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Zinc in PDB 5ewa: Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor L-VC26

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor L-VC26

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Imp-1 in Complex with the Bisthiazolidine Inhibitor L-VC26:
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 L-VC26, PDB code: 5ewa was solved by M.Kosmopoulou, P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.054, 78.448, 260.608, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.2

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 L-VC26 (pdb code 5ewa). 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 L-VC26, PDB code: 5ewa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:25.7
occ:1.00
 ND1 A:HIS79 2.0 25.7 1.0
NE2 A:HIS139 2.0 29.6 1.0
NE2 A:HIS77 2.2 22.1 1.0
S01 A:9BZ303 2.4 21.9 1.0
CD2 A:HIS77 2.9 21.7 1.0
CE1 A:HIS79 2.9 26.3 1.0
CD2 A:HIS139 3.0 31.1 1.0
CG A:HIS79 3.0 28.1 1.0
CE1 A:HIS139 3.1 30.9 1.0
CE1 A:HIS77 3.3 22.6 1.0
CB A:HIS79 3.4 25.6 1.0
ZN A:ZN302 3.7 26.2 1.0
C02 A:9BZ303 3.8 65.9 1.0
CB A:CYS158 4.0 28.1 1.0
SG A:CYS158 4.0 31.6 1.0
NE2 A:HIS79 4.0 28.4 1.0
CD2 A:HIS79 4.1 25.0 1.0
CG A:HIS139 4.1 32.4 1.0
ND1 A:HIS139 4.1 31.0 1.0
CG A:HIS77 4.2 23.7 1.0
OD2 A:ASP81 4.2 24.6 1.0
ND1 A:HIS77 4.3 23.2 1.0
OD1 A:ASP81 4.4 30.7 1.0
CG2 A:THR140 4.5 30.2 1.0
CG A:ASP81 4.7 28.2 1.0
CA A:HIS79 4.8 23.3 1.0

Zinc binding site 2 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:26.2
occ:1.00
 OD1 A:ASP81 1.9 30.7 1.0
NE2 A:HIS197 2.1 28.0 1.0
S01 A:9BZ303 2.3 21.9 1.0
SG A:CYS158 2.3 31.6 1.0
C02 A:9BZ303 2.9 65.9 1.0
CG A:ASP81 2.9 28.2 1.0
CE1 A:HIS197 2.9 25.1 1.0
CD2 A:HIS197 3.2 25.0 1.0
OD2 A:ASP81 3.4 24.6 1.0
CB A:CYS158 3.5 28.1 1.0
C03 A:9BZ303 3.5 59.1 1.0
ZN A:ZN301 3.7 25.7 1.0
ND1 A:HIS197 4.1 29.9 1.0
CB A:ASP81 4.2 29.1 1.0
NE2 A:HIS77 4.2 22.1 1.0
CE1 A:HIS77 4.2 22.6 1.0
CG A:HIS197 4.2 32.7 1.0
S04 A:9BZ303 4.3 55.4 1.0
CB A:SER196 4.4 25.9 1.0
CE A:LYS33 4.4 20.1 1.0
CD A:LYS33 4.5 19.5 1.0
CA A:CYS158 4.6 31.2 1.0
NE2 A:HIS139 4.7 29.6 1.0
OG A:SER196 4.7 25.3 1.0
N07 A:9BZ303 4.8 56.5 1.0
O10 A:9BZ303 4.9 53.3 1.0

Zinc binding site 3 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:29.4
occ:1.00
 ND1 B:HIS79 1.9 29.0 1.0
NE2 B:HIS139 2.0 32.5 1.0
NE2 B:HIS77 2.2 30.2 1.0
S01 B:9BZ303 2.4 25.9 1.0
CE1 B:HIS79 2.8 33.1 1.0
CG B:HIS79 2.9 27.2 1.0
CD2 B:HIS77 3.0 26.8 1.0
CD2 B:HIS139 3.0 30.6 1.0
CE1 B:HIS139 3.0 32.5 1.0
CE1 B:HIS77 3.3 32.9 1.0
CB B:HIS79 3.3 25.0 1.0
C02 B:9BZ303 3.5 94.5 1.0
ZN B:ZN302 3.6 29.1 1.0
NE2 B:HIS79 4.0 31.4 1.0
CD2 B:HIS79 4.0 28.2 1.0
SG B:CYS158 4.1 31.8 1.0
CB B:CYS158 4.1 31.7 1.0
ND1 B:HIS139 4.1 33.2 1.0
OD1 B:ASP81 4.2 26.2 1.0
CG B:HIS139 4.2 34.8 1.0
CG B:HIS77 4.2 31.2 1.0
ND1 B:HIS77 4.3 31.5 1.0
CG2 B:THR140 4.4 31.5 1.0
OD2 B:ASP81 4.6 30.7 1.0
CA B:HIS79 4.8 29.1 1.0
CG B:ASP81 4.8 27.5 1.0
C03 B:9BZ303 4.8 91.2 1.0

Zinc binding site 4 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:29.1
occ:1.00
 OD2 B:ASP81 1.8 30.7 1.0
S01 B:9BZ303 2.0 25.9 1.0
NE2 B:HIS197 2.1 34.0 1.0
SG B:CYS158 2.4 31.8 1.0
CG B:ASP81 2.9 27.5 1.0
CE1 B:HIS197 3.0 32.8 1.0
CD2 B:HIS197 3.2 35.5 1.0
OD1 B:ASP81 3.3 26.2 1.0
C02 B:9BZ303 3.4 94.5 1.0
CB B:CYS158 3.5 31.7 1.0
C03 B:9BZ303 3.6 91.2 1.0
ZN B:ZN301 3.6 29.4 1.0
ND1 B:HIS197 4.1 38.5 1.0
CB B:ASP81 4.2 25.0 1.0
CE1 B:HIS77 4.2 32.9 1.0
NE2 B:HIS77 4.2 30.2 1.0
CG B:HIS197 4.2 38.8 1.0
CB B:SER196 4.4 31.0 1.0
NE2 B:HIS139 4.5 32.5 1.0
CE B:LYS33 4.6 23.9 1.0
CD B:LYS33 4.6 23.4 1.0
N07 B:9BZ303 4.7 89.0 1.0
CA B:CYS158 4.7 34.1 1.0
S04 B:9BZ303 4.7 77.1 1.0
OG B:SER196 4.8 32.4 1.0
C08 B:9BZ303 4.8 83.2 1.0

Zinc binding site 5 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:21.3
occ:1.00
 ND1 C:HIS79 2.0 20.9 1.0
NE2 C:HIS139 2.0 19.8 1.0
NE2 C:HIS77 2.2 22.0 1.0
S01 C:9BZ304 2.3 28.3 1.0
CD2 C:HIS77 2.9 19.6 1.0
CE1 C:HIS79 3.0 21.4 1.0
CD2 C:HIS139 3.0 18.6 1.0
CG C:HIS79 3.0 19.2 1.0
CE1 C:HIS139 3.1 19.0 1.0
CE1 C:HIS77 3.3 23.1 1.0
CB C:HIS79 3.4 21.8 1.0
C02 C:9BZ304 3.6 78.2 1.0
ZN C:ZN302 3.7 20.2 1.0
CB C:CYS158 4.0 20.2 1.0
SG C:CYS158 4.1 23.2 1.0
NE2 C:HIS79 4.1 20.9 1.0
CD2 C:HIS79 4.1 20.4 1.0
ND1 C:HIS139 4.1 19.6 1.0
CG C:HIS139 4.2 22.4 1.0
CG C:HIS77 4.2 21.8 1.0
OD1 C:ASP81 4.2 23.3 1.0
ND1 C:HIS77 4.3 23.2 1.0
OD2 C:ASP81 4.4 25.8 1.0
O C:HOH473 4.4 46.7 1.0
CG2 C:THR140 4.5 17.6 1.0
O C:HOH407 4.6 43.7 1.0
CG C:ASP81 4.7 27.1 1.0
CA C:HIS79 4.8 21.8 1.0
C03 C:9BZ304 5.0 76.0 1.0

Zinc binding site 6 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:20.2
occ:1.00
 OD2 C:ASP81 1.9 25.8 1.0
NE2 C:HIS197 2.2 23.1 1.0
SG C:CYS158 2.3 23.2 1.0
S01 C:9BZ304 2.4 28.3 1.0
CG C:ASP81 2.9 27.1 1.0
CE1 C:HIS197 3.2 27.0 1.0
CD2 C:HIS197 3.2 25.8 1.0
C02 C:9BZ304 3.4 78.2 1.0
OD1 C:ASP81 3.4 23.3 1.0
CB C:CYS158 3.4 20.2 1.0
C03 C:9BZ304 3.6 76.0 1.0
ZN C:ZN301 3.7 21.3 1.0
O C:HOH407 4.1 43.7 1.0
NE2 C:HIS77 4.1 22.0 1.0
CE1 C:HIS77 4.1 23.1 1.0
CB C:ASP81 4.2 26.1 1.0
ND1 C:HIS197 4.3 28.6 1.0
CG C:HIS197 4.3 28.2 1.0
S04 C:9BZ304 4.3 56.5 1.0
CE C:LYS33 4.3 25.6 1.0
CB C:SER196 4.3 24.0 1.0
CD C:LYS33 4.4 25.4 1.0
CA C:CYS158 4.5 23.6 1.0
NE2 C:HIS139 4.6 19.8 1.0
OG C:SER196 4.6 27.5 1.0
O11 C:9BZ304 4.9 58.4 1.0
N07 C:9BZ304 4.9 72.8 1.0

Zinc binding site 7 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:28.6
occ:1.00
 ND1 D:HIS79 2.0 26.4 1.0
NE2 D:HIS139 2.1 24.8 1.0
NE2 D:HIS77 2.2 40.2 1.0
CE1 D:HIS79 2.8 34.2 1.0
CD2 D:HIS77 2.9 23.5 1.0
CD2 D:HIS139 3.0 28.8 1.0
CG D:HIS79 3.0 31.6 1.0
CE1 D:HIS139 3.1 25.8 1.0
CE1 D:HIS77 3.3 39.8 1.0
CB D:HIS79 3.5 29.4 1.0
ZN D:ZN302 3.5 34.1 1.0
CB D:CYS158 3.9 24.9 1.0
NE2 D:HIS79 4.0 27.0 1.0
SG D:CYS158 4.0 30.2 1.0
CD2 D:HIS79 4.1 30.0 1.0
OD1 D:ASP81 4.1 31.8 1.0
CG D:HIS77 4.2 29.0 1.0
CG D:HIS139 4.2 27.9 1.0
ND1 D:HIS139 4.2 26.9 1.0
ND1 D:HIS77 4.3 34.1 1.0
CG2 D:THR140 4.5 25.9 1.0
OD2 D:ASP81 4.5 32.1 1.0
CG D:ASP81 4.7 34.9 1.0
CA D:HIS79 4.9 28.9 1.0

Zinc binding site 8 out of 8 in 5ewa

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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 L-VC26


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 L-VC26 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:34.1
occ:1.00
 OD2 D:ASP81 2.0 32.1 1.0
NE2 D:HIS197 2.3 39.8 1.0
SG D:CYS158 2.3 30.2 1.0
CG D:ASP81 3.0 34.9 1.0
CE1 D:HIS197 3.1 41.1 1.0
CD2 D:HIS197 3.3 37.7 1.0
CB D:CYS158 3.4 24.9 1.0
OD1 D:ASP81 3.5 31.8 1.0
ZN D:ZN301 3.5 28.6 1.0
NE2 D:HIS77 4.1 40.2 1.0
CE1 D:HIS77 4.2 39.8 1.0
ND1 D:HIS197 4.3 40.1 1.0
CB D:ASP81 4.3 33.9 1.0
CE D:LYS33 4.4 32.9 1.0
CG D:HIS197 4.4 45.4 1.0
CB D:SER196 4.4 31.8 1.0
CD D:LYS33 4.5 29.4 1.0
NE2 D:HIS139 4.6 24.8 1.0
CA D:CYS158 4.6 26.1 1.0
OG D:SER196 4.7 33.9 1.0

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 15:35:19 2024

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