Zinc in PDB 8hxe: Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
Enzymatic activity of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
All present enzymatic activity of Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)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- Propylbenzyl)Thiazole-4-Carboxylic Acid, PDB code: 8hxe
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)
|
32.65 /
2.38
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.525,
75.525,
181.039,
90,
90,
90
|
R / Rfree (%)
|
21.4 /
29.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
(pdb code 8hxe). 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- Propylbenzyl)Thiazole-4-Carboxylic Acid, PDB code: 8hxe:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8hxe
Go back to
Zinc Binding Sites List in 8hxe
Zinc binding site 1 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxe-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxe-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- Propylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:71.6
occ:1.00
|
O
|
A:HOH402
|
2.0
|
73.8
|
1.0
|
NE2
|
A:HIS160
|
2.2
|
69.7
|
1.0
|
NE2
|
A:HIS84
|
2.2
|
73.1
|
1.0
|
ND1
|
A:HIS86
|
2.2
|
61.6
|
1.0
|
S
|
A:SCN304
|
2.6
|
88.4
|
1.0
|
CD2
|
A:HIS160
|
3.1
|
74.3
|
1.0
|
CE1
|
A:HIS86
|
3.1
|
62.7
|
1.0
|
CE1
|
A:HIS84
|
3.2
|
67.7
|
1.0
|
CE1
|
A:HIS160
|
3.2
|
72.6
|
1.0
|
CD2
|
A:HIS84
|
3.2
|
75.5
|
1.0
|
CG
|
A:HIS86
|
3.3
|
65.3
|
1.0
|
ZN
|
A:ZN302
|
3.4
|
71.1
|
1.0
|
CB
|
A:HIS86
|
3.6
|
62.4
|
1.0
|
O07
|
A:51I303
|
3.7
|
68.0
|
1.0
|
C05
|
A:51I303
|
4.1
|
71.5
|
1.0
|
CG
|
A:HIS160
|
4.2
|
63.0
|
1.0
|
OD1
|
A:ASP88
|
4.3
|
74.4
|
1.0
|
NE2
|
A:HIS86
|
4.3
|
62.0
|
1.0
|
ND1
|
A:HIS160
|
4.3
|
68.2
|
1.0
|
ND1
|
A:HIS84
|
4.3
|
67.5
|
1.0
|
CD2
|
A:HIS89
|
4.3
|
67.5
|
1.0
|
NE2
|
A:HIS89
|
4.3
|
60.2
|
1.0
|
C
|
A:SCN304
|
4.3
|
72.4
|
1.0
|
N03
|
A:51I303
|
4.3
|
72.2
|
1.0
|
CD2
|
A:HIS86
|
4.3
|
59.4
|
1.0
|
CG
|
A:HIS84
|
4.4
|
69.3
|
1.0
|
C04
|
A:51I303
|
4.6
|
74.8
|
1.0
|
O06
|
A:51I303
|
4.6
|
86.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8hxe
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Zinc Binding Sites List in 8hxe
Zinc binding site 2 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxe-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxe-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- Propylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:71.1
occ:1.00
|
NE2
|
A:HIS89
|
2.1
|
60.2
|
1.0
|
NE2
|
A:HIS225
|
2.2
|
76.9
|
1.0
|
OD2
|
A:ASP88
|
2.3
|
63.0
|
1.0
|
N03
|
A:51I303
|
2.3
|
72.2
|
1.0
|
O
|
A:HOH402
|
2.3
|
73.8
|
1.0
|
O07
|
A:51I303
|
2.5
|
68.0
|
1.0
|
CE1
|
A:HIS89
|
3.0
|
70.2
|
1.0
|
C04
|
A:51I303
|
3.1
|
74.8
|
1.0
|
CE1
|
A:HIS225
|
3.1
|
68.8
|
1.0
|
C05
|
A:51I303
|
3.1
|
71.5
|
1.0
|
CD2
|
A:HIS89
|
3.2
|
67.5
|
1.0
|
CD2
|
A:HIS225
|
3.2
|
72.7
|
1.0
|
CG
|
A:ASP88
|
3.2
|
72.0
|
1.0
|
OD1
|
A:ASP88
|
3.3
|
74.4
|
1.0
|
C02
|
A:51I303
|
3.4
|
84.4
|
1.0
|
ZN
|
A:ZN301
|
3.4
|
71.6
|
1.0
|
N01
|
A:51I303
|
3.9
|
81.9
|
1.0
|
ND1
|
A:HIS89
|
4.2
|
63.8
|
1.0
|
ND1
|
A:HIS225
|
4.2
|
77.7
|
1.0
|
CE1
|
A:HIS84
|
4.2
|
67.7
|
1.0
|
CG
|
A:HIS225
|
4.2
|
78.7
|
1.0
|
CG
|
A:HIS89
|
4.3
|
64.9
|
1.0
|
NE2
|
A:HIS84
|
4.3
|
73.1
|
1.0
|
O06
|
A:51I303
|
4.3
|
86.0
|
1.0
|
S
|
A:SCN304
|
4.4
|
88.4
|
1.0
|
C08
|
A:51I303
|
4.5
|
74.8
|
1.0
|
NE2
|
A:HIS160
|
4.6
|
69.7
|
1.0
|
CB
|
A:ASP88
|
4.6
|
66.9
|
1.0
|
S19
|
A:51I303
|
4.8
|
77.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8hxe
Go back to
Zinc Binding Sites List in 8hxe
Zinc binding site 3 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxe-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxe-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- Propylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:70.0
occ:1.00
|
NE2
|
B:HIS160
|
2.1
|
71.6
|
1.0
|
O
|
B:HOH407
|
2.1
|
80.9
|
1.0
|
NE2
|
B:HIS84
|
2.1
|
66.8
|
1.0
|
ND1
|
B:HIS86
|
2.2
|
59.9
|
1.0
|
CD2
|
B:HIS160
|
3.0
|
63.9
|
1.0
|
CD2
|
B:HIS84
|
3.0
|
58.8
|
1.0
|
CE1
|
B:HIS160
|
3.1
|
70.9
|
1.0
|
CE1
|
B:HIS86
|
3.1
|
63.6
|
1.0
|
CE1
|
B:HIS84
|
3.2
|
66.8
|
1.0
|
CG
|
B:HIS86
|
3.2
|
67.3
|
1.0
|
S
|
B:SCN304
|
3.2
|
97.8
|
1.0
|
CB
|
B:HIS86
|
3.5
|
66.0
|
1.0
|
O07
|
B:51I303
|
3.6
|
78.6
|
1.0
|
ZN
|
B:ZN302
|
3.7
|
75.9
|
1.0
|
CG
|
B:HIS160
|
4.1
|
71.0
|
1.0
|
ND1
|
B:HIS160
|
4.1
|
67.5
|
1.0
|
CG
|
B:HIS84
|
4.2
|
65.0
|
1.0
|
ND1
|
B:HIS84
|
4.2
|
69.0
|
1.0
|
NE2
|
B:HIS86
|
4.2
|
60.6
|
1.0
|
CD2
|
B:HIS86
|
4.3
|
64.8
|
1.0
|
OD1
|
B:ASP88
|
4.3
|
78.6
|
1.0
|
N03
|
B:51I303
|
4.3
|
82.6
|
1.0
|
CD2
|
B:HIS89
|
4.4
|
65.5
|
1.0
|
C05
|
B:51I303
|
4.4
|
83.1
|
1.0
|
NE2
|
B:HIS89
|
4.6
|
62.8
|
1.0
|
C04
|
B:51I303
|
4.8
|
93.0
|
1.0
|
OD2
|
B:ASP88
|
4.9
|
79.2
|
1.0
|
C
|
B:SCN304
|
4.9
|
163.6
|
1.0
|
CA
|
B:HIS86
|
5.0
|
65.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8hxe
Go back to
Zinc Binding Sites List in 8hxe
Zinc binding site 4 out
of 4 in the Crystal Structure of B3 L1 Mbl in Complex with 2-Amino-5-(4- Propylbenzyl)Thiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxe-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxe-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- Propylbenzyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:75.9
occ:1.00
|
O
|
B:HOH407
|
2.0
|
80.9
|
1.0
|
NE2
|
B:HIS89
|
2.2
|
62.8
|
1.0
|
NE2
|
B:HIS225
|
2.2
|
80.2
|
1.0
|
OD2
|
B:ASP88
|
2.2
|
79.2
|
1.0
|
N03
|
B:51I303
|
2.4
|
82.6
|
1.0
|
O07
|
B:51I303
|
2.7
|
78.6
|
1.0
|
CD2
|
B:HIS89
|
3.0
|
65.5
|
1.0
|
CE1
|
B:HIS225
|
3.0
|
76.4
|
1.0
|
CG
|
B:ASP88
|
3.1
|
79.8
|
1.0
|
CE1
|
B:HIS89
|
3.2
|
67.6
|
1.0
|
C04
|
B:51I303
|
3.3
|
93.0
|
1.0
|
CD2
|
B:HIS225
|
3.3
|
71.3
|
1.0
|
C02
|
B:51I303
|
3.3
|
102.2
|
1.0
|
OD1
|
B:ASP88
|
3.3
|
78.6
|
1.0
|
C05
|
B:51I303
|
3.4
|
83.1
|
1.0
|
N01
|
B:51I303
|
3.6
|
114.8
|
1.0
|
ZN
|
B:ZN301
|
3.7
|
70.0
|
1.0
|
CG
|
B:HIS89
|
4.2
|
62.4
|
1.0
|
ND1
|
B:HIS225
|
4.2
|
78.4
|
1.0
|
ND1
|
B:HIS89
|
4.2
|
66.8
|
1.0
|
CE1
|
B:HIS84
|
4.3
|
66.8
|
1.0
|
NE2
|
B:HIS84
|
4.3
|
66.8
|
1.0
|
CG
|
B:HIS225
|
4.3
|
61.8
|
1.0
|
CB
|
B:ASP88
|
4.4
|
76.8
|
1.0
|
S
|
B:SCN304
|
4.5
|
97.8
|
1.0
|
C08
|
B:51I303
|
4.5
|
106.2
|
1.0
|
O06
|
B:51I303
|
4.6
|
87.3
|
1.0
|
NE2
|
B:HIS160
|
4.6
|
71.6
|
1.0
|
S19
|
B:51I303
|
4.7
|
106.4
|
1.0
|
OG
|
B:SER185
|
5.0
|
75.4
|
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
|