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Zinc in PDB 4fw4: Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor

Protein crystallography data

The structure of Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor, PDB code: 4fw4 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) 43.21 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.674, 89.332, 170.674, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor (pdb code 4fw4). 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-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor, PDB code: 4fw4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4fw4

Go back to Zinc Binding Sites List in 4fw4
Zinc binding site 1 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-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-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:20.0
occ:1.00
 O01 A:3P3301 2.0 30.4 1.0
NE2 A:HIS237 2.1 19.7 1.0
OD1 A:ASP241 2.1 21.7 1.0
NE2 A:HIS78 2.1 21.9 1.0
O04 A:3P3301 2.3 32.3 1.0
CG A:ASP241 2.7 21.5 1.0
OD2 A:ASP241 2.8 20.6 1.0
C02 A:3P3301 2.8 32.6 1.0
CE1 A:HIS237 3.0 19.0 1.0
CD2 A:HIS78 3.0 22.0 1.0
N03 A:3P3301 3.0 31.9 1.0
CD2 A:HIS237 3.1 19.7 1.0
CE1 A:HIS78 3.1 21.6 1.0
OG1 A:THR190 4.0 23.5 1.0
ND1 A:HIS237 4.1 19.7 1.0
CG A:HIS237 4.2 18.4 1.0
CG A:HIS78 4.2 21.2 1.0
CB A:ASP241 4.2 16.9 1.0
OE2 A:GLU77 4.2 27.1 1.0
ND1 A:HIS78 4.2 22.7 1.0
C05 A:3P3301 4.2 33.9 1.0
CG A:GLU77 4.3 25.0 1.0
CB A:THR190 4.3 23.4 1.0
C25 A:3P3301 4.5 36.1 1.0
CD A:GLU77 4.8 35.2 1.0
O A:HIS237 4.8 19.1 1.0
CA A:ASP241 4.8 15.8 1.0
CE1 A:HIS264 4.8 22.6 1.0
CA A:THR190 4.9 18.1 1.0
NE2 A:HIS264 4.9 23.1 1.0
N06 A:3P3301 4.9 33.1 1.0

Zinc binding site 2 out of 4 in 4fw4

Go back to Zinc Binding Sites List in 4fw4
Zinc binding site 2 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-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-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:18.9
occ:1.00
 O01 B:3P3302 1.9 23.6 1.0
OD1 B:ASP241 2.0 23.2 1.0
NE2 B:HIS237 2.1 18.0 1.0
NE2 B:HIS78 2.1 24.9 1.0
O04 B:3P3302 2.3 28.8 1.0
CG B:ASP241 2.7 23.0 1.0
OD2 B:ASP241 2.8 25.2 1.0
C02 B:3P3302 2.8 26.5 1.0
CE1 B:HIS237 3.0 18.1 1.0
CD2 B:HIS78 3.0 24.9 1.0
N03 B:3P3302 3.0 26.4 1.0
CD2 B:HIS237 3.1 18.6 1.0
CE1 B:HIS78 3.1 25.0 1.0
OG1 B:THR190 4.0 23.2 1.0
ND1 B:HIS237 4.2 19.0 1.0
CG B:HIS237 4.2 17.7 1.0
CG B:HIS78 4.2 23.3 1.0
CB B:ASP241 4.2 17.0 1.0
OE2 B:GLU77 4.2 25.2 1.0
CB B:THR190 4.2 21.5 1.0
ND1 B:HIS78 4.2 25.4 1.0
C05 B:3P3302 4.2 29.8 1.0
CG B:GLU77 4.3 23.9 1.0
C25 B:3P3302 4.6 33.7 1.0
CD B:GLU77 4.8 31.8 1.0
O B:HIS237 4.8 19.0 1.0
CA B:ASP241 4.8 16.0 1.0
CE1 B:HIS264 4.9 22.1 1.0
CA B:THR190 4.9 17.7 1.0
N06 B:3P3302 4.9 30.2 1.0
NE2 B:HIS264 5.0 22.8 1.0

Zinc binding site 3 out of 4 in 4fw4

Go back to Zinc Binding Sites List in 4fw4
Zinc binding site 3 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-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-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:23.2
occ:1.00
 NE2 C:HIS78 1.9 25.6 1.0
OD1 C:ASP241 2.0 23.0 1.0
NE2 C:HIS237 2.0 18.4 1.0
O04 C:3P3302 2.1 35.1 1.0
O01 C:3P3302 2.2 33.5 1.0
CG C:ASP241 2.7 24.1 1.0
OD2 C:ASP241 2.8 25.5 1.0
C02 C:3P3302 2.9 36.8 1.0
CE1 C:HIS78 2.9 25.7 1.0
CE1 C:HIS237 2.9 18.6 1.0
CD2 C:HIS78 3.0 25.7 1.0
N03 C:3P3302 3.0 36.0 1.0
CD2 C:HIS237 3.0 18.6 1.0
ND1 C:HIS237 4.1 19.9 1.0
ND1 C:HIS78 4.1 26.6 1.0
OG1 C:THR190 4.1 25.7 1.0
CG C:HIS78 4.1 24.4 1.0
CG C:HIS237 4.1 18.2 1.0
CB C:ASP241 4.1 19.0 1.0
CG C:GLU77 4.2 31.0 1.0
OE2 C:GLU77 4.3 31.6 1.0
C05 C:3P3302 4.3 40.1 1.0
CB C:THR190 4.3 26.6 1.0
C25 C:3P3302 4.7 42.7 1.0
CA C:ASP241 4.7 18.1 1.0
O C:HIS237 4.8 21.2 1.0
CD C:GLU77 4.8 40.4 1.0
CE1 C:HIS264 4.8 25.1 1.0
NE2 C:HIS264 4.9 25.7 1.0
CA C:THR190 4.9 22.6 1.0

Zinc binding site 4 out of 4 in 4fw4

Go back to Zinc Binding Sites List in 4fw4
Zinc binding site 4 out of 4 in the Crystal Structure of the Lpxc in Complex with N-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-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-[(1S,2R)-2-Hydroxy-1- (Hydroxycarbamoyl)Propyl]-4-(4-Phenylbuta-1,3-Diyn-1-Yl)Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:23.0
occ:1.00
 OD1 D:ASP241 2.0 25.9 1.0
NE2 D:HIS78 2.0 25.9 1.0
NE2 D:HIS237 2.1 18.2 1.0
O01 D:3P3302 2.1 31.5 1.0
O04 D:3P3302 2.2 33.5 1.0
CG D:ASP241 2.7 26.4 1.0
OD2 D:ASP241 2.8 29.1 1.0
C02 D:3P3302 2.8 35.1 1.0
CE1 D:HIS237 3.0 18.0 1.0
N03 D:3P3302 3.0 34.5 1.0
CE1 D:HIS78 3.0 26.1 1.0
CD2 D:HIS78 3.0 26.0 1.0
CD2 D:HIS237 3.1 18.3 1.0
OG1 D:THR190 4.1 26.6 1.0
ND1 D:HIS237 4.1 18.9 1.0
CB D:ASP241 4.1 19.3 1.0
CG D:HIS78 4.1 24.9 1.0
ND1 D:HIS78 4.1 27.3 1.0
CG D:HIS237 4.2 17.5 1.0
CB D:THR190 4.3 29.4 1.0
C05 D:3P3302 4.3 37.8 1.0
CG D:GLU77 4.3 29.2 1.0
OE2 D:GLU77 4.3 31.1 1.0
C25 D:3P3302 4.6 40.0 1.0
O D:HIS237 4.8 18.8 1.0
CA D:ASP241 4.8 17.9 1.0
CD D:GLU77 4.8 38.3 1.0
CE1 D:HIS264 4.8 25.4 1.0
CA D:THR190 4.9 21.9 1.0
NE2 D:HIS264 4.9 26.1 1.0
CD2 D:LEU240 5.0 22.3 1.0

Reference:

Y.N.Kang, J.A.Stuckey. Crystal Structure of the Lpxc To Be Published.
Page generated: Sat Oct 26 22:58:55 2024

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