Zinc in PDB 6lvj: Imp-6 Metallo-Beta-Lactamase

Enzymatic activity of Imp-6 Metallo-Beta-Lactamase

All present enzymatic activity of Imp-6 Metallo-Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Imp-6 Metallo-Beta-Lactamase, PDB code: 6lvj was solved by K.Yamamoto, H.Tanaka, G.Kurisu, R.Nakano, H.Yano, H.Sakai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.40 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.146, 78.434, 260.431, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 29.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Imp-6 Metallo-Beta-Lactamase (pdb code 6lvj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Imp-6 Metallo-Beta-Lactamase, PDB code: 6lvj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6lvj

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Zinc binding site 1 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:36.5
occ:1.00
 ND1 A:HIS79 1.9 29.5 1.0
NE2 A:HIS139 1.9 52.9 1.0
NE2 A:HIS77 2.1 34.6 1.0
O A:HOH602 2.1 29.2 1.0
CE1 A:HIS79 2.8 34.3 1.0
CD2 A:HIS139 2.9 45.2 1.0
CD2 A:HIS77 3.0 29.8 1.0
CE1 A:HIS139 3.0 47.5 1.0
CG A:HIS79 3.0 31.8 1.0
CE1 A:HIS77 3.1 33.9 1.0
ZN A:ZN502 3.3 37.3 1.0
CB A:HIS79 3.5 34.9 1.0
CB A:CYS158 3.8 34.1 1.0
OD1 A:ASP81 3.8 37.0 1.0
NE2 A:HIS79 3.9 33.5 1.0
CG A:HIS139 4.0 44.5 1.0
OD2 A:ASP81 4.1 42.4 1.0
ND1 A:HIS139 4.1 42.5 1.0
SG A:CYS158 4.1 33.4 1.0
CD2 A:HIS79 4.1 34.2 1.0
CG A:HIS77 4.2 32.8 1.0
ND1 A:HIS77 4.2 36.6 1.0
CG A:ASP81 4.4 43.1 1.0
CG2 A:THR140 4.8 38.7 1.0
NE2 A:HIS197 4.9 49.5 1.0
CA A:HIS79 4.9 37.0 1.0

Zinc binding site 2 out of 8 in 6lvj

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Zinc binding site 2 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:37.3
occ:1.00
 O A:HOH602 1.9 29.2 1.0
OD2 A:ASP81 1.9 42.4 1.0
NE2 A:HIS197 2.0 49.5 1.0
SG A:CYS158 2.2 33.4 1.0
CG A:ASP81 2.9 43.1 1.0
CE1 A:HIS197 2.9 46.9 1.0
CD2 A:HIS197 3.0 42.6 1.0
CB A:CYS158 3.2 34.1 1.0
OD1 A:ASP81 3.3 37.0 1.0
ZN A:ZN501 3.3 36.5 1.0
CE1 A:HIS77 4.0 33.9 1.0
ND1 A:HIS197 4.0 49.5 1.0
CG A:HIS197 4.1 41.7 1.0
NE2 A:HIS77 4.1 34.6 1.0
CB A:ASP81 4.1 37.5 1.0
CD A:LYS33 4.3 30.2 1.0
NE2 A:HIS139 4.3 52.9 1.0
CE A:LYS33 4.4 28.4 1.0
CA A:CYS158 4.5 36.8 1.0
ND1 A:HIS79 4.9 29.5 1.0
CE1 A:HIS139 4.9 47.5 1.0

Zinc binding site 3 out of 8 in 6lvj

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Zinc binding site 3 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:33.1
occ:1.00
 ND1 B:HIS79 1.9 24.9 1.0
NE2 B:HIS139 2.1 36.3 1.0
O B:HOH401 2.1 34.8 1.0
NE2 B:HIS77 2.2 31.6 1.0
CE1 B:HIS79 2.8 33.7 1.0
CD2 B:HIS77 2.9 33.8 1.0
CD2 B:HIS139 3.0 35.0 1.0
CG B:HIS79 3.0 30.9 1.0
CE1 B:HIS139 3.1 36.2 1.0
CE1 B:HIS77 3.4 35.4 1.0
ZN B:ZN302 3.4 35.6 1.0
CB B:HIS79 3.5 30.1 1.0
O B:HOH437 3.8 42.4 1.0
CB B:CYS158 3.8 35.4 1.0
NE2 B:HIS79 4.0 34.0 1.0
OD1 B:ASP81 4.0 35.9 1.0
CD2 B:HIS79 4.1 35.3 1.0
CG B:HIS77 4.1 32.8 1.0
CG B:HIS139 4.1 36.1 1.0
SG B:CYS158 4.2 31.3 1.0
ND1 B:HIS139 4.2 32.3 1.0
OD2 B:ASP81 4.2 38.8 1.0
ND1 B:HIS77 4.3 33.2 1.0
CG2 B:THR140 4.5 36.7 1.0
CG B:ASP81 4.5 37.0 1.0
CA B:HIS79 4.9 31.1 1.0

Zinc binding site 4 out of 8 in 6lvj

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Zinc binding site 4 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:35.6
occ:1.00
 O B:HOH401 1.8 34.8 1.0
OD2 B:ASP81 1.9 38.8 1.0
NE2 B:HIS197 2.1 37.3 1.0
SG B:CYS158 2.3 31.3 1.0
CG B:ASP81 2.9 37.0 1.0
O B:HOH437 3.0 42.4 1.0
CD2 B:HIS197 3.0 33.8 1.0
CE1 B:HIS197 3.0 32.0 1.0
CB B:CYS158 3.2 35.4 1.0
OD1 B:ASP81 3.3 35.9 1.0
ZN B:ZN301 3.4 33.1 1.0
NE2 B:HIS77 3.9 31.6 1.0
CE1 B:HIS77 4.1 35.4 1.0
ND1 B:HIS197 4.1 34.8 1.0
CG B:HIS197 4.2 37.0 1.0
CB B:ASP81 4.2 31.0 1.0
CD B:LYS33 4.3 32.4 1.0
CE B:LYS33 4.4 31.1 1.0
NE2 B:HIS139 4.4 36.3 1.0
CA B:CYS158 4.5 35.2 1.0
ND1 B:HIS79 4.9 24.9 1.0

Zinc binding site 5 out of 8 in 6lvj

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Zinc binding site 5 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:41.4
occ:1.00
 ND1 C:HIS79 1.6 27.7 1.0
NE2 C:HIS139 1.9 36.8 1.0
CE1 C:HIS79 2.3 38.5 1.0
NE2 C:HIS77 2.3 46.0 1.0
CG C:HIS79 2.9 35.4 1.0
CD2 C:HIS139 2.9 39.6 1.0
CE1 C:HIS139 2.9 37.7 1.0
CD2 C:HIS77 3.0 44.4 1.0
ZN C:ZN302 3.3 45.2 1.0
CE1 C:HIS77 3.4 41.8 1.0
NE2 C:HIS79 3.5 36.0 1.0
CB C:HIS79 3.6 38.0 1.0
CD2 C:HIS79 3.8 32.6 1.0
CB C:CYS158 3.8 46.4 1.0
ND1 C:HIS139 4.0 40.8 1.0
OD1 C:ASP81 4.0 46.9 1.0
CG C:HIS139 4.0 38.0 1.0
SG C:CYS158 4.1 43.5 1.0
CG C:HIS77 4.2 44.6 1.0
OD2 C:ASP81 4.3 41.5 1.0
ND1 C:HIS77 4.4 43.1 1.0
CG C:ASP81 4.6 44.8 1.0
CG2 C:THR140 4.7 43.2 1.0

Zinc binding site 6 out of 8 in 6lvj

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Zinc binding site 6 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:45.2
occ:1.00
 OD2 C:ASP81 2.0 41.5 1.0
SG C:CYS158 2.3 43.5 1.0
NE2 C:HIS197 2.5 42.5 1.0
CG C:ASP81 2.9 44.8 1.0
CD2 C:HIS197 3.2 47.8 1.0
OD1 C:ASP81 3.3 46.9 1.0
CB C:CYS158 3.3 46.4 1.0
ZN C:ZN301 3.3 41.4 1.0
CE1 C:HIS197 3.5 38.9 1.0
NE2 C:HIS77 4.0 46.0 1.0
CE1 C:HIS77 4.1 41.8 1.0
CD C:LYS33 4.2 43.7 1.0
CB C:ASP81 4.3 43.9 1.0
CE C:LYS33 4.3 38.2 1.0
CG C:HIS197 4.3 47.6 1.0
NE2 C:HIS139 4.3 36.8 1.0
ND1 C:HIS197 4.4 42.1 1.0
ND1 C:HIS79 4.4 27.7 1.0
CA C:CYS158 4.6 44.0 1.0
NZ C:LYS161 4.9 49.0 1.0
CE1 C:HIS139 4.9 37.7 1.0

Zinc binding site 7 out of 8 in 6lvj

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Zinc binding site 7 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:30.4
occ:1.00
 ND1 D:HIS79 1.9 25.5 1.0
NE2 D:HIS139 2.0 23.7 1.0
O D:HOH401 2.1 34.7 1.0
NE2 D:HIS77 2.2 35.0 1.0
CE1 D:HIS79 2.8 30.1 1.0
CE1 D:HIS139 3.0 25.6 1.0
CG D:HIS79 3.0 29.1 1.0
CD2 D:HIS77 3.0 29.3 1.0
CD2 D:HIS139 3.0 28.7 1.0
CE1 D:HIS77 3.2 34.8 1.0
ZN D:ZN302 3.4 34.0 1.0
CB D:HIS79 3.4 30.5 1.0
CB D:CYS158 3.8 31.6 1.0
O D:HOH407 3.9 31.7 1.0
NE2 D:HIS79 4.0 29.8 1.0
OD1 D:ASP81 4.0 34.6 1.0
CD2 D:HIS79 4.1 30.5 1.0
SG D:CYS158 4.1 31.0 1.0
ND1 D:HIS139 4.1 24.8 1.0
CG D:HIS139 4.1 24.4 1.0
CG D:HIS77 4.2 31.9 1.0
OD2 D:ASP81 4.3 33.0 1.0
ND1 D:HIS77 4.3 31.9 1.0
CG D:ASP81 4.5 30.8 1.0
CG2 D:THR140 4.6 29.9 1.0
CA D:HIS79 4.8 27.6 1.0

Zinc binding site 8 out of 8 in 6lvj

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Zinc binding site 8 out of 8 in the Imp-6 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Imp-6 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:34.0
occ:1.00
 O D:HOH401 1.8 34.7 1.0
OD2 D:ASP81 1.9 33.0 1.0
NE2 D:HIS197 2.1 38.1 1.0
SG D:CYS158 2.2 31.0 1.0
CG D:ASP81 2.8 30.8 1.0
CD2 D:HIS197 3.0 37.8 1.0
OD1 D:ASP81 3.1 34.6 1.0
CE1 D:HIS197 3.2 37.1 1.0
CB D:CYS158 3.3 31.6 1.0
O D:HOH407 3.3 31.7 1.0
ZN D:ZN301 3.4 30.4 1.0
CD D:LYS33 4.1 34.0 1.0
NE2 D:HIS77 4.1 35.0 1.0
CE D:LYS33 4.1 35.9 1.0
CG D:HIS197 4.1 38.5 1.0
CE1 D:HIS77 4.1 34.8 1.0
CB D:ASP81 4.2 32.0 1.0
ND1 D:HIS197 4.2 34.3 1.0
NE2 D:HIS139 4.4 23.7 1.0
CA D:CYS158 4.5 32.2 1.0
ND1 D:HIS79 5.0 25.5 1.0
CE1 D:HIS139 5.0 25.6 1.0

Reference:

K.Yamamoto, H.Tanaka, G.Kurisu, R.Nakano, H.Yano, H.Sakai. Crystal Structure of Imp-6 Metallo-Beta-Lactamase From Escherichia Coli To Be Published.
Page generated: Wed Dec 16 12:17:13 2020

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