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Zinc in PDB 8hyb: 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: 8hyb 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) 19.34 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.899, 201.103, 52.319, 90, 89.97, 90
R / Rfree (%) 17.7 / 22.7

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 8hyb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 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: 8hyb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8hyb

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Zinc binding site 1 out of 8 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:40.0
occ:1.00
 O A:HOH426 1.9 37.4 1.0
ND1 A:HIS79 2.0 38.0 1.0
NE2 A:HIS139 2.0 40.3 1.0
NE2 A:HIS77 2.1 42.6 1.0
CE1 A:HIS79 2.9 43.9 1.0
CD2 A:HIS139 3.0 40.4 1.0
CG A:HIS79 3.0 39.9 1.0
CE1 A:HIS139 3.0 40.6 1.0
CD2 A:HIS77 3.0 41.5 1.0
CE1 A:HIS77 3.1 45.2 1.0
CB A:HIS79 3.3 38.6 1.0
ZN A:ZN302 3.5 42.0 1.0
CH3 A:ACT306 3.6 36.6 1.0
SG A:CYS158 3.7 38.1 1.0
OD1 A:ASP81 3.8 43.1 1.0
O03 A:5ZX303 3.9 41.4 1.0
CB A:CYS158 3.9 30.7 1.0
NE2 A:HIS79 4.0 46.4 1.0
CD2 A:HIS79 4.1 42.8 1.0
ND1 A:HIS139 4.1 42.7 1.0
CG A:HIS139 4.1 42.4 1.0
CG A:HIS77 4.2 39.0 1.0
ND1 A:HIS77 4.2 44.5 1.0
OD2 A:ASP81 4.4 41.9 1.0
CG A:ASP81 4.6 39.0 1.0
C A:ACT306 4.6 59.9 1.0
CG2 A:THR140 4.6 41.6 1.0
C02 A:5ZX303 4.6 42.9 1.0
N17 A:5ZX303 4.7 42.0 1.0
CA A:HIS79 4.8 40.3 1.0
O A:ACT306 4.8 64.0 1.0

Zinc binding site 2 out of 8 in 8hyb

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Zinc binding site 2 out of 8 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:42.0
occ:1.00
 NE2 A:HIS197 2.1 36.0 1.0
OD2 A:ASP81 2.1 41.9 1.0
O03 A:5ZX303 2.2 41.4 1.0
O A:HOH426 2.3 37.4 1.0
N17 A:5ZX303 2.3 42.0 1.0
SG A:CYS158 2.5 38.1 1.0
CE1 A:HIS197 2.9 35.5 1.0
C02 A:5ZX303 2.9 42.9 1.0
C04 A:5ZX303 3.0 43.3 1.0
CD2 A:HIS197 3.2 33.4 1.0
CG A:ASP81 3.2 39.0 1.0
C15 A:5ZX303 3.4 42.9 1.0
CB A:CYS158 3.5 30.7 1.0
ZN A:ZN301 3.5 40.0 1.0
OD1 A:ASP81 3.6 43.1 1.0
N16 A:5ZX303 3.9 36.5 1.0
ND1 A:HIS197 4.1 34.6 1.0
O01 A:5ZX303 4.2 44.6 1.0
NE2 A:HIS139 4.2 40.3 1.0
CG A:HIS197 4.2 33.9 1.0
C05 A:5ZX303 4.3 45.7 1.0
CH3 A:ACT306 4.4 36.6 1.0
CE1 A:HIS139 4.5 40.6 1.0
CB A:ASP81 4.5 39.2 1.0
NE2 A:HIS77 4.6 42.6 1.0
S14 A:5ZX303 4.7 44.0 1.0
CA A:CYS158 4.7 39.0 1.0
CB A:SER196 4.7 34.2 1.0
CE1 A:HIS77 4.8 45.2 1.0
NZ A:LYS161 4.9 36.4 1.0

Zinc binding site 3 out of 8 in 8hyb

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Zinc binding site 3 out of 8 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:42.9
occ:1.00
 NE2 B:HIS77 2.0 43.3 1.0
O B:HOH427 2.0 47.1 1.0
NE2 B:HIS139 2.1 39.8 1.0
ND1 B:HIS79 2.1 41.7 1.0
CD2 B:HIS77 2.9 39.2 1.0
CD2 B:HIS139 2.9 37.1 1.0
CG B:HIS79 3.1 39.4 1.0
CE1 B:HIS77 3.1 40.5 1.0
CE1 B:HIS79 3.2 42.8 1.0
CE1 B:HIS139 3.2 37.9 1.0
CB B:HIS79 3.3 38.9 1.0
ZN B:ZN302 3.5 46.5 1.0
SG B:CYS158 3.7 35.8 1.0
CB B:CYS158 3.8 34.9 1.0
OD1 B:ASP81 3.9 45.8 1.0
O01 B:5ZX303 3.9 44.9 1.0
O B:HOH435 4.0 53.7 1.0
CG B:HIS77 4.1 43.2 1.0
ND1 B:HIS77 4.1 46.3 1.0
CG B:HIS139 4.1 36.0 1.0
CD2 B:HIS79 4.2 40.1 1.0
NE2 B:HIS79 4.3 47.3 1.0
ND1 B:HIS139 4.3 38.4 1.0
OD2 B:ASP81 4.4 44.4 1.0
CG2 B:THR140 4.4 47.0 1.0
CG B:ASP81 4.6 40.0 1.0
CA B:HIS79 4.7 45.6 1.0
C02 B:5ZX303 4.8 46.2 1.0
N17 B:5ZX303 4.8 42.8 1.0

Zinc binding site 4 out of 8 in 8hyb

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Zinc binding site 4 out of 8 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:46.5
occ:1.00
 OD2 B:ASP81 2.1 44.4 1.0
NE2 B:HIS197 2.1 44.4 1.0
O B:HOH427 2.2 47.1 1.0
O01 B:5ZX303 2.4 44.9 1.0
N17 B:5ZX303 2.4 42.8 1.0
SG B:CYS158 2.5 35.8 1.0
CE1 B:HIS197 3.1 35.4 1.0
C04 B:5ZX303 3.1 43.3 1.0
C02 B:5ZX303 3.1 46.2 1.0
CD2 B:HIS197 3.2 40.8 1.0
CG B:ASP81 3.2 40.0 1.0
C15 B:5ZX303 3.4 42.2 1.0
ZN B:ZN301 3.5 42.9 1.0
CB B:CYS158 3.6 34.9 1.0
OD1 B:ASP81 3.6 45.8 1.0
N16 B:5ZX303 3.8 40.0 1.0
OG B:SER196 4.0 52.4 1.0
ND1 B:HIS197 4.2 40.9 1.0
NE2 B:HIS139 4.2 39.8 1.0
CG B:HIS197 4.3 41.9 1.0
O03 B:5ZX303 4.3 45.2 1.0
O B:HOH435 4.4 53.7 1.0
C05 B:5ZX303 4.4 48.5 1.0
CB B:ASP81 4.5 44.6 1.0
NE2 B:HIS77 4.5 43.3 1.0
CE1 B:HIS77 4.7 40.5 1.0
CE1 B:HIS139 4.7 37.9 1.0
CA B:CYS158 4.7 39.5 1.0
S14 B:5ZX303 4.8 49.4 1.0
O B:HOH433 4.8 50.4 1.0
CD B:LYS33 4.9 34.6 1.0
NZ B:LYS161 4.9 48.2 1.0

Zinc binding site 5 out of 8 in 8hyb

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Zinc binding site 5 out of 8 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 5 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
C:Zn301

b:43.2
occ:1.00
 NE2 C:HIS77 2.0 38.8 1.0
O C:HOH427 2.1 42.9 1.0
NE2 C:HIS139 2.1 40.0 1.0
ND1 C:HIS79 2.1 37.2 1.0
CD2 C:HIS77 2.8 38.7 1.0
CD2 C:HIS139 2.9 36.5 1.0
CG C:HIS79 3.0 39.5 1.0
CE1 C:HIS77 3.1 39.4 1.0
CE1 C:HIS79 3.2 41.0 1.0
CE1 C:HIS139 3.2 37.6 1.0
CB C:HIS79 3.3 39.1 1.0
ZN C:ZN302 3.5 47.3 1.0
SG C:CYS158 3.7 39.0 1.0
OD1 C:ASP81 3.8 48.2 1.0
CB C:CYS158 3.8 36.4 1.0
O01 C:5ZX303 3.9 40.2 1.0
CG C:HIS77 4.1 39.7 1.0
ND1 C:HIS77 4.1 42.8 1.0
CG C:HIS139 4.2 36.7 1.0
CD2 C:HIS79 4.2 40.0 1.0
NE2 C:HIS79 4.2 44.0 1.0
ND1 C:HIS139 4.3 37.3 1.0
OD2 C:ASP81 4.3 41.7 1.0
CG2 C:THR140 4.4 45.9 1.0
CG C:ASP81 4.5 37.3 1.0
CA C:HIS79 4.7 43.5 1.0
O C:HOH432 4.7 54.4 1.0
C02 C:5ZX303 4.8 46.2 1.0
N17 C:5ZX303 4.8 40.6 1.0

Zinc binding site 6 out of 8 in 8hyb

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Zinc binding site 6 out of 8 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 6 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
C:Zn302

b:47.3
occ:1.00
 OD2 C:ASP81 2.1 41.7 1.0
NE2 C:HIS197 2.1 43.4 1.0
O01 C:5ZX303 2.2 40.2 1.0
O C:HOH427 2.3 42.9 1.0
N17 C:5ZX303 2.4 40.6 1.0
SG C:CYS158 2.5 39.0 1.0
C02 C:5ZX303 3.0 46.2 1.0
C04 C:5ZX303 3.1 40.5 1.0
CE1 C:HIS197 3.1 36.1 1.0
CD2 C:HIS197 3.2 42.8 1.0
CG C:ASP81 3.2 37.3 1.0
C15 C:5ZX303 3.4 41.3 1.0
ZN C:ZN301 3.5 43.2 1.0
CB C:CYS158 3.5 36.4 1.0
OD1 C:ASP81 3.6 48.2 1.0
N16 C:5ZX303 3.9 39.5 1.0
NE2 C:HIS139 4.2 40.0 1.0
ND1 C:HIS197 4.2 38.6 1.0
O03 C:5ZX303 4.2 44.3 1.0
CG C:HIS197 4.3 42.2 1.0
C05 C:5ZX303 4.4 45.6 1.0
NE2 C:HIS77 4.5 38.8 1.0
CB C:ASP81 4.5 43.9 1.0
CE1 C:HIS139 4.6 37.6 1.0
CB C:SER196 4.7 37.5 1.0
CE1 C:HIS77 4.7 39.4 1.0
CA C:CYS158 4.7 39.6 1.0
S14 C:5ZX303 4.8 50.9 1.0
O C:HOH429 4.8 47.7 1.0
NZ C:LYS161 4.8 44.9 1.0
OG C:SER196 4.9 42.2 1.0
CD C:LYS33 4.9 35.9 1.0

Zinc binding site 7 out of 8 in 8hyb

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Zinc binding site 7 out of 8 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 7 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
D:Zn301

b:38.5
occ:1.00
 O D:HOH427 1.8 34.8 1.0
NE2 D:HIS139 2.0 37.8 1.0
ND1 D:HIS79 2.0 34.8 1.0
NE2 D:HIS77 2.1 43.8 1.0
CE1 D:HIS139 2.9 41.0 1.0
CE1 D:HIS79 3.0 42.3 1.0
CD2 D:HIS139 3.0 41.1 1.0
CG D:HIS79 3.0 41.6 1.0
CD2 D:HIS77 3.0 41.5 1.0
CE1 D:HIS77 3.1 42.8 1.0
CB D:HIS79 3.3 36.9 1.0
ZN D:ZN302 3.5 42.4 1.0
O D:HOH430 3.7 39.6 1.0
SG D:CYS158 3.7 37.0 1.0
OD1 D:ASP81 3.8 44.2 1.0
O01 D:5ZX303 3.8 43.6 1.0
CB D:CYS158 3.9 29.6 1.0
NE2 D:HIS79 4.1 47.6 1.0
ND1 D:HIS139 4.1 41.1 1.0
CD2 D:HIS79 4.1 41.0 1.0
CG D:HIS139 4.1 39.5 1.0
CG D:HIS77 4.2 39.5 1.0
ND1 D:HIS77 4.2 42.7 1.0
OD2 D:ASP81 4.4 43.3 1.0
CG D:ASP81 4.5 39.4 1.0
C02 D:5ZX303 4.6 42.4 1.0
CG2 D:THR140 4.6 39.7 1.0
N17 D:5ZX303 4.7 43.7 1.0
CA D:HIS79 4.7 41.9 1.0

Zinc binding site 8 out of 8 in 8hyb

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Zinc binding site 8 out of 8 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 8 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
D:Zn302

b:42.4
occ:1.00
 NE2 D:HIS197 2.1 37.8 1.0
OD2 D:ASP81 2.1 43.3 1.0
O01 D:5ZX303 2.1 43.6 1.0
N17 D:5ZX303 2.3 43.7 1.0
O D:HOH427 2.3 34.8 1.0
SG D:CYS158 2.5 37.0 1.0
C02 D:5ZX303 2.9 42.4 1.0
C04 D:5ZX303 2.9 41.7 1.0
CE1 D:HIS197 3.0 36.7 1.0
CD2 D:HIS197 3.1 35.6 1.0
CG D:ASP81 3.2 39.4 1.0
C15 D:5ZX303 3.4 41.4 1.0
OD1 D:ASP81 3.5 44.2 1.0
CB D:CYS158 3.5 29.6 1.0
ZN D:ZN301 3.5 38.5 1.0
N16 D:5ZX303 4.0 31.9 1.0
ND1 D:HIS197 4.1 36.2 1.0
O03 D:5ZX303 4.1 42.5 1.0
NE2 D:HIS139 4.2 37.8 1.0
CG D:HIS197 4.2 33.1 1.0
C05 D:5ZX303 4.3 45.2 1.0
O D:HOH430 4.4 39.6 1.0
CE1 D:HIS139 4.5 41.0 1.0
CB D:ASP81 4.5 40.5 1.0
NE2 D:HIS77 4.6 43.8 1.0
S14 D:5ZX303 4.7 41.5 1.0
CE1 D:HIS77 4.7 42.8 1.0
CB D:SER196 4.7 34.8 1.0
CA D:CYS158 4.7 40.0 1.0
NZ D:LYS161 4.9 35.7 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.
Page generated: Thu Oct 31 07:33:05 2024

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