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

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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


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- 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 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


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- 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

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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- Propylbenzyl)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- 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

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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


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- 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 Oct 31 07:28:15 2024

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