3.1 13.7 1.0
H13 A:L63302 3.8 18.4 1.0
H16 A:L63302 3.9 21.4 1.0
O A:HOH540 3.9 39.1 1.0
OG1 A:THR190 4.0 16.7 1.0
CG A:HIS237 4.2 11.2 1.0
ND1 A:HIS237 4.2 11.8 1.0
CG A:HIS78 4.2 13.1 1.0
ND1 A:HIS78 4.2 15.9 1.0
CG A:GLU77 4.2 12.8 1.0
C14 A:L63302 4.3 21.0 1.0
CB A:ASP241 4.3 11.6 1.0
CB A:THR190 4.3 17.3 1.0
OE2 A:GLU77 4.3 18.3 1.0
H3 A:L63302 4.5 20.3 1.0
O4 A:L63302 4.6 28.8 1.0
C17 A:L63302 4.7 20.5 1.0
C16 A:L63302 4.8 24.8 1.0
CD A:GLU77 4.8 14.5 1.0
H18 A:L63302 4.8 28.7 1.0
CA A:THR190 4.8 12.0 1.0
CA A:ASP241 4.8 9.4 1.0
CE1 A:HIS264 4.9 15.1 1.0
H1 A:L63302 4.9 21.2 1.0
N1 A:L63302 4.9 20.1 1.0
O A:HIS237 4.9 12.0 1.0
NE2 A:HIS264 5.0 15.8 1.0

Zinc binding site 2 out of 4 in 4fw7

Go back to Zinc Binding Sites List in 4fw7
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]Biphenyl-4-Carboxamide 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]Biphenyl-4-Carboxamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:12.8
occ:1.00
NE2 B:HIS237 2.1 11.8 1.0
OD1 B:ASP241 2.1 12.1 1.0
NE2 B:HIS78 2.1 14.4 1.0
O2 B:L63403 2.1 19.6 1.0
H14 B:L63403 2.2 17.8 1.0
O3 B:L63403 2.2 18.7 1.0
CG B:ASP241 2.7 11.6 1.0
OD2 B:ASP241 2.8 14.0 1.0
C15 B:L63403 2.9 19.8 1.0
N2 B:L63403 3.0 19.4 1.0
CE1 B:HIS237 3.0 12.0 1.0
CD2 B:HIS78 3.0 13.6 1.0
CE1 B:HIS78 3.1 14.6 1.0
CD2 B:HIS237 3.1 12.8 1.0
H13 B:L63403 3.8 19.7 1.0
O B:HOH636 3.9 40.5 1.0
H16 B:L63403 4.0 21.7 1.0
OG1 B:THR190 4.0 17.7 1.0
ND1 B:HIS237 4.2 11.5 1.0
CG B:HIS237 4.2 11.0 1.0
CG B:HIS78 4.2 12.9 1.0
CG B:GLU77 4.2 13.6 1.0
ND1 B:HIS78 4.2 15.7 1.0
CB B:ASP241 4.2 10.4 1.0
C14 B:L63403 4.3 20.1 1.0
CB B:THR190 4.3 15.7 1.0
OE2 B:GLU77 4.3 16.2 1.0
H18 B:L63403 4.4 29.4 1.0
H3 B:L63403 4.6 21.6 1.0
O4 B:L63403 4.8 30.0 1.0
C17 B:L63403 4.8 20.7 1.0
CA B:ASP241 4.8 9.4 1.0
CD B:GLU77 4.8 14.1 1.0
CE1 B:HIS264 4.8 15.8 1.0
O B:HIS237 4.9 11.2 1.0
CA B:THR190 4.9 12.1 1.0
C16 B:L63403 4.9 24.7 1.0
H1 B:L63403 4.9 20.5 1.0
NE2 B:HIS264 4.9 16.6 1.0
N1 B:L63403 4.9 20.3 1.0

Zinc binding site 3 out of 4 in 4fw7

Go back to Zinc Binding Sites List in 4fw7
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]Biphenyl-4-Carboxamide 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]Biphenyl-4-Carboxamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:15.4
occ:1.00
OD1 C:ASP241 2.0 13.4 1.0
NE2 C:HIS78 2.1 15.9 1.0
NE2 C:HIS237 2.1 14.7 1.0
O2 C:L63302 2.2 19.2 1.0
O3 C:L63302 2.2 21.5 1.0
H14 C:L63302 2.5 21.4 1.0
CG C:ASP241 2.7 14.2 1.0
OD2 C:ASP241 2.7 16.1 1.0
C15 C:L63302 2.8 20.4 1.0
N2 C:L63302 3.0 21.8 1.0
CD2 C:HIS78 3.0 15.2 1.0
CD2 C:HIS237 3.1 15.1 1.0
CE1 C:HIS237 3.1 15.3 1.0
CE1 C:HIS78 3.1 17.1 1.0
H13 C:L63302 3.6 22.9 1.0
H16 C:L63302 3.8 27.5 1.0
OG1 C:THR190 4.1 17.6 1.0
CB C:ASP241 4.1 13.7 1.0
CG C:HIS78 4.2 14.6 1.0
CG C:HIS237 4.2 13.9 1.0
ND1 C:HIS237 4.2 15.2 1.0
CG C:GLU77 4.2 16.9 1.0
ND1 C:HIS78 4.2 16.9 1.0
C14 C:L63302 4.3 25.1 1.0
CB C:THR190 4.3 19.2 1.0
H18 C:L63302 4.3 28.1 1.0
OE2 C:GLU77 4.3 19.1 1.0
O4 C:L63302 4.5 28.7 1.0
H3 C:L63302 4.7 24.5 1.0
C17 C:L63302 4.7 26.6 1.0
C16 C:L63302 4.7 28.0 1.0
CA C:ASP241 4.8 11.7 1.0
CD C:GLU77 4.8 25.0 1.0
CA C:THR190 4.8 14.0 1.0
CE1 C:HIS264 4.9 18.2 1.0
O C:HIS237 4.9 12.2 1.0
H1 C:L63302 4.9 25.3 1.0
NE2 C:HIS264 5.0 18.6 1.0
N1 C:L63302 5.0 24.6 1.0

Zinc binding site 4 out of 4 in 4fw7

Go back to Zinc Binding Sites List in 4fw7
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]Biphenyl-4-Carboxamide 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]Biphenyl-4-Carboxamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:15.2
occ:1.00
NE2 D:HIS78 2.1 15.2 1.0
OD1 D:ASP241 2.1 13.3 1.0
NE2 D:HIS237 2.1 14.2 1.0
O2 D:L63302 2.1 17.9 1.0
O3 D:L63302 2.1 20.6 1.0
H14 D:L63302 2.4 20.7 1.0
OD2 D:ASP241 2.7 16.8 1.0
CG D:ASP241 2.7 12.7 1.0
C15 D:L63302 2.8 19.7 1.0
N2 D:L63302 2.9 21.3 1.0
CD2 D:HIS78 3.0 14.9 1.0
CD2 D:HIS237 3.1 15.3 1.0
CE1 D:HIS78 3.1 16.2 1.0
CE1 D:HIS237 3.1 15.7 1.0
H13 D:L63302 3.6 22.7 1.0
H16 D:L63302 3.8 24.0 1.0
H18 D:L63302 4.0 27.7 1.0
OG1 D:THR190 4.1 19.5 1.0
CB D:ASP241 4.2 12.0 1.0
CG D:HIS78 4.2 13.2 1.0
CG D:HIS237 4.2 14.7 1.0
ND1 D:HIS237 4.2 15.6 1.0
ND1 D:HIS78 4.2 15.8 1.0
CG D:GLU77 4.3 14.8 1.0
C14 D:L63302 4.3 22.6 1.0
OE2 D:GLU77 4.3 19.5 1.0
CB D:THR190 4.3 19.0 1.0
H3 D:L63302 4.6 23.4 1.0
O4 D:L63302 4.6 28.2 1.0
C17 D:L63302 4.6 24.0 1.0
C16 D:L63302 4.7 24.8 1.0
CA D:ASP241 4.8 10.5 1.0
CD D:GLU77 4.8 25.4 1.0
CA D:THR190 4.9 13.3 1.0
H1 D:L63302 4.9 22.8 1.0
CE1 D:HIS264 4.9 18.2 1.0
H15 D:L63302 4.9 25.1 1.0
O D:HIS237 4.9 12.4 1.0
N1 D:L63302 4.9 23.3 1.0
NE2 D:HIS264 4.9 19.1 1.0

Reference:

Y.N.Kang, J.A.Stuckey. Crystal Structure of the Lpxc To Be Published.
Page generated: Wed Dec 16 05:18:32 2020

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