Zinc in PDB 5ev6: Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1

Enzymatic activity of Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1

All present enzymatic activity of Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1, PDB code: 5ev6 was solved by J.Spencer, P.Hinchliffe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.57 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.189, 78.000, 260.129, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 (pdb code 5ev6). 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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1, PDB code: 5ev6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ev6

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Zinc binding site 1 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.5
occ:1.00
 NE2 A:HIS139 2.1 23.0 1.0
ND1 A:HIS79 2.1 20.9 1.0
NE2 A:HIS77 2.1 20.6 1.0
O A:HOH478 2.4 26.6 1.0
CD2 A:HIS139 3.0 28.2 1.0
CD2 A:HIS77 3.0 21.8 1.0
CE1 A:HIS79 3.0 21.8 1.0
CG A:HIS79 3.1 21.3 1.0
CE1 A:HIS139 3.1 25.5 1.0
CE1 A:HIS77 3.2 23.6 1.0
O A:HOH508 3.3 50.5 1.0
CB A:HIS79 3.4 21.0 1.0
ZN A:ZN302 3.4 31.2 1.0
O A:HOH426 3.8 48.8 1.0
OD2 A:ASP81 3.8 29.7 1.0
SG A:CYS158 3.8 30.4 1.0
CB A:CYS158 3.9 27.7 1.0
NE2 A:HIS79 4.1 24.2 1.0
CG A:HIS139 4.2 25.6 1.0
ND1 A:HIS139 4.2 25.1 1.0
CD2 A:HIS79 4.2 22.3 1.0
CG A:HIS77 4.2 19.7 1.0
ND1 A:HIS77 4.3 24.6 1.0
OD1 A:ASP81 4.4 27.3 1.0
O A:HOH506 4.5 44.5 1.0
CG A:ASP81 4.6 29.1 1.0
CG2 A:THR140 4.7 25.5 1.0
O A:HOH491 4.8 34.4 1.0
CA A:HIS79 4.8 21.6 1.0

Zinc binding site 2 out of 8 in 5ev6

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Zinc binding site 2 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:31.2
occ:1.00
 O A:HOH478 1.9 26.6 1.0
OD1 A:ASP81 2.0 27.3 1.0
NE2 A:HIS197 2.1 27.8 1.0
O A:HOH426 2.3 48.8 1.0
SG A:CYS158 2.3 30.4 1.0
CG A:ASP81 3.0 29.1 1.0
CE1 A:HIS197 3.1 26.2 1.0
CD2 A:HIS197 3.1 26.9 1.0
O A:HOH506 3.1 44.5 1.0
OD2 A:ASP81 3.3 29.7 1.0
CB A:CYS158 3.3 27.7 1.0
ZN A:ZN301 3.4 24.5 1.0
O A:HOH491 4.0 34.4 1.0
ND1 A:HIS197 4.2 26.8 1.0
CG A:HIS197 4.2 29.6 1.0
NE2 A:HIS77 4.2 20.6 1.0
CE1 A:HIS77 4.3 23.6 1.0
NE2 A:HIS139 4.3 23.0 1.0
CB A:ASP81 4.3 26.0 1.0
O A:HOH508 4.4 50.5 1.0
CB A:SER196 4.4 28.3 1.0
CA A:CYS158 4.5 27.2 1.0
CD A:LYS33 4.6 22.0 1.0
CE A:LYS33 4.6 24.6 1.0
OG A:SER196 4.7 26.0 1.0
CE1 A:HIS139 4.8 25.5 1.0

Zinc binding site 3 out of 8 in 5ev6

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Zinc binding site 3 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:27.1
occ:1.00
 NE2 B:HIS139 2.0 28.8 1.0
ND1 B:HIS79 2.0 24.3 1.0
NE2 B:HIS77 2.1 25.4 1.0
O B:HOH476 2.2 25.7 1.0
CE1 B:HIS139 3.0 29.3 1.0
CG B:HIS79 3.0 24.8 1.0
CD2 B:HIS139 3.0 29.8 1.0
CD2 B:HIS77 3.0 22.4 1.0
CE1 B:HIS79 3.0 28.6 1.0
CE1 B:HIS77 3.2 20.6 1.0
CB B:HIS79 3.3 21.9 1.0
ZN B:ZN302 3.4 35.3 1.0
OD2 B:ASP81 3.8 26.9 1.0
SG B:CYS158 3.9 31.7 1.0
CB B:CYS158 4.0 30.7 1.0
NE2 B:HIS79 4.1 28.0 1.0
ND1 B:HIS139 4.1 27.8 1.0
CD2 B:HIS79 4.1 25.9 1.0
CG B:HIS139 4.2 28.4 1.0
CG B:HIS77 4.2 25.3 1.0
O B:HOH508 4.2 41.0 1.0
ND1 B:HIS77 4.2 24.7 1.0
OD1 B:ASP81 4.4 28.4 1.0
CG B:ASP81 4.5 29.0 1.0
CG2 B:THR140 4.7 29.3 1.0
CA B:HIS79 4.8 21.1 1.0

Zinc binding site 4 out of 8 in 5ev6

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Zinc binding site 4 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:35.3
occ:1.00
 O B:HOH476 1.9 25.7 1.0
NE2 B:HIS197 2.0 27.3 1.0
OD1 B:ASP81 2.0 28.4 1.0
SG B:CYS158 2.3 31.7 1.0
CE1 B:HIS197 2.9 25.7 1.0
CD2 B:HIS197 3.0 28.2 1.0
CG B:ASP81 3.0 29.0 1.0
CB B:CYS158 3.3 30.7 1.0
O B:HOH508 3.4 41.0 1.0
ZN B:ZN301 3.4 27.1 1.0
OD2 B:ASP81 3.4 26.9 1.0
ND1 B:HIS197 4.0 29.2 1.0
CG B:HIS197 4.1 30.1 1.0
NE2 B:HIS77 4.2 25.4 1.0
CE1 B:HIS77 4.2 20.6 1.0
NE2 B:HIS139 4.3 28.8 1.0
CB B:ASP81 4.4 25.2 1.0
CB B:SER196 4.4 26.7 1.0
CA B:CYS158 4.5 29.7 1.0
CD B:LYS33 4.6 24.8 1.0
CE B:LYS33 4.6 28.6 1.0
OG B:SER196 4.7 29.1 1.0
CE1 B:HIS139 4.7 29.3 1.0

Zinc binding site 5 out of 8 in 5ev6

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Zinc binding site 5 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:26.5
occ:1.00
 O C:HOH515 1.9 23.7 1.0
OD1 C:ASP81 2.0 20.7 1.0
NE2 C:HIS197 2.1 20.8 1.0
SG C:CYS158 2.3 26.6 1.0
CE1 C:HIS197 3.0 22.5 1.0
CG C:ASP81 3.1 27.0 1.0
CD2 C:HIS197 3.2 21.1 1.0
O C:HOH405 3.3 31.8 1.0
CB C:CYS158 3.3 25.9 1.0
ZN C:ZN302 3.3 21.5 1.0
OD2 C:ASP81 3.4 25.0 1.0
O C:HOH534 3.9 40.4 1.0
O C:HOH424 4.1 47.9 1.0
NE2 C:HIS77 4.1 20.7 1.0
CE1 C:HIS77 4.2 21.4 1.0
ND1 C:HIS197 4.2 22.1 1.0
CG C:HIS197 4.3 22.3 1.0
NE2 C:HIS139 4.3 21.0 1.0
CD C:LYS33 4.3 23.7 1.0
CE C:LYS33 4.3 22.0 1.0
CB C:ASP81 4.4 27.2 1.0
CB C:SER196 4.4 26.4 1.0
CA C:CYS158 4.5 27.6 1.0
OG C:SER196 4.7 28.0 1.0
CE1 C:HIS139 4.9 20.9 1.0

Zinc binding site 6 out of 8 in 5ev6

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Zinc binding site 6 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:21.5
occ:1.00
 ND1 C:HIS79 2.0 21.9 1.0
NE2 C:HIS139 2.0 21.0 1.0
NE2 C:HIS77 2.1 20.7 1.0
O C:HOH515 2.1 23.7 1.0
CD2 C:HIS77 3.0 20.8 1.0
CE1 C:HIS79 3.0 25.1 1.0
CD2 C:HIS139 3.0 22.9 1.0
CE1 C:HIS139 3.0 20.9 1.0
CG C:HIS79 3.0 20.9 1.0
CE1 C:HIS77 3.2 21.4 1.0
ZN C:ZN301 3.3 26.5 1.0
CB C:HIS79 3.4 19.9 1.0
O C:HOH534 3.6 40.4 1.0
CB C:CYS158 3.9 25.9 1.0
SG C:CYS158 3.9 26.6 1.0
OD2 C:ASP81 3.9 25.0 1.0
NE2 C:HIS79 4.1 21.1 1.0
ND1 C:HIS139 4.1 18.3 1.0
CD2 C:HIS79 4.1 20.0 1.0
O C:HOH405 4.1 31.8 1.0
CG C:HIS77 4.2 21.6 1.0
CG C:HIS139 4.2 17.4 1.0
ND1 C:HIS77 4.2 20.3 1.0
OD1 C:ASP81 4.4 20.7 1.0
CG C:ASP81 4.6 27.0 1.0
CG2 C:THR140 4.7 21.0 1.0
CA C:HIS79 4.8 19.7 1.0
O C:HOH494 4.9 39.3 1.0

Zinc binding site 7 out of 8 in 5ev6

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Zinc binding site 7 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:34.9
occ:1.00
 NE2 D:HIS139 2.0 35.9 1.0
ND1 D:HIS79 2.0 38.9 1.0
NE2 D:HIS77 2.2 43.4 1.0
O D:HOH429 2.3 30.5 1.0
CE1 D:HIS139 3.0 36.3 1.0
CE1 D:HIS79 3.0 42.8 1.0
CD2 D:HIS77 3.0 36.8 1.0
CD2 D:HIS139 3.0 37.9 1.0
CG D:HIS79 3.0 41.5 1.0
CE1 D:HIS77 3.3 41.0 1.0
ZN D:ZN302 3.4 42.3 1.0
CB D:HIS79 3.4 40.4 1.0
SG D:CYS158 3.8 42.2 1.0
CB D:CYS158 3.9 36.4 1.0
OD2 D:ASP81 3.9 42.8 1.0
ND1 D:HIS139 4.1 34.5 1.0
NE2 D:HIS79 4.1 38.7 1.0
CD2 D:HIS79 4.1 39.6 1.0
CG D:HIS139 4.1 32.9 1.0
CG D:HIS77 4.2 40.7 1.0
ND1 D:HIS77 4.3 41.3 1.0
OD1 D:ASP81 4.4 42.7 1.0
CG D:ASP81 4.6 45.1 1.0
O D:HOH445 4.6 40.0 1.0
CG2 D:THR140 4.7 44.7 1.0
CA D:HIS79 4.8 40.4 1.0

Zinc binding site 8 out of 8 in 5ev6

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Zinc binding site 8 out of 8 in the Crystal Structure of the Native, Di-Zinc Metallo-Beta-Lactamase Imp-1


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 Native, Di-Zinc Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:42.3
occ:1.00
 O D:HOH429 1.9 30.5 1.0
OD1 D:ASP81 2.0 42.7 1.0
NE2 D:HIS197 2.1 42.6 1.0
SG D:CYS158 2.4 42.2 1.0
CE1 D:HIS197 3.0 41.9 1.0
CG D:ASP81 3.0 45.1 1.0
CD2 D:HIS197 3.1 39.6 1.0
ZN D:ZN301 3.4 34.9 1.0
CB D:CYS158 3.4 36.4 1.0
OD2 D:ASP81 3.4 42.8 1.0
O D:HOH445 3.9 40.0 1.0
ND1 D:HIS197 4.1 45.8 1.0
CG D:HIS197 4.2 46.4 1.0
NE2 D:HIS77 4.2 43.4 1.0
CE1 D:HIS77 4.3 41.0 1.0
NE2 D:HIS139 4.3 35.9 1.0
CB D:ASP81 4.4 47.4 1.0
CB D:SER196 4.4 34.4 1.0
CD D:LYS33 4.5 43.2 1.0
CA D:CYS158 4.6 37.7 1.0
CE D:LYS33 4.6 41.1 1.0
CE1 D:HIS139 4.8 36.3 1.0
OG D:SER196 4.8 36.5 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: Wed Dec 16 06:10:32 2020

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