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Zinc in PDB 8hy6: Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid

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

All present enzymatic activity of Crystal Structure of B1 Ndm-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 Ndm-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid, PDB code: 8hy6 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) 30.80 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.313, 79.301, 133.698, 90, 90, 90
R / Rfree (%) 14.3 / 16.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid (pdb code 8hy6). 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 Ndm-1 Mbl in Complex with 2-Amino-5- Phenethylthiazole-4-Carboxylic Acid, PDB code: 8hy6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8hy6

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Zinc binding site 1 out of 4 in the Crystal Structure of B1 Ndm-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 Ndm-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:11.5
occ:1.00
 O A:HOH452 1.9 12.2 1.0
NE2 A:HIS189 2.0 9.7 1.0
ND1 A:HIS122 2.0 11.3 1.0
NE2 A:HIS120 2.1 8.6 1.0
CD2 A:HIS189 3.0 10.9 1.0
CE1 A:HIS122 3.0 12.7 1.0
CE1 A:HIS120 3.0 9.2 1.0
CD2 A:HIS120 3.0 8.5 1.0
CG A:HIS122 3.1 10.8 1.0
CE1 A:HIS189 3.1 9.8 1.0
O A:HOH435 3.3 19.9 1.0
CB A:HIS122 3.4 9.4 1.0
ZN A:ZN302 3.5 13.8 1.0
SG A:CYS208 3.9 10.5 1.0
OD1 A:ASP124 4.0 15.9 1.0
O03 A:5ZX303 4.0 11.7 1.0
CB A:CYS208 4.1 12.4 1.0
NE2 A:HIS122 4.1 14.8 1.0
CG A:HIS189 4.1 10.0 1.0
ND1 A:HIS120 4.1 9.5 1.0
ND1 A:HIS189 4.1 10.1 1.0
CD2 A:HIS122 4.2 14.7 1.0
CG A:HIS120 4.2 9.2 1.0
CG2 A:THR190 4.4 10.7 1.0
OD2 A:ASP124 4.5 12.5 1.0
N17 A:5ZX303 4.6 14.9 1.0
CG A:ASP124 4.7 13.4 1.0
CA A:HIS122 4.9 8.8 1.0
O B:HOH496 4.9 25.7 1.0
C02 A:5ZX303 5.0 14.1 1.0

Zinc binding site 2 out of 4 in 8hy6

Go back to Zinc Binding Sites List in 8hy6
Zinc binding site 2 out of 4 in the Crystal Structure of B1 Ndm-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 Ndm-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:13.8
occ:1.00
 O A:HOH452 2.0 12.2 1.0
OD2 A:ASP124 2.1 12.5 1.0
O03 A:5ZX303 2.1 11.7 1.0
NE2 A:HIS250 2.2 11.9 1.0
N17 A:5ZX303 2.3 14.9 1.0
SG A:CYS208 2.4 10.5 1.0
C02 A:5ZX303 3.0 14.1 1.0
C04 A:5ZX303 3.0 15.5 1.0
CE1 A:HIS250 3.1 11.4 1.0
CG A:ASP124 3.2 13.4 1.0
CD2 A:HIS250 3.2 13.2 1.0
C15 A:5ZX303 3.4 16.0 1.0
CB A:CYS208 3.4 12.4 1.0
OD1 A:ASP124 3.5 15.9 1.0
ZN A:ZN301 3.5 11.5 1.0
N16 A:5ZX303 3.8 16.9 1.0
O A:HOH435 4.1 19.9 1.0
NE2 A:HIS189 4.1 9.7 1.0
O01 A:5ZX303 4.2 14.8 1.0
ND1 A:HIS250 4.3 12.0 1.0
C05 A:5ZX303 4.3 16.8 1.0
CG A:HIS250 4.3 12.7 1.0
CE1 A:HIS189 4.4 9.8 1.0
CB A:ASP124 4.5 10.7 1.0
CB A:SER249 4.6 10.6 1.0
NE2 A:HIS120 4.7 8.6 1.0
S14 A:5ZX303 4.7 17.4 1.0
CA A:CYS208 4.7 11.8 1.0
CE1 A:HIS120 4.8 9.2 1.0
OG A:SER249 4.9 9.8 1.0

Zinc binding site 3 out of 4 in 8hy6

Go back to Zinc Binding Sites List in 8hy6
Zinc binding site 3 out of 4 in the Crystal Structure of B1 Ndm-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 Ndm-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:11.8
occ:1.00
 O B:HOH459 1.9 11.8 1.0
NE2 B:HIS189 2.0 11.2 1.0
ND1 B:HIS122 2.1 12.1 1.0
NE2 B:HIS120 2.1 10.0 1.0
CE1 B:HIS120 3.0 10.8 1.0
CD2 B:HIS189 3.0 9.7 1.0
CE1 B:HIS122 3.0 11.6 1.0
CE1 B:HIS189 3.1 11.1 1.0
CG B:HIS122 3.1 10.0 1.0
CD2 B:HIS120 3.1 9.6 1.0
O B:HOH534 3.2 18.2 1.0
CB B:HIS122 3.4 10.0 1.0
ZN B:ZN302 3.6 14.5 1.0
SG B:CYS208 3.9 11.8 1.0
OD1 B:ASP124 4.0 15.2 1.0
O01 B:5ZX303 4.1 13.1 1.0
NE2 B:HIS122 4.1 12.5 1.0
CB B:CYS208 4.1 15.8 1.0
ND1 B:HIS120 4.1 10.5 1.0
ND1 B:HIS189 4.1 11.6 1.0
CG B:HIS189 4.2 9.9 1.0
CD2 B:HIS122 4.2 11.3 1.0
CG B:HIS120 4.2 8.6 1.0
CG2 B:THR190 4.4 11.9 1.0
N17 B:5ZX303 4.5 16.1 1.0
OD2 B:ASP124 4.5 12.5 1.0
O A:HOH525 4.7 25.2 1.0
CG B:ASP124 4.7 11.8 1.0
CA B:HIS122 4.9 8.7 1.0
C02 B:5ZX303 5.0 17.0 1.0

Zinc binding site 4 out of 4 in 8hy6

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Zinc binding site 4 out of 4 in the Crystal Structure of B1 Ndm-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 Ndm-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:14.5
occ:1.00
 O B:HOH459 2.1 11.8 1.0
OD2 B:ASP124 2.1 12.5 1.0
O01 B:5ZX303 2.1 13.1 1.0
NE2 B:HIS250 2.2 13.4 1.0
N17 B:5ZX303 2.3 16.1 1.0
SG B:CYS208 2.4 11.8 1.0
C02 B:5ZX303 2.9 17.0 1.0
C04 B:5ZX303 3.0 17.9 1.0
CE1 B:HIS250 3.2 13.1 1.0
CG B:ASP124 3.2 11.8 1.0
CD2 B:HIS250 3.2 13.8 1.0
C15 B:5ZX303 3.3 14.5 1.0
CB B:CYS208 3.4 15.8 1.0
OD1 B:ASP124 3.5 15.2 1.0
ZN B:ZN301 3.6 11.8 1.0
N16 B:5ZX303 3.8 17.2 1.0
O B:HOH534 4.0 18.2 1.0
O03 B:5ZX303 4.1 16.7 1.0
NE2 B:HIS189 4.2 11.2 1.0
C05 B:5ZX303 4.3 21.1 1.0
ND1 B:HIS250 4.3 14.2 1.0
CG B:HIS250 4.3 13.9 1.0
CE1 B:HIS189 4.3 11.1 1.0
CB B:ASP124 4.5 10.9 1.0
CB B:SER249 4.6 12.5 1.0
S14 B:5ZX303 4.7 19.1 1.0
NE2 B:HIS120 4.7 10.0 1.0
CA B:CYS208 4.7 13.4 1.0
CE1 B:HIS120 4.8 10.8 1.0
OG B:SER249 4.9 11.6 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 Oct 31 07:32:24 2024

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