Zinc in PDB 7wzu: 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: 7wzu was solved by Y.Yamaguchi, H.Kurosaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.42 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.799, 76.098, 82.114, 83.45, 75.32, 74.06
R / Rfree (%) 19 / 22.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 7wzu

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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:Zn301

b:22.7
occ:1.00
 NE2 A:HIS139 2.0 20.2 1.0
ND1 A:HIS79 2.0 19.5 1.0
NE2 A:HIS77 2.1 20.4 1.0
CD2 A:HIS77 2.9 19.9 1.0
CE1 A:HIS79 2.9 22.1 1.0
CD2 A:HIS139 3.0 20.1 1.0
CG A:HIS79 3.1 21.8 1.0
CE1 A:HIS139 3.1 20.4 1.0
CE1 A:HIS77 3.2 21.3 1.0
CB A:HIS79 3.4 21.2 1.0
ZN A:ZN302 3.5 30.1 1.0
CB A:CYS158 3.8 23.4 1.0
OD1 A:ASP81 3.9 24.5 1.0
NE2 A:HIS79 4.1 22.3 1.0
CG A:HIS77 4.1 19.8 1.0
CG A:HIS139 4.1 20.0 1.0
SG A:CYS158 4.1 25.6 1.0
ND1 A:HIS139 4.1 19.2 1.0
CD2 A:HIS79 4.1 22.7 1.0
ND1 A:HIS77 4.2 20.1 1.0
OD2 A:ASP81 4.4 27.6 1.0
CG2 A:THR140 4.5 18.6 1.0
CG A:ASP81 4.6 25.6 1.0
CA A:HIS79 4.9 20.5 1.0

Zinc binding site 2 out of 8 in 7wzu

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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:Zn302

b:30.1
occ:1.00
 OD2 A:ASP81 1.9 27.6 1.0
NE2 A:HIS197 2.0 31.5 1.0
SG A:CYS158 2.2 25.6 1.0
CD2 A:HIS197 2.9 30.1 1.0
CG A:ASP81 2.9 25.6 1.0
CE1 A:HIS197 3.1 29.9 1.0
CB A:CYS158 3.3 23.4 1.0
OD1 A:ASP81 3.3 24.5 1.0
ZN A:ZN301 3.5 22.7 1.0
CG A:HIS197 4.1 30.2 1.0
NE2 A:HIS77 4.1 20.4 1.0
ND1 A:HIS197 4.1 30.1 1.0
CE1 A:HIS77 4.2 21.3 1.0
CB A:ASP81 4.3 24.3 1.0
CD A:LYS33 4.3 23.1 1.0
NE2 A:HIS139 4.4 20.2 1.0
CE A:LYS33 4.5 22.5 1.0
CA A:CYS158 4.5 21.8 1.0

Zinc binding site 3 out of 8 in 7wzu

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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:24.8
occ:1.00
 ND1 B:HIS79 2.0 23.5 1.0
NE2 B:HIS139 2.1 25.6 1.0
NE2 B:HIS77 2.2 20.0 1.0
CD2 B:HIS77 2.9 20.1 1.0
CE1 B:HIS79 2.9 26.3 1.0
CD2 B:HIS139 3.0 26.1 1.0
CG B:HIS79 3.0 24.4 1.0
CE1 B:HIS139 3.1 26.4 1.0
CE1 B:HIS77 3.3 21.7 1.0
CB B:HIS79 3.4 23.6 1.0
ZN B:ZN302 3.5 33.3 1.0
CB B:CYS158 3.8 26.5 1.0
OD1 B:ASP81 4.0 26.9 1.0
NE2 B:HIS79 4.1 25.2 1.0
SG B:CYS158 4.1 26.7 1.0
CD2 B:HIS79 4.1 25.5 1.0
CG B:HIS139 4.1 25.8 1.0
CG B:HIS77 4.2 19.7 1.0
ND1 B:HIS139 4.2 24.9 1.0
ND1 B:HIS77 4.3 20.2 1.0
OD2 B:ASP81 4.4 27.4 1.0
CG2 B:THR140 4.6 22.6 1.0
CG B:ASP81 4.6 26.9 1.0
CA B:HIS79 4.9 22.6 1.0

Zinc binding site 4 out of 8 in 7wzu

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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:33.3
occ:1.00
 OD2 B:ASP81 2.0 27.4 1.0
NE2 B:HIS197 2.1 39.8 1.0
SG B:CYS158 2.2 26.7 1.0
CG B:ASP81 3.0 26.9 1.0
CD2 B:HIS197 3.0 38.2 1.0
CE1 B:HIS197 3.1 39.9 1.0
CB B:CYS158 3.2 26.5 1.0
OD1 B:ASP81 3.3 26.9 1.0
ZN B:ZN301 3.5 24.8 1.0
NE2 B:HIS77 4.1 20.0 1.0
ND1 B:HIS197 4.1 37.7 1.0
CG B:HIS197 4.1 38.6 1.0
CE1 B:HIS77 4.2 21.7 1.0
CB B:ASP81 4.3 25.3 1.0
CD B:LYS33 4.4 22.9 1.0
NE2 B:HIS139 4.4 25.6 1.0
CA B:CYS158 4.5 25.8 1.0
CE B:LYS33 4.5 22.0 1.0
NZ B:LYS161 4.9 31.7 1.0

Zinc binding site 5 out of 8 in 7wzu

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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:24.6
occ:1.00
 ND1 C:HIS79 2.0 22.3 1.0
NE2 C:HIS139 2.0 24.4 1.0
NE2 C:HIS77 2.1 22.7 1.0
CD2 C:HIS77 2.9 22.1 1.0
CD2 C:HIS139 2.9 24.0 1.0
CE1 C:HIS79 2.9 24.5 1.0
CG C:HIS79 3.0 24.1 1.0
CE1 C:HIS139 3.1 24.4 1.0
CE1 C:HIS77 3.2 23.4 1.0
CB C:HIS79 3.4 23.3 1.0
ZN C:ZN302 3.5 30.8 1.0
CB C:CYS158 3.9 25.5 1.0
OD1 C:ASP81 3.9 23.9 1.0
NE2 C:HIS79 4.1 23.4 1.0
CG C:HIS139 4.1 23.8 1.0
CD2 C:HIS79 4.1 24.3 1.0
CG C:HIS77 4.1 21.4 1.0
SG C:CYS158 4.1 24.2 1.0
ND1 C:HIS139 4.2 23.2 1.0
ND1 C:HIS77 4.2 22.5 1.0
OD2 C:ASP81 4.5 27.4 1.0
CG2 C:THR140 4.6 23.4 1.0
CG C:ASP81 4.6 24.9 1.0
CA C:HIS79 4.8 22.6 1.0

Zinc binding site 6 out of 8 in 7wzu

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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:30.8
occ:1.00
 OD2 C:ASP81 2.0 27.4 1.0
NE2 C:HIS197 2.1 31.6 1.0
SG C:CYS158 2.2 24.2 1.0
CG C:ASP81 3.0 24.9 1.0
CD2 C:HIS197 3.0 30.2 1.0
CE1 C:HIS197 3.2 30.7 1.0
OD1 C:ASP81 3.2 23.9 1.0
CB C:CYS158 3.3 25.5 1.0
ZN C:ZN301 3.5 24.6 1.0
NE2 C:HIS77 4.1 22.7 1.0
CG C:HIS197 4.1 31.1 1.0
CE1 C:HIS77 4.2 23.4 1.0
ND1 C:HIS197 4.2 29.2 1.0
CD C:LYS33 4.2 23.9 1.0
CB C:ASP81 4.3 23.7 1.0
CE C:LYS33 4.4 23.2 1.0
NE2 C:HIS139 4.5 24.4 1.0
CA C:CYS158 4.6 24.1 1.0
NZ C:LYS161 5.0 33.7 1.0

Zinc binding site 7 out of 8 in 7wzu

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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:24.0
occ:1.00
 ND1 D:HIS79 2.0 20.8 1.0
NE2 D:HIS139 2.0 22.4 1.0
NE2 D:HIS77 2.1 22.1 1.0
CD2 D:HIS139 2.9 22.5 1.0
CD2 D:HIS77 2.9 21.1 1.0
CE1 D:HIS79 2.9 23.1 1.0
CG D:HIS79 3.0 23.5 1.0
CE1 D:HIS139 3.2 22.5 1.0
CE1 D:HIS77 3.2 24.0 1.0
CB D:HIS79 3.4 22.4 1.0
ZN D:ZN302 3.4 31.6 1.0
OD1 D:ASP81 3.8 23.8 1.0
CB D:CYS158 3.8 26.3 1.0
NE2 D:HIS79 4.1 22.5 1.0
SG D:CYS158 4.1 28.0 1.0
CG D:HIS139 4.1 21.7 1.0
CD2 D:HIS79 4.1 23.7 1.0
CG D:HIS77 4.1 20.8 1.0
ND1 D:HIS139 4.2 21.7 1.0
ND1 D:HIS77 4.2 23.1 1.0
OD2 D:ASP81 4.4 24.3 1.0
CG D:ASP81 4.5 24.1 1.0
CG2 D:THR140 4.6 21.2 1.0
CA D:HIS79 4.8 21.4 1.0

Zinc binding site 8 out of 8 in 7wzu

Go back to Zinc Binding Sites List in 7wzu
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:31.6
occ:1.00
 OD2 D:ASP81 2.0 24.3 1.0
NE2 D:HIS197 2.0 30.3 1.0
SG D:CYS158 2.2 28.0 1.0
CE1 D:HIS197 2.9 32.1 1.0
CG D:ASP81 2.9 24.1 1.0
CD2 D:HIS197 3.1 30.2 1.0
OD1 D:ASP81 3.3 23.8 1.0
CB D:CYS158 3.3 26.3 1.0
ZN D:ZN301 3.4 24.0 1.0
ND1 D:HIS197 4.0 32.2 1.0
CE1 D:HIS77 4.1 24.0 1.0
NE2 D:HIS77 4.1 22.1 1.0
CG D:HIS197 4.1 31.6 1.0
CB D:ASP81 4.3 23.4 1.0
CE D:LYS33 4.3 23.8 1.0
CD D:LYS33 4.3 24.2 1.0
NE2 D:HIS139 4.4 22.4 1.0
CA D:CYS158 4.6 24.9 1.0
NZ D:LYS161 5.0 33.0 1.0

Reference:

Y.Yamaguchi, K.Kato, Y.Ichimaru, Y.Uenosono, S.Tawara, R.Ito, N.Matsuse, J.I.Wachino, S.Toma-Fukai, W.Jin, Y.Arakawa, M.Otsuka, M.Fujita, N.Fukuishi, K.Sugiura, M.Imai, H.Kurosaki. Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates From the Zn(II) Active Site of Metallo-Beta-Lactamases (Imp-1 and Imp-6) Associated with A Single Amino Acid Substitution. Acs Infect Dis. 2022.
ISSN: ESSN 2373-8227
PubMed: 36519431
DOI: 10.1021/ACSINFECDIS.2C00395
Page generated: Wed Oct 30 14:39:29 2024

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