Zinc in PDB 8hxi: Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
Enzymatic activity of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
All present enzymatic activity of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid:
3.5.2.6;
Protein crystallography data
The structure of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid, PDB code: 8hxi
was solved by
Y.-H.Yan,
K.-R.Zhu,
G.-B.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.69 /
1.81
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.82,
75.82,
184.52,
90,
90,
90
|
R / Rfree (%)
|
17.5 /
21.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
(pdb code 8hxi). 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 B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid, PDB code: 8hxi:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8hxi
Go back to
Zinc Binding Sites List in 8hxi
Zinc binding site 1 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:34.9
occ:1.00
|
O
|
A:HOH444
|
1.9
|
26.7
|
1.0
|
NE2
|
A:HIS160
|
2.1
|
32.6
|
1.0
|
ND1
|
A:HIS86
|
2.2
|
22.8
|
1.0
|
NE2
|
A:HIS84
|
2.2
|
30.0
|
1.0
|
S
|
A:SCN304
|
2.3
|
48.2
|
1.0
|
CD2
|
A:HIS160
|
3.0
|
26.9
|
1.0
|
CE1
|
A:HIS86
|
3.1
|
25.1
|
1.0
|
CE1
|
A:HIS84
|
3.2
|
30.2
|
1.0
|
CE1
|
A:HIS160
|
3.2
|
33.5
|
1.0
|
CD2
|
A:HIS84
|
3.2
|
26.5
|
1.0
|
CG
|
A:HIS86
|
3.3
|
24.4
|
1.0
|
O07
|
A:5A5303
|
3.4
|
31.0
|
0.4
|
O07
|
A:5A5303
|
3.5
|
31.4
|
0.6
|
CB
|
A:HIS86
|
3.6
|
28.7
|
1.0
|
ZN
|
A:ZN302
|
3.7
|
32.6
|
1.0
|
C
|
A:SCN304
|
4.1
|
38.4
|
1.0
|
C05
|
A:5A5303
|
4.1
|
32.6
|
0.4
|
C05
|
A:5A5303
|
4.2
|
32.5
|
0.6
|
CG
|
A:HIS160
|
4.2
|
29.0
|
1.0
|
NE2
|
A:HIS86
|
4.2
|
23.1
|
1.0
|
ND1
|
A:HIS160
|
4.2
|
30.4
|
1.0
|
ND1
|
A:HIS84
|
4.2
|
31.5
|
1.0
|
OD1
|
A:ASP88
|
4.3
|
28.6
|
1.0
|
CG
|
A:HIS84
|
4.3
|
28.4
|
1.0
|
N03
|
A:5A5303
|
4.3
|
29.2
|
0.6
|
CD2
|
A:HIS86
|
4.3
|
21.9
|
1.0
|
CD2
|
A:HIS89
|
4.4
|
26.7
|
1.0
|
N03
|
A:5A5303
|
4.5
|
29.6
|
0.4
|
NE2
|
A:HIS89
|
4.6
|
28.4
|
1.0
|
C04
|
A:5A5303
|
4.6
|
34.4
|
0.4
|
C04
|
A:5A5303
|
4.6
|
34.6
|
0.6
|
O06
|
A:5A5303
|
4.8
|
33.6
|
0.4
|
OD2
|
A:ASP88
|
4.9
|
28.2
|
1.0
|
O06
|
A:5A5303
|
4.9
|
33.7
|
0.6
|
|
Zinc binding site 2 out
of 4 in 8hxi
Go back to
Zinc Binding Sites List in 8hxi
Zinc binding site 2 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:32.6
occ:1.00
|
O07
|
A:5A5303
|
2.1
|
31.0
|
0.4
|
O
|
A:HOH444
|
2.1
|
26.7
|
1.0
|
NE2
|
A:HIS225
|
2.1
|
25.5
|
1.0
|
OD2
|
A:ASP88
|
2.2
|
28.2
|
1.0
|
N03
|
A:5A5303
|
2.2
|
29.6
|
0.4
|
NE2
|
A:HIS89
|
2.2
|
28.4
|
1.0
|
N03
|
A:5A5303
|
2.3
|
29.2
|
0.6
|
O07
|
A:5A5303
|
2.3
|
31.4
|
0.6
|
C05
|
A:5A5303
|
2.9
|
32.6
|
0.4
|
C04
|
A:5A5303
|
3.0
|
34.4
|
0.4
|
CG
|
A:ASP88
|
3.1
|
28.1
|
1.0
|
C04
|
A:5A5303
|
3.1
|
34.6
|
0.6
|
C05
|
A:5A5303
|
3.1
|
32.5
|
0.6
|
CD2
|
A:HIS225
|
3.1
|
28.2
|
1.0
|
CE1
|
A:HIS225
|
3.1
|
33.2
|
1.0
|
CD2
|
A:HIS89
|
3.2
|
26.7
|
1.0
|
CE1
|
A:HIS89
|
3.2
|
25.5
|
1.0
|
C02
|
A:5A5303
|
3.3
|
32.1
|
0.6
|
C02
|
A:5A5303
|
3.3
|
32.2
|
0.4
|
OD1
|
A:ASP88
|
3.3
|
28.6
|
1.0
|
N01
|
A:5A5303
|
3.6
|
29.8
|
0.6
|
ZN
|
A:ZN301
|
3.7
|
34.9
|
1.0
|
N01
|
A:5A5303
|
3.7
|
30.3
|
0.4
|
O06
|
A:5A5303
|
4.1
|
33.6
|
0.4
|
CE1
|
A:HIS84
|
4.2
|
30.2
|
1.0
|
ND1
|
A:HIS225
|
4.2
|
30.7
|
1.0
|
CG
|
A:HIS225
|
4.3
|
29.6
|
1.0
|
ND1
|
A:HIS89
|
4.3
|
27.7
|
1.0
|
CG
|
A:HIS89
|
4.3
|
28.8
|
1.0
|
NE2
|
A:HIS84
|
4.3
|
30.0
|
1.0
|
O06
|
A:5A5303
|
4.3
|
33.7
|
0.6
|
C08
|
A:5A5303
|
4.3
|
33.4
|
0.4
|
CB
|
A:ASP88
|
4.4
|
27.9
|
1.0
|
C08
|
A:5A5303
|
4.4
|
33.3
|
0.6
|
S
|
A:SCN304
|
4.5
|
48.2
|
1.0
|
S19
|
A:5A5303
|
4.7
|
33.9
|
0.6
|
S19
|
A:5A5303
|
4.7
|
33.9
|
0.4
|
OG
|
A:SER185
|
4.7
|
34.7
|
1.0
|
NE2
|
A:HIS160
|
4.9
|
32.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8hxi
Go back to
Zinc Binding Sites List in 8hxi
Zinc binding site 3 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:38.2
occ:1.00
|
O
|
B:HOH408
|
1.9
|
33.2
|
1.0
|
ND1
|
B:HIS86
|
2.1
|
27.8
|
1.0
|
NE2
|
B:HIS160
|
2.2
|
32.9
|
1.0
|
NE2
|
B:HIS84
|
2.3
|
25.9
|
1.0
|
S
|
B:SCN307
|
2.3
|
53.5
|
1.0
|
CE1
|
B:HIS86
|
3.0
|
28.0
|
1.0
|
CD2
|
B:HIS160
|
3.1
|
34.4
|
1.0
|
CG
|
B:HIS86
|
3.1
|
28.5
|
1.0
|
CE1
|
B:HIS84
|
3.2
|
31.5
|
1.0
|
CD2
|
B:HIS84
|
3.2
|
33.9
|
1.0
|
CE1
|
B:HIS160
|
3.2
|
34.4
|
1.0
|
CB
|
B:HIS86
|
3.5
|
31.1
|
1.0
|
O07
|
B:5A5303
|
3.7
|
36.4
|
1.0
|
ZN
|
B:ZN302
|
3.7
|
39.2
|
1.0
|
C
|
B:SCN307
|
4.0
|
38.4
|
1.0
|
NE2
|
B:HIS86
|
4.1
|
28.2
|
1.0
|
OD1
|
B:ASP88
|
4.2
|
32.6
|
1.0
|
CD2
|
B:HIS86
|
4.2
|
28.9
|
1.0
|
CG
|
B:HIS160
|
4.3
|
36.0
|
1.0
|
ND1
|
B:HIS84
|
4.3
|
30.1
|
1.0
|
ND1
|
B:HIS160
|
4.3
|
32.8
|
1.0
|
C05
|
B:5A5303
|
4.3
|
40.8
|
1.0
|
CG
|
B:HIS84
|
4.3
|
29.9
|
1.0
|
N03
|
B:5A5303
|
4.4
|
36.2
|
1.0
|
CD2
|
B:HIS89
|
4.4
|
31.5
|
1.0
|
NE2
|
B:HIS89
|
4.5
|
33.4
|
1.0
|
C04
|
B:5A5303
|
4.7
|
37.0
|
1.0
|
OD2
|
B:ASP88
|
4.9
|
33.7
|
1.0
|
O06
|
B:5A5303
|
4.9
|
39.8
|
1.0
|
CA
|
B:HIS86
|
5.0
|
29.4
|
1.0
|
CG
|
B:ASP88
|
5.0
|
29.9
|
1.0
|
OH
|
B:TYR191
|
5.0
|
30.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8hxi
Go back to
Zinc Binding Sites List in 8hxi
Zinc binding site 4 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxi-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Isopropylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:39.2
occ:1.00
|
O
|
B:HOH408
|
2.1
|
33.2
|
1.0
|
OD2
|
B:ASP88
|
2.2
|
33.7
|
1.0
|
NE2
|
B:HIS225
|
2.2
|
35.6
|
1.0
|
NE2
|
B:HIS89
|
2.2
|
33.4
|
1.0
|
N03
|
B:5A5303
|
2.3
|
36.2
|
1.0
|
O07
|
B:5A5303
|
2.3
|
36.4
|
1.0
|
CG
|
B:ASP88
|
3.1
|
29.9
|
1.0
|
C04
|
B:5A5303
|
3.1
|
37.0
|
1.0
|
CD2
|
B:HIS225
|
3.1
|
36.0
|
1.0
|
C05
|
B:5A5303
|
3.1
|
40.8
|
1.0
|
CD2
|
B:HIS89
|
3.2
|
31.5
|
1.0
|
CE1
|
B:HIS225
|
3.2
|
37.9
|
1.0
|
CE1
|
B:HIS89
|
3.2
|
32.0
|
1.0
|
C02
|
B:5A5303
|
3.2
|
44.1
|
1.0
|
OD1
|
B:ASP88
|
3.3
|
32.6
|
1.0
|
N01
|
B:5A5303
|
3.5
|
42.5
|
1.0
|
ZN
|
B:ZN301
|
3.7
|
38.2
|
1.0
|
ND1
|
B:HIS89
|
4.2
|
29.0
|
1.0
|
ND1
|
B:HIS225
|
4.3
|
36.0
|
1.0
|
CG
|
B:HIS89
|
4.3
|
29.5
|
1.0
|
CG
|
B:HIS225
|
4.3
|
41.4
|
1.0
|
CE1
|
B:HIS84
|
4.3
|
31.5
|
1.0
|
O06
|
B:5A5303
|
4.4
|
39.8
|
1.0
|
NE2
|
B:HIS84
|
4.4
|
25.9
|
1.0
|
CB
|
B:ASP88
|
4.4
|
29.6
|
1.0
|
C08
|
B:5A5303
|
4.4
|
45.6
|
1.0
|
S
|
B:SCN307
|
4.5
|
53.5
|
1.0
|
S19
|
B:5A5303
|
4.7
|
40.4
|
1.0
|
OG
|
B:SER185
|
4.7
|
34.5
|
1.0
|
NE2
|
B:HIS160
|
4.8
|
32.9
|
1.0
|
|
Reference:
Y.H.Yan,
T.T.Zhang,
R.Li,
S.Y.Wang,
L.L.Wei,
X.Y.Wang,
K.R.Zhu,
S.R.Li,
G.Q.Liang,
Z.B.Yang,
L.L.Yang,
S.Qin,
G.B.Li.
Discovery of 2-Aminothiazole-4-Carboxylic Acids As Broad-Spectrum Metallo-Beta-Lactamase Inhibitors By Mimicking Carbapenem Hydrolysate Binding. J.Med.Chem. V. 66 13746 2023.
ISSN: ISSN 0022-2623
PubMed: 37791640
DOI: 10.1021/ACS.JMEDCHEM.3C01189
Page generated: Thu Dec 28 13:14:24 2023
|