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Zinc in PDB 8hyc: Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid

Enzymatic activity of Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid

All present enzymatic activity of Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-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-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid, PDB code: 8hyc 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) 19.53 / 1.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.053, 78.384, 131.614, 90, 90, 90
R / Rfree (%) 24.9 / 27.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 8hyc

Go back to Zinc Binding Sites List in 8hyc
Zinc binding site 1 out of 4 in the Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)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 B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.9
occ:1.00
 O A:HOH471 1.8 27.4 1.0
NE2 A:HIS120 2.0 28.5 1.0
ND1 A:HIS122 2.0 26.8 1.0
NE2 A:HIS189 2.1 22.0 1.0
HB2 A:HIS122 2.9 30.6 1.0
CE1 A:HIS120 2.9 26.1 1.0
CG A:HIS122 2.9 27.0 1.0
CE1 A:HIS122 3.0 31.9 1.0
CD2 A:HIS120 3.0 25.2 1.0
CE1 A:HIS189 3.1 22.2 1.0
CD2 A:HIS189 3.1 29.3 1.0
HE1 A:HIS120 3.1 31.3 1.0
HE1 A:HIS122 3.2 38.3 1.0
HD2 A:HIS120 3.2 30.3 1.0
HD2 A:HIS189 3.2 35.2 1.0
HE1 A:HIS189 3.2 26.6 1.0
CB A:HIS122 3.3 25.5 1.0
HB3 A:HIS122 3.4 30.6 1.0
O A:HOH458 3.4 34.0 1.0
ZN A:ZN302 3.6 30.8 1.0
HB2 A:CYS208 3.8 29.5 1.0
HG21 A:THR190 3.9 32.8 1.0
HG23 A:THR190 3.9 32.8 1.0
SG A:CYS208 4.0 27.6 1.0
ND1 A:HIS120 4.0 26.0 1.0
O06 A:60J303 4.0 31.4 1.0
NE2 A:HIS122 4.0 29.6 1.0
CD2 A:HIS122 4.1 31.2 1.0
CG A:HIS120 4.1 25.1 1.0
OD1 A:ASP124 4.1 26.8 1.0
HB3 A:CYS208 4.1 29.5 1.0
ND1 A:HIS189 4.2 31.8 1.0
CB A:CYS208 4.2 24.6 1.0
CG A:HIS189 4.2 27.4 1.0
CG2 A:THR190 4.3 27.4 1.0
N03 A:60J303 4.4 33.2 1.0
OD2 A:ASP124 4.4 23.9 1.0
HG3 A:LYS125 4.6 30.0 1.0
HG22 A:THR190 4.6 32.8 1.0
CG A:ASP124 4.7 31.1 1.0
CA A:HIS122 4.7 27.6 1.0
H2 A:60J303 4.8 42.5 1.0
HD1 A:HIS120 4.8 31.2 1.0
HE2 A:HIS122 4.8 35.5 1.0
C05 A:60J303 4.8 29.7 1.0
HG2 A:LYS125 4.9 30.0 1.0
HD2 A:HIS122 4.9 37.4 1.0
O B:HOH525 4.9 36.2 1.0
HD1 A:HIS189 5.0 38.2 1.0

Zinc binding site 2 out of 4 in 8hyc

Go back to Zinc Binding Sites List in 8hyc
Zinc binding site 2 out of 4 in the Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)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 B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:30.8
occ:1.00
 O06 A:60J303 2.1 31.4 1.0
OD2 A:ASP124 2.1 23.9 1.0
NE2 A:HIS250 2.1 27.3 1.0
O A:HOH471 2.2 27.4 1.0
N03 A:60J303 2.3 33.2 1.0
SG A:CYS208 2.4 27.6 1.0
C05 A:60J303 2.8 29.7 1.0
C04 A:60J303 2.9 32.1 1.0
CE1 A:HIS250 3.1 31.9 1.0
CD2 A:HIS250 3.2 32.4 1.0
CG A:ASP124 3.2 31.1 1.0
HE1 A:HIS250 3.2 38.2 1.0
HB3 A:CYS208 3.3 29.5 1.0
HD2 A:HIS250 3.4 38.9 1.0
C02 A:60J303 3.4 27.7 1.0
CB A:CYS208 3.5 24.6 1.0
ZN A:ZN301 3.6 28.9 1.0
H2 A:60J303 3.7 42.5 1.0
OD1 A:ASP124 3.7 26.8 1.0
N01 A:60J303 3.9 35.4 1.0
HB2 A:CYS208 4.0 29.5 1.0
HE1 A:HIS120 4.0 31.3 1.0
O07 A:60J303 4.0 34.9 1.0
HB3 A:SER249 4.2 30.3 1.0
C08 A:60J303 4.2 34.5 1.0
NE2 A:HIS189 4.2 22.0 1.0
ND1 A:HIS250 4.2 31.5 1.0
HE1 A:HIS189 4.2 26.6 1.0
O A:HOH458 4.2 34.0 1.0
CG A:HIS250 4.3 33.4 1.0
HG A:SER249 4.3 32.9 1.0
HE3 A:LYS125 4.3 36.2 1.0
HB2 A:SER249 4.3 30.3 1.0
CE1 A:HIS189 4.4 22.2 1.0
CB A:ASP124 4.4 24.6 1.0
HB2 A:ASP124 4.5 29.5 1.0
NE2 A:HIS120 4.6 28.5 1.0
CE1 A:HIS120 4.6 26.1 1.0
HB3 A:ASP124 4.6 29.5 1.0
S16 A:60J303 4.6 32.4 1.0
CB A:SER249 4.7 25.2 1.0
HA A:CYS208 4.7 31.8 1.0
HG2 A:LYS125 4.7 30.0 1.0
CA A:CYS208 4.7 26.5 1.0
HD2 A:LYS125 4.7 30.5 1.0
H1 A:60J303 4.7 42.5 1.0
H6 A:60J303 4.9 48.6 1.0
HZ1 A:LYS211 4.9 39.8 1.0
OG A:SER249 4.9 27.4 1.0
HD1 A:HIS250 5.0 37.8 1.0
HB2 A:HIS122 5.0 30.6 1.0

Zinc binding site 3 out of 4 in 8hyc

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

b:26.9
occ:1.00
 O B:HOH474 1.7 26.9 1.0
NE2 B:HIS120 2.0 26.6 1.0
ND1 B:HIS122 2.0 23.3 1.0
NE2 B:HIS189 2.0 22.9 1.0
CE1 B:HIS120 2.9 27.1 1.0
CE1 B:HIS122 2.9 27.9 1.0
CD2 B:HIS189 3.0 29.0 1.0
CD2 B:HIS120 3.0 25.0 1.0
O B:HOH485 3.0 26.9 1.0
CG B:HIS122 3.0 25.7 1.0
HB2 B:HIS122 3.0 29.8 1.0
CE1 B:HIS189 3.0 30.6 1.0
HE1 B:HIS120 3.1 32.6 1.0
HE1 B:HIS122 3.1 33.5 1.0
HD2 B:HIS189 3.1 34.8 1.0
HD2 B:HIS120 3.2 30.0 1.0
HE1 B:HIS189 3.3 36.7 1.0
CB B:HIS122 3.4 24.8 1.0
HB3 B:HIS122 3.5 29.8 1.0
ZN B:ZN302 3.6 29.6 1.0
HB2 B:CYS208 3.6 38.0 1.0
HB3 B:CYS208 3.7 38.0 1.0
O06 B:60J303 3.8 27.3 1.0
SG B:CYS208 3.9 24.8 1.0
HG23 B:THR190 3.9 30.3 1.0
CB B:CYS208 3.9 31.6 1.0
ND1 B:HIS120 4.0 26.1 1.0
NE2 B:HIS122 4.0 25.1 1.0
OD1 B:ASP124 4.0 26.6 1.0
CD2 B:HIS122 4.1 30.9 1.0
CG B:HIS120 4.1 26.9 1.0
ND1 B:HIS189 4.1 28.7 1.0
CG B:HIS189 4.1 26.7 1.0
HG21 B:THR190 4.2 30.3 1.0
N03 B:60J303 4.5 31.7 1.0
CG2 B:THR190 4.5 25.3 1.0
OD2 B:ASP124 4.5 25.5 1.0
CG B:ASP124 4.7 30.7 1.0
HG3 B:LYS125 4.7 33.8 1.0
HD22 B:ASN220 4.7 49.1 1.0
HG2 B:LYS125 4.8 33.8 1.0
HD1 B:HIS120 4.8 31.3 1.0
HE2 B:HIS122 4.8 30.1 1.0
C05 B:60J303 4.8 30.0 1.0
HG22 B:THR190 4.8 30.3 1.0
CA B:HIS122 4.9 23.5 1.0
HD1 B:HIS189 4.9 34.4 1.0
HD2 B:HIS122 4.9 37.0 1.0

Zinc binding site 4 out of 4 in 8hyc

Go back to Zinc Binding Sites List in 8hyc
Zinc binding site 4 out of 4 in the Crystal Structure of B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)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 B1 Ndm-1 Mbl in Complex with 2-Amino-5-(2- (Thiophen-2-Yl)Ethyl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:29.6
occ:1.00
 NE2 B:HIS250 2.1 25.1 1.0
OD2 B:ASP124 2.1 25.5 1.0
O06 B:60J303 2.1 27.3 1.0
O B:HOH474 2.2 26.9 1.0
N03 B:60J303 2.3 31.7 1.0
SG B:CYS208 2.5 24.8 1.0
C05 B:60J303 2.9 30.0 1.0
C04 B:60J303 2.9 32.0 1.0
CE1 B:HIS250 3.0 25.0 1.0
CD2 B:HIS250 3.1 28.6 1.0
CG B:ASP124 3.2 30.7 1.0
HE1 B:HIS250 3.2 30.0 1.0
HD2 B:HIS250 3.3 34.4 1.0
C02 B:60J303 3.3 34.8 1.0
HB3 B:CYS208 3.4 38.0 1.0
CB B:CYS208 3.6 31.6 1.0
ZN B:ZN301 3.6 26.9 1.0
OD1 B:ASP124 3.6 26.6 1.0
H2 B:60J303 3.6 41.1 1.0
O B:HOH485 3.9 26.9 1.0
N01 B:60J303 3.9 34.3 1.0
O07 B:60J303 4.1 31.1 1.0
HB2 B:CYS208 4.1 38.0 1.0
HE1 B:HIS120 4.1 32.6 1.0
HB2 B:SER249 4.2 28.6 1.0
ND1 B:HIS250 4.2 28.6 1.0
C08 B:60J303 4.2 32.8 1.0
HB3 B:SER249 4.2 28.6 1.0
CG B:HIS250 4.3 27.2 1.0
NE2 B:HIS189 4.3 22.9 1.0
HG B:SER249 4.3 28.1 1.0
HE1 B:HIS189 4.3 36.7 1.0
CB B:ASP124 4.4 30.6 1.0
HA B:CYS208 4.5 29.2 1.0
CE1 B:HIS189 4.5 30.6 1.0
HD2 B:LYS125 4.5 38.8 1.0
S16 B:60J303 4.5 36.4 1.0
HB2 B:ASP124 4.5 36.7 1.0
HZ1 B:LYS211 4.6 34.1 1.0
CB B:SER249 4.6 23.8 1.0
HB3 B:ASP124 4.7 36.7 1.0
NE2 B:HIS120 4.7 26.6 1.0
CA B:CYS208 4.7 24.4 1.0
CE1 B:HIS120 4.7 27.1 1.0
HE3 B:LYS125 4.8 31.9 1.0
H1 B:60J303 4.8 41.1 1.0
HG2 B:LYS125 4.9 33.8 1.0
OG B:SER249 4.9 23.4 1.0
H6 B:60J303 4.9 43.4 1.0
HD1 B:HIS250 4.9 34.3 1.0

Reference:

Y.-H.Yan, K.-R.Zhu, L.-L.Yang, G.-B.Li. 2-Aminothiazole-4-Carboxylic Acids As Cross-Class Metallo-Beta-Lactamase Inhibitors By Mimicking Beta-Lactam Hydrolysate Binding To Be Published.
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