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Zinc in PDB 8jao: Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid

Enzymatic activity of Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid

All present enzymatic activity of Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid, PDB code: 8jao was solved by Y.-H.Yan, G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.67 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.758, 52.231, 200.973, 90, 90, 90
R / Rfree (%) 17.9 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid (pdb code 8jao). 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 B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid, PDB code: 8jao:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8jao

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Zinc binding site 1 out of 4 in the Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-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 B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:21.0
occ:1.00
 O A:HOH454 1.7 18.2 1.0
NE2 A:HIS139 1.9 19.8 1.0
ND1 A:HIS79 2.0 18.4 1.0
NE2 A:HIS77 2.1 27.7 1.0
CD2 A:HIS139 2.9 25.2 1.0
CE1 A:HIS139 2.9 25.8 1.0
CE1 A:HIS79 3.0 27.3 1.0
CG A:HIS79 3.0 23.7 1.0
CD2 A:HIS77 3.0 27.2 1.0
CE1 A:HIS77 3.1 26.0 1.0
CB A:HIS79 3.4 20.2 1.0
ZN A:ZN302 3.5 24.1 1.0
SG A:CYS158 3.6 20.6 1.0
O A:HOH469 3.7 31.4 1.0
CB A:CYS158 3.8 20.6 1.0
O03 A:5ZX303 3.9 26.2 1.0
OD1 A:ASP81 3.9 31.2 1.0
ND1 A:HIS139 4.0 23.3 1.0
CG A:HIS139 4.1 23.9 1.0
NE2 A:HIS79 4.1 30.1 1.0
CD2 A:HIS79 4.1 29.4 1.0
ND1 A:HIS77 4.2 25.9 1.0
CG A:HIS77 4.2 24.1 1.0
OD2 A:ASP81 4.4 26.5 1.0
CG2 A:THR140 4.5 26.5 1.0
CG A:ASP81 4.6 26.1 1.0
C02 A:5ZX303 4.7 25.6 1.0
N17 A:5ZX303 4.7 23.6 1.0
CA A:HIS79 4.8 23.2 1.0

Zinc binding site 2 out of 4 in 8jao

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Zinc binding site 2 out of 4 in the Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-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 B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:24.1
occ:1.00
 NE2 A:HIS197 2.1 21.1 1.0
OD2 A:ASP81 2.1 26.5 1.0
O03 A:5ZX303 2.3 26.2 1.0
N17 A:5ZX303 2.3 23.6 1.0
O A:HOH454 2.3 18.2 1.0
SG A:CYS158 2.4 20.6 1.0
CE1 A:HIS197 3.0 23.6 1.0
C04 A:5ZX303 3.0 24.4 1.0
C02 A:5ZX303 3.0 25.6 1.0
CD2 A:HIS197 3.1 17.4 1.0
CG A:ASP81 3.2 26.1 1.0
C15 A:5ZX303 3.3 23.3 1.0
ZN A:ZN301 3.5 21.0 1.0
CB A:CYS158 3.6 20.6 1.0
OD1 A:ASP81 3.6 31.2 1.0
N16 A:5ZX303 3.7 21.9 1.0
ND1 A:HIS197 4.1 18.2 1.0
NE2 A:HIS139 4.2 19.8 1.0
CG A:HIS197 4.2 14.9 1.0
O01 A:5ZX303 4.2 30.3 1.0
O A:HOH469 4.3 31.4 1.0
C05 A:5ZX303 4.3 23.8 1.0
CB A:ASP81 4.5 23.1 1.0
CE1 A:HIS139 4.6 25.8 1.0
S14 A:5ZX303 4.7 26.2 1.0
NE2 A:HIS77 4.7 27.7 1.0
CA A:CYS158 4.7 21.9 1.0
CB A:SER196 4.7 17.8 1.0
CE1 A:HIS77 4.7 26.0 1.0
NZ A:LYS161 5.0 19.9 1.0

Zinc binding site 3 out of 4 in 8jao

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Zinc binding site 3 out of 4 in the Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-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 B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:29.6
occ:1.00
 OD2 B:ASP81 2.1 26.4 1.0
O B:HOH447 2.1 26.4 1.0
NE2 B:HIS197 2.1 26.8 1.0
O01 B:5ZX303 2.3 20.7 1.0
N17 B:5ZX303 2.3 23.5 1.0
SG B:CYS158 2.5 21.8 1.0
C02 B:5ZX303 3.0 26.3 1.0
C04 B:5ZX303 3.1 27.5 1.0
CE1 B:HIS197 3.1 21.0 1.0
CD2 B:HIS197 3.1 26.6 1.0
CG B:ASP81 3.2 26.2 1.0
C15 B:5ZX303 3.3 33.4 1.0
ZN B:ZN302 3.5 24.9 1.0
CB B:CYS158 3.6 24.2 1.0
OD1 B:ASP81 3.6 30.3 1.0
N16 B:5ZX303 3.6 28.9 1.0
O03 B:5ZX303 4.2 26.5 1.0
ND1 B:HIS197 4.2 22.5 1.0
NE2 B:HIS139 4.2 23.3 1.0
CG B:HIS197 4.3 23.9 1.0
C05 B:5ZX303 4.4 32.2 1.0
CB B:ASP81 4.4 25.2 1.0
NE2 B:HIS77 4.5 25.8 1.0
CE1 B:HIS139 4.6 32.1 1.0
CA B:CYS158 4.7 22.4 1.0
CB B:SER196 4.7 22.6 1.0
S14 B:5ZX303 4.7 33.4 1.0
CE1 B:HIS77 4.7 25.3 1.0
O B:HOH463 4.7 31.6 1.0
NZ B:LYS161 4.9 25.6 1.0
CD B:LYS33 4.9 18.5 1.0
OG B:SER196 5.0 24.0 1.0

Zinc binding site 4 out of 4 in 8jao

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Zinc binding site 4 out of 4 in the Crystal Structure of B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-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 B1 Imp-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:24.9
occ:1.00
 O B:HOH447 1.9 26.4 1.0
NE2 B:HIS139 2.0 23.3 1.0
NE2 B:HIS77 2.0 25.8 1.0
ND1 B:HIS79 2.0 22.9 1.0
CD2 B:HIS77 2.9 22.1 1.0
CD2 B:HIS139 2.9 21.8 1.0
CG B:HIS79 3.0 26.8 1.0
CE1 B:HIS79 3.0 25.8 1.0
CE1 B:HIS139 3.1 32.1 1.0
CE1 B:HIS77 3.1 25.3 1.0
CB B:HIS79 3.3 23.0 1.0
ZN B:ZN301 3.5 29.6 1.0
SG B:CYS158 3.6 21.8 1.0
CB B:CYS158 3.6 24.2 1.0
OD1 B:ASP81 3.8 30.3 1.0
O01 B:5ZX303 3.9 20.7 1.0
CG B:HIS77 4.1 23.2 1.0
CG B:HIS139 4.1 22.4 1.0
CD2 B:HIS79 4.1 22.8 1.0
NE2 B:HIS79 4.1 29.0 1.0
ND1 B:HIS139 4.1 22.4 1.0
ND1 B:HIS77 4.1 27.1 1.0
OD2 B:ASP81 4.3 26.4 1.0
CG2 B:THR140 4.4 28.3 1.0
CG B:ASP81 4.5 26.2 1.0
CA B:HIS79 4.7 26.7 1.0
C02 B:5ZX303 4.7 26.3 1.0
N17 B:5ZX303 4.8 23.5 1.0
O B:HOH463 5.0 31.6 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 13:21:28 2023

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