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
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]-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
|
Other elements in 4fw6:
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:
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]-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 4fw6
Go back to
Zinc Binding Sites List in 4fw6
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 4fw6
Go back to
Zinc Binding Sites List in 4fw6
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 4fw6
Go back to
Zinc Binding Sites List in 4fw6
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 4fw6
Go back to
Zinc Binding Sites List in 4fw6
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
|
|
Reference:
Y.N.Kang,
J.A.Stuckey.
Crystal Structure of the Lpxc To Be Published.
Page generated: Sat Oct 26 22:58:55 2024
|