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Zinc in PDB 5ev8: Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319, PDB code: 5ev8 was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.24 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.560, 77.713, 261.638, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22

Other elements in 5ev8:

The structure of Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 (pdb code 5ev8). 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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319, PDB code: 5ev8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ev8

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Zinc binding site 1 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.7
occ:1.00
 NE2 A:HIS139 2.1 31.9 1.0
ND1 A:HIS79 2.1 21.7 1.0
NE2 A:HIS77 2.2 29.9 1.0
SAC A:3R9303 2.2 29.7 0.9
CD2 A:HIS77 3.0 20.8 1.0
CE1 A:HIS139 3.0 31.5 1.0
CD2 A:HIS139 3.1 29.8 1.0
CE1 A:HIS79 3.1 24.8 1.0
CG A:HIS79 3.1 27.1 1.0
CE1 A:HIS77 3.3 24.1 1.0
CB A:HIS79 3.4 25.9 1.0
CAD A:3R9303 3.4 42.2 0.9
ZN A:ZN302 3.5 46.5 1.0
SG A:CYS158 3.7 35.5 1.0
CB A:CYS158 3.9 29.0 1.0
OD1 A:ASP81 4.0 28.4 0.2
CAJ A:3R9303 4.1 50.7 0.9
ND1 A:HIS139 4.1 32.1 1.0
OXT A:3R9303 4.1 38.1 0.9
NE2 A:HIS79 4.2 25.0 1.0
CG A:HIS139 4.2 35.2 1.0
CD2 A:HIS79 4.2 28.7 1.0
CG A:HIS77 4.2 23.2 1.0
ND1 A:HIS77 4.3 26.1 1.0
OD2 A:ASP81 4.5 32.7 0.2
CG A:ASP81 4.6 31.6 0.2
CG2 A:THR140 4.6 30.0 1.0
C A:3R9303 4.8 37.5 0.9
CA A:HIS79 4.8 28.6 1.0
N A:3R9303 4.8 43.0 0.9

Zinc binding site 2 out of 8 in 5ev8

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Zinc binding site 2 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:46.5
occ:1.00
 NE2 A:HIS197 2.0 34.6 1.0
OXT A:3R9303 2.0 38.1 0.9
SAC A:3R9303 2.1 29.7 0.9
SG A:CYS158 2.5 35.5 1.0
CD2 A:HIS197 2.9 34.4 1.0
OD2 A:ASP81 3.0 32.7 0.2
CE1 A:HIS197 3.0 31.2 1.0
N A:3R9303 3.1 43.0 0.9
C A:3R9303 3.2 37.5 0.9
CAD A:3R9303 3.3 42.2 0.9
CB A:CYS158 3.4 29.0 1.0
ZN A:ZN301 3.5 28.7 1.0
CAJ A:3R9303 3.6 50.7 0.9
CA A:3R9303 3.7 42.5 0.9
CAM A:3R9303 3.8 42.9 0.9
CG A:ASP81 3.9 31.6 0.2
ND1 A:HIS197 4.1 34.4 1.0
CG A:HIS197 4.1 38.0 1.0
OD2 A:ASP81 4.2 40.4 0.8
O A:3R9303 4.3 34.9 0.9
NE2 A:HIS139 4.3 31.9 1.0
OD1 A:ASP81 4.4 28.4 0.2
CB A:3R9303 4.4 42.8 0.9
CE1 A:HIS139 4.4 31.5 1.0
SAH A:3R9303 4.4 50.1 0.9
CA A:CYS158 4.5 33.3 1.0
CB A:SER196 4.6 31.6 1.0
CG A:ASP81 4.6 39.5 0.8
NE2 A:HIS77 4.7 29.9 1.0
CB A:ASP81 4.8 32.4 0.8
CE1 A:HIS77 4.9 24.1 1.0
NZ A:LYS161 4.9 40.5 1.0
CE A:LYS161 5.0 39.4 1.0
CB A:ASP81 5.0 32.2 0.2

Zinc binding site 3 out of 8 in 5ev8

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Zinc binding site 3 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:48.1
occ:1.00
 O B:3R9303 2.1 44.9 0.9
SAC B:3R9303 2.1 37.8 0.9
NE2 B:HIS197 2.2 37.0 1.0
SG B:CYS158 2.5 36.2 1.0
N B:3R9303 2.8 46.2 0.9
OD2 B:ASP81 2.9 33.7 0.3
C B:3R9303 3.1 46.0 0.9
CD2 B:HIS197 3.1 33.7 1.0
CAD B:3R9303 3.2 39.0 0.9
CE1 B:HIS197 3.2 33.4 1.0
CAJ B:3R9303 3.3 47.0 0.9
CA B:3R9303 3.4 45.2 0.9
CB B:CYS158 3.5 30.7 1.0
ZN B:ZN302 3.6 30.3 1.0
CAM B:3R9303 3.6 43.9 0.9
OD2 B:ASP81 3.7 39.1 0.7
CG B:ASP81 3.8 31.9 0.3
CB B:3R9303 3.9 42.8 0.9
OD1 B:ASP81 4.1 28.9 0.3
NE2 B:HIS139 4.2 37.1 1.0
OXT B:3R9303 4.2 45.5 0.9
CE1 B:HIS139 4.2 36.3 1.0
CG B:HIS197 4.2 35.5 1.0
ND1 B:HIS197 4.3 34.2 1.0
CG B:ASP81 4.4 37.8 0.7
CB B:SER196 4.6 37.4 1.0
CB B:ASP81 4.6 32.5 0.7
SAH B:3R9303 4.6 59.8 0.9
CA B:CYS158 4.7 38.1 1.0
CAF B:3R9303 4.7 48.3 0.9
NE2 B:HIS77 4.8 30.8 1.0
NZ B:LYS161 4.8 37.3 1.0
OG B:SER196 4.9 38.9 1.0
CE1 B:HIS77 5.0 28.6 1.0
CB B:ASP81 5.0 32.8 0.3

Zinc binding site 4 out of 8 in 5ev8

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Zinc binding site 4 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:30.3
occ:1.00
 SAC B:3R9303 1.9 37.8 0.9
ND1 B:HIS79 2.0 27.3 1.0
NE2 B:HIS139 2.0 37.1 1.0
NE2 B:HIS77 2.2 30.8 1.0
CE1 B:HIS139 2.9 36.3 1.0
CE1 B:HIS79 2.9 33.0 1.0
CG B:HIS79 3.0 36.3 1.0
CD2 B:HIS139 3.0 36.9 1.0
CD2 B:HIS77 3.1 32.7 1.0
CAD B:3R9303 3.1 39.0 0.9
CE1 B:HIS77 3.3 28.6 1.0
CB B:HIS79 3.4 25.7 1.0
ZN B:ZN301 3.6 48.1 1.0
CAJ B:3R9303 3.7 47.0 0.9
O B:3R9303 3.7 44.9 0.9
SG B:CYS158 3.9 36.2 1.0
NE2 B:HIS79 4.0 32.1 1.0
CB B:CYS158 4.0 30.7 1.0
ND1 B:HIS139 4.1 44.6 1.0
CD2 B:HIS79 4.1 31.1 1.0
CG B:HIS139 4.1 42.7 1.0
OD1 B:ASP81 4.2 28.9 0.3
CG B:HIS77 4.3 31.6 1.0
ND1 B:HIS77 4.3 31.3 1.0
N B:3R9303 4.5 46.2 0.9
CG2 B:THR140 4.5 33.7 1.0
C B:3R9303 4.6 46.0 0.9
CA B:HIS79 4.8 28.8 1.0
CG B:ASP81 4.8 31.9 0.3
OD2 B:ASP81 4.8 33.7 0.3

Zinc binding site 5 out of 8 in 5ev8

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Zinc binding site 5 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:23.1
occ:1.00
 ND1 C:HIS79 2.0 24.1 1.0
NE2 C:HIS139 2.0 28.9 1.0
NE2 C:HIS77 2.1 27.4 1.0
SAC C:3R9303 2.3 24.9 1.0
CE1 C:HIS79 2.9 25.3 1.0
CD2 C:HIS77 3.0 23.0 1.0
CD2 C:HIS139 3.0 22.6 1.0
CG C:HIS79 3.0 25.4 1.0
CE1 C:HIS139 3.0 25.1 1.0
CE1 C:HIS77 3.1 24.4 1.0
CAD C:3R9303 3.3 34.5 1.0
CB C:HIS79 3.4 22.0 1.0
ZN C:ZN302 3.6 26.1 1.0
SG C:CYS158 3.7 22.5 1.0
CAJ C:3R9303 3.9 33.7 1.0
NE2 C:HIS79 4.0 23.9 1.0
CB C:CYS158 4.0 22.1 1.0
CD2 C:HIS79 4.1 28.1 1.0
ND1 C:HIS139 4.1 25.0 1.0
CG C:HIS139 4.1 25.8 1.0
CG C:HIS77 4.2 24.6 1.0
ND1 C:HIS77 4.2 25.7 1.0
O C:3R9303 4.2 26.4 1.0
O C:HOH485 4.3 34.1 1.0
N C:3R9303 4.7 27.3 1.0
CG2 C:THR140 4.7 24.9 1.0
CA C:HIS79 4.8 26.2 1.0
C C:3R9303 4.9 27.4 1.0

Zinc binding site 6 out of 8 in 5ev8

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Zinc binding site 6 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:26.1
occ:1.00
 NE2 C:HIS197 1.9 24.9 1.0
O C:3R9303 2.0 26.4 1.0
SAC C:3R9303 2.3 24.9 1.0
SG C:CYS158 2.5 22.5 1.0
N C:3R9303 2.8 27.3 1.0
CD2 C:HIS197 2.9 27.3 1.0
C C:3R9303 3.0 27.4 1.0
CE1 C:HIS197 3.0 27.2 1.0
CAJ C:3R9303 3.3 33.7 1.0
CA C:3R9303 3.4 30.0 1.0
CAD C:3R9303 3.4 34.5 1.0
CB C:CYS158 3.4 22.1 1.0
CAM C:3R9303 3.6 33.2 1.0
ZN C:ZN301 3.6 23.1 1.0
CB C:3R9303 4.0 37.9 1.0
CG C:HIS197 4.0 27.3 1.0
ND1 C:HIS197 4.1 28.4 1.0
OXT C:3R9303 4.1 26.1 1.0
NE2 C:HIS139 4.1 28.9 1.0
CE1 C:HIS139 4.2 25.1 1.0
SAH C:3R9303 4.3 34.3 1.0
OD2 C:ASP81 4.4 41.7 1.0
CB C:SER196 4.5 23.4 1.0
CA C:CYS158 4.6 27.0 1.0
NZ C:LYS161 4.6 23.0 1.0
CE C:LYS161 4.8 25.4 1.0
NE2 C:HIS77 4.9 27.4 1.0
OG C:SER196 5.0 28.2 1.0

Zinc binding site 7 out of 8 in 5ev8

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Zinc binding site 7 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:42.7
occ:1.00
 ND1 D:HIS79 2.0 37.0 1.0
NE2 D:HIS139 2.0 41.7 1.0
NE2 D:HIS77 2.3 43.2 1.0
SAC D:3R9303 2.6 45.6 0.9
CE1 D:HIS79 2.8 42.8 1.0
CD2 D:HIS77 2.9 32.8 1.0
CD2 D:HIS139 3.0 47.4 1.0
CE1 D:HIS139 3.0 50.9 1.0
CG D:HIS79 3.1 39.7 1.0
ZN D:ZN302 3.4 49.2 1.0
CAD D:3R9303 3.4 51.2 0.9
CE1 D:HIS77 3.5 45.0 1.0
CB D:HIS79 3.5 39.2 1.0
SG D:CYS158 3.8 43.5 1.0
CB D:CYS158 4.0 42.2 1.0
NE2 D:HIS79 4.0 39.1 1.0
CAJ D:3R9303 4.0 57.6 0.9
OD1 D:ASP81 4.1 47.5 0.1
CD2 D:HIS79 4.1 37.8 1.0
ND1 D:HIS139 4.1 43.2 1.0
O D:3R9303 4.2 48.5 0.9
CG D:HIS139 4.2 45.3 1.0
CG D:HIS77 4.2 46.5 1.0
ND1 D:HIS77 4.4 40.8 1.0
OD2 D:ASP81 4.5 48.0 0.1
CG D:ASP81 4.6 48.7 0.1
CG2 D:THR140 4.7 47.5 1.0
N D:3R9303 4.7 54.0 0.9
C D:3R9303 4.8 54.7 0.9
CA D:HIS79 4.9 46.7 1.0

Zinc binding site 8 out of 8 in 5ev8

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Zinc binding site 8 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319


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 the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor D-CS319 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:49.2
occ:1.00
 SAC D:3R9303 2.1 45.6 0.9
NE2 D:HIS197 2.2 54.0 1.0
O D:3R9303 2.2 48.5 0.9
SG D:CYS158 2.5 43.5 1.0
N D:3R9303 2.9 54.0 0.9
CD2 D:HIS197 3.0 54.0 1.0
C D:3R9303 3.2 54.7 0.9
OD2 D:ASP81 3.2 48.0 0.1
CE1 D:HIS197 3.3 49.8 1.0
CAD D:3R9303 3.4 51.2 0.9
CAJ D:3R9303 3.4 57.6 0.9
CB D:CYS158 3.4 42.2 1.0
ZN D:ZN301 3.4 42.7 1.0
CA D:3R9303 3.6 59.6 0.9
CAM D:3R9303 3.6 59.7 0.9
OD2 D:ASP81 4.0 56.8 0.8
NE2 D:HIS139 4.1 41.7 1.0
CG D:ASP81 4.1 48.7 0.1
CB D:3R9303 4.1 57.2 0.9
CG D:HIS197 4.2 55.0 1.0
ND1 D:HIS197 4.3 49.7 1.0
CE1 D:HIS139 4.3 50.9 1.0
OXT D:3R9303 4.4 54.6 0.9
SAH D:3R9303 4.5 64.8 0.9
OD1 D:ASP81 4.5 47.5 0.1
NE2 D:HIS77 4.5 43.2 1.0
CA D:CYS158 4.6 43.4 1.0
CB D:SER196 4.7 40.9 1.0
CAF D:3R9303 4.9 61.8 0.9
CE1 D:HIS77 4.9 45.0 1.0
CB D:ASP81 4.9 51.2 0.8
CD2 D:HIS139 4.9 47.4 1.0
CG D:ASP81 5.0 56.0 0.8

Reference:

P.Hinchliffe, M.M.Gonzalez, M.F.Mojica, J.M.Gonzalez, V.Castillo, C.Saiz, M.Kosmopoulou, C.L.Tooke, L.I.Llarrull, G.Mahler, R.A.Bonomo, A.J.Vila, J.Spencer. Cross-Class Metallo-Beta-Lactamase Inhibition By Bisthiazolidines Reveals Multiple Binding Modes. Proc.Natl.Acad.Sci.Usa V. 113 E3745 2016.
ISSN: ESSN 1091-6490
PubMed: 27303030
DOI: 10.1073/PNAS.1601368113
Page generated: Sun Oct 27 15:30:50 2024

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