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


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 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

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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


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 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

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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


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 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


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 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 Oct 31 07:28:39 2024

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