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Zinc in PDB 7xhx: Crystal Structure of Metallo-Beta-Lactamase Imp-6

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-6

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

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-6, PDB code: 7xhx 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) 48.30 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.156, 78.34, 260.225, 90, 90, 90
R / Rfree (%) 20.4 / 23.8

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:28.4
occ:1.00
 ND1 A:HIS79 1.9 26.1 1.0
O A:HOH706 2.0 28.7 1.0
NE2 A:HIS139 2.0 29.6 1.0
NE2 A:HIS77 2.1 27.1 1.0
CE1 A:HIS79 2.9 31.9 1.0
CD2 A:HIS77 2.9 26.4 1.0
CE1 A:HIS139 3.0 33.0 1.0
CG A:HIS79 3.0 25.2 1.0
CD2 A:HIS139 3.0 32.0 1.0
CE1 A:HIS77 3.2 27.5 1.0
CB A:HIS79 3.4 26.2 1.0
ZN A:ZN502 3.4 28.0 1.0
CB A:CYS158 3.8 29.1 1.0
OD1 A:ASP81 3.9 26.6 1.0
NE2 A:HIS79 4.0 31.2 1.0
CD2 A:HIS79 4.1 31.4 1.0
ND1 A:HIS139 4.1 30.1 1.0
CG A:HIS77 4.1 25.2 1.0
CG A:HIS139 4.2 27.2 1.0
SG A:CYS158 4.2 28.5 1.0
ND1 A:HIS77 4.2 24.9 1.0
OD2 A:ASP81 4.4 27.2 1.0
CG A:ASP81 4.5 27.6 1.0
CG2 A:THR140 4.6 27.1 1.0
CA A:HIS79 4.8 24.5 1.0

Zinc binding site 2 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:28.0
occ:1.00
 O A:HOH706 1.9 28.7 1.0
NE2 A:HIS197 2.0 28.0 1.0
OD2 A:ASP81 2.0 27.2 1.0
SG A:CYS158 2.3 28.5 1.0
CE1 A:HIS197 2.9 28.1 1.0
CG A:ASP81 2.9 27.6 1.0
CD2 A:HIS197 3.0 27.3 1.0
OD1 A:ASP81 3.2 26.6 1.0
CB A:CYS158 3.3 29.1 1.0
ZN A:ZN501 3.4 28.4 1.0
ND1 A:HIS197 4.0 30.1 1.0
CE1 A:HIS77 4.0 27.5 1.0
NE2 A:HIS77 4.0 27.1 1.0
CG A:HIS197 4.1 28.6 1.0
CD A:LYS33 4.2 24.6 1.0
CB A:ASP81 4.2 24.5 1.0
CE A:LYS33 4.3 24.4 1.0
NE2 A:HIS139 4.4 29.6 1.0
CA A:CYS158 4.5 28.2 1.0
CE1 A:HIS139 4.8 33.0 1.0
ND1 A:HIS79 4.9 26.1 1.0

Zinc binding site 3 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:27.6
occ:1.00
 O B:HOH491 1.9 28.3 1.0
ND1 B:HIS79 2.0 27.0 1.0
NE2 B:HIS77 2.0 32.1 1.0
NE2 B:HIS139 2.1 24.4 1.0
CE1 B:HIS79 2.9 29.4 1.0
CD2 B:HIS77 2.9 25.8 1.0
CD2 B:HIS139 3.0 27.7 1.0
CG B:HIS79 3.1 24.9 1.0
CE1 B:HIS139 3.1 31.1 1.0
CE1 B:HIS77 3.1 28.4 1.0
ZN B:ZN302 3.4 29.6 1.0
CB B:HIS79 3.4 24.8 1.0
CB B:CYS158 3.8 24.1 1.0
O B:HOH448 4.0 34.6 1.0
OD1 B:ASP81 4.0 26.9 1.0
NE2 B:HIS79 4.1 31.6 1.0
SG B:CYS158 4.1 28.1 1.0
CD2 B:HIS79 4.1 31.4 1.0
CG B:HIS77 4.1 23.9 1.0
CG B:HIS139 4.2 25.4 1.0
ND1 B:HIS139 4.2 27.3 1.0
ND1 B:HIS77 4.2 25.7 1.0
OD2 B:ASP81 4.4 26.5 1.0
CG B:ASP81 4.6 27.1 1.0
CG2 B:THR140 4.6 27.0 1.0
CA B:HIS79 4.9 23.0 1.0

Zinc binding site 4 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:29.6
occ:1.00
 OD2 B:ASP81 2.0 26.5 1.0
O B:HOH491 2.0 28.3 1.0
NE2 B:HIS197 2.1 29.5 1.0
SG B:CYS158 2.2 28.1 1.0
CG B:ASP81 2.9 27.1 1.0
CE1 B:HIS197 3.0 28.2 1.0
CD2 B:HIS197 3.1 31.0 1.0
OD1 B:ASP81 3.2 26.9 1.0
CB B:CYS158 3.3 24.1 1.0
ZN B:ZN301 3.4 27.6 1.0
O B:HOH448 3.5 34.6 1.0
CE1 B:HIS77 4.0 28.4 1.0
NE2 B:HIS77 4.1 32.1 1.0
ND1 B:HIS197 4.1 28.5 1.0
CG B:HIS197 4.1 31.4 1.0
CD B:LYS33 4.2 25.5 1.0
CB B:ASP81 4.2 23.5 1.0
CE B:LYS33 4.4 25.9 1.0
NE2 B:HIS139 4.5 24.4 1.0
CA B:CYS158 4.5 26.6 1.0
ND1 B:HIS79 5.0 27.0 1.0

Zinc binding site 5 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:42.3
occ:1.00
 ND1 C:HIS79 1.8 33.7 1.0
NE2 C:HIS139 1.9 46.8 1.0
NE2 C:HIS77 2.2 38.8 1.0
O C:HOH401 2.6 26.4 1.0
CE1 C:HIS79 2.7 42.6 1.0
CD2 C:HIS139 2.9 43.2 1.0
CE1 C:HIS139 3.0 42.2 1.0
CD2 C:HIS77 3.0 40.7 1.0
CG C:HIS79 3.0 37.5 1.0
CE1 C:HIS77 3.3 38.9 1.0
CB C:HIS79 3.5 37.1 1.0
ZN C:ZN302 3.5 41.1 1.0
NE2 C:HIS79 3.9 38.5 1.0
CB C:CYS158 3.9 38.0 1.0
OD1 C:ASP81 3.9 41.8 1.0
CD2 C:HIS79 4.0 39.3 1.0
ND1 C:HIS139 4.0 44.6 1.0
CG C:HIS139 4.1 39.9 1.0
SG C:CYS158 4.1 39.8 1.0
CG C:HIS77 4.2 38.6 1.0
OD2 C:ASP81 4.2 43.7 1.0
ND1 C:HIS77 4.3 37.5 1.0
CG C:ASP81 4.5 49.6 1.0
CG2 C:THR140 4.6 38.9 1.0
CA C:HIS79 4.9 39.5 1.0

Zinc binding site 6 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:41.1
occ:1.00
 O C:HOH401 1.4 26.4 1.0
OD2 C:ASP81 1.9 43.7 1.0
SG C:CYS158 2.1 39.8 1.0
NE2 C:HIS197 2.3 41.5 1.0
CG C:ASP81 2.9 49.6 1.0
CD2 C:HIS197 3.1 49.2 1.0
CE1 C:HIS197 3.2 49.1 1.0
CB C:CYS158 3.2 38.0 1.0
OD1 C:ASP81 3.3 41.8 1.0
ZN C:ZN301 3.5 42.3 1.0
CD C:LYS33 3.9 41.1 1.0
CE1 C:HIS77 4.1 38.9 1.0
NE2 C:HIS77 4.1 38.8 1.0
CE C:LYS33 4.1 33.8 1.0
CG C:HIS197 4.2 50.6 1.0
CB C:ASP81 4.2 42.8 1.0
ND1 C:HIS197 4.2 47.2 1.0
CA C:CYS158 4.4 37.5 1.0
NE2 C:HIS139 4.5 46.8 1.0
ND1 C:HIS79 5.0 33.7 1.0

Zinc binding site 7 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:24.7
occ:1.00
 O D:HOH491 1.9 26.0 1.0
ND1 D:HIS79 2.0 25.4 1.0
NE2 D:HIS139 2.0 23.3 1.0
NE2 D:HIS77 2.1 23.1 1.0
CE1 D:HIS79 2.9 25.8 1.0
CD2 D:HIS77 3.0 23.0 1.0
CD2 D:HIS139 3.0 25.2 1.0
CG D:HIS79 3.0 23.6 1.0
CE1 D:HIS139 3.1 27.0 1.0
CE1 D:HIS77 3.2 26.9 1.0
ZN D:ZN302 3.4 27.7 1.0
CB D:HIS79 3.4 23.5 1.0
CB D:CYS158 3.8 24.7 1.0
OD1 D:ASP81 4.0 29.9 1.0
O D:HOH453 4.0 32.3 1.0
NE2 D:HIS79 4.1 25.1 1.0
ND1 D:HIS139 4.1 22.0 1.0
CD2 D:HIS79 4.1 26.4 1.0
CG D:HIS139 4.1 21.5 1.0
SG D:CYS158 4.1 26.5 1.0
CG D:HIS77 4.2 23.8 1.0
ND1 D:HIS77 4.2 25.4 1.0
OD2 D:ASP81 4.4 28.8 1.0
CG D:ASP81 4.6 28.4 1.0
CG2 D:THR140 4.6 23.6 1.0
CA D:HIS79 4.9 23.9 1.0
O D:HOH503 4.9 46.7 1.0

Zinc binding site 8 out of 8 in 7xhx

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


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 Metallo-Beta-Lactamase Imp-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:27.7
occ:1.00
 OD2 D:ASP81 2.0 28.8 1.0
O D:HOH491 2.0 26.0 1.0
NE2 D:HIS197 2.1 26.3 1.0
SG D:CYS158 2.2 26.5 1.0
CG D:ASP81 2.9 28.4 1.0
CD2 D:HIS197 3.0 28.3 1.0
CE1 D:HIS197 3.1 31.1 1.0
OD1 D:ASP81 3.2 29.9 1.0
CB D:CYS158 3.3 24.7 1.0
ZN D:ZN301 3.4 24.7 1.0
O D:HOH453 3.5 32.3 1.0
CE1 D:HIS77 4.0 26.9 1.0
NE2 D:HIS77 4.1 23.1 1.0
CE D:LYS33 4.1 28.3 1.0
CD D:LYS33 4.1 26.3 1.0
CG D:HIS197 4.2 30.9 1.0
ND1 D:HIS197 4.2 30.9 1.0
CB D:ASP81 4.3 26.5 1.0
CA D:CYS158 4.5 26.2 1.0
NE2 D:HIS139 4.5 23.3 1.0
NZ D:LYS161 5.0 35.2 1.0

Reference:

K.Yamamoto, H.Tanaka, G.Kurisu, R.Nakano, H.Yano, H.Sakai. Structural Insights Into the Substrate Specificity of Imp-6 and Imp-1 Metallo-Beta-Lactamases. J.Biochem. V. 173 21 2022.
ISSN: ISSN 0021-924X
PubMed: 36174533
DOI: 10.1093/JB/MVAC080
Page generated: Wed Oct 30 15:06:15 2024

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