Zinc in PDB 7xhw: Crystal Structure of Metallo-Beta-Lactamase Imp-1

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1, PDB code: 7xhw 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) 46.11 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.321, 78.332, 259.945, 90, 90, 90
R / Rfree (%) 24.9 / 29.2

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 7xhw

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Zinc binding site 1 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:41.7
occ:1.00
 ND1 A:HIS79 1.9 36.1 1.0
NE2 A:HIS139 2.0 59.5 1.0
NE2 A:HIS77 2.2 43.2 1.0
O A:HOH630 2.3 32.7 1.0
CG A:HIS79 2.9 41.3 1.0
CE1 A:HIS79 2.9 41.2 1.0
CD2 A:HIS139 2.9 52.5 1.0
CE1 A:HIS139 3.1 48.2 1.0
CD2 A:HIS77 3.1 39.0 1.0
CB A:HIS79 3.2 42.4 1.0
CE1 A:HIS77 3.2 43.4 1.0
ZN A:ZN502 3.4 46.1 1.0
OD1 A:ASP81 3.9 39.1 1.0
CB A:CYS158 3.9 42.2 1.0
CD2 A:HIS79 4.0 42.0 1.0
O A:HOH643 4.0 47.1 1.0
NE2 A:HIS79 4.0 39.9 1.0
SG A:CYS158 4.1 44.1 1.0
CG A:HIS139 4.1 56.1 1.0
ND1 A:HIS139 4.1 54.0 1.0
CG A:HIS77 4.2 41.1 1.0
ND1 A:HIS77 4.3 40.5 1.0
OD2 A:ASP81 4.4 42.1 1.0
CG A:ASP81 4.6 38.8 1.0
CG2 A:THR140 4.6 38.7 1.0
CA A:HIS79 4.7 44.5 1.0

Zinc binding site 2 out of 8 in 7xhw

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Zinc binding site 2 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:46.1
occ:1.00
 O A:HOH630 1.9 32.7 1.0
OD2 A:ASP81 2.0 42.1 1.0
NE2 A:HIS197 2.1 48.7 1.0
SG A:CYS158 2.3 44.1 1.0
CG A:ASP81 3.0 38.8 1.0
CD2 A:HIS197 3.0 44.1 1.0
O A:HOH643 3.1 47.1 1.0
CE1 A:HIS197 3.1 45.1 1.0
OD1 A:ASP81 3.3 39.1 1.0
CB A:CYS158 3.3 42.2 1.0
ZN A:ZN501 3.4 41.7 1.0
CG A:HIS197 4.2 42.2 1.0
CE1 A:HIS77 4.2 43.4 1.0
ND1 A:HIS197 4.2 48.1 1.0
NE2 A:HIS77 4.2 43.2 1.0
NE2 A:HIS139 4.2 59.5 1.0
CB A:SER196 4.3 42.4 1.0
CB A:ASP81 4.4 37.4 1.0
CA A:CYS158 4.5 45.2 1.0
CD A:LYS33 4.5 38.4 1.0
OG A:SER196 4.6 40.8 1.0
CE A:LYS33 4.6 38.3 1.0
CE1 A:HIS139 4.6 48.2 1.0
ND1 A:HIS79 4.9 36.1 1.0

Zinc binding site 3 out of 8 in 7xhw

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Zinc binding site 3 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:42.9
occ:1.00
 ND1 B:HIS79 1.8 30.5 1.0
NE2 B:HIS139 2.0 59.9 1.0
O B:HOH436 2.2 32.1 1.0
NE2 B:HIS77 2.3 45.9 1.0
CE1 B:HIS79 2.7 31.6 1.0
CG B:HIS79 2.9 33.5 1.0
CE1 B:HIS139 3.0 55.7 1.0
CD2 B:HIS77 3.0 35.8 1.0
CD2 B:HIS139 3.0 59.5 1.0
CB B:HIS79 3.3 35.9 1.0
ZN B:ZN302 3.4 48.0 1.0
CE1 B:HIS77 3.4 43.6 1.0
OD1 B:ASP81 3.8 43.7 1.0
NE2 B:HIS79 3.9 34.0 1.0
CD2 B:HIS79 4.0 32.6 1.0
CB B:CYS158 4.0 40.9 1.0
O B:HOH432 4.1 50.1 1.0
ND1 B:HIS139 4.1 52.7 1.0
SG B:CYS158 4.1 46.2 1.0
CG B:HIS139 4.1 53.7 1.0
CG B:HIS77 4.2 34.9 1.0
ND1 B:HIS77 4.4 34.8 1.0
OD2 B:ASP81 4.5 49.2 1.0
CG B:ASP81 4.5 42.3 1.0
CG2 B:THR140 4.6 45.2 1.0
CA B:HIS79 4.7 37.2 1.0

Zinc binding site 4 out of 8 in 7xhw

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Zinc binding site 4 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:48.0
occ:1.00
 O B:HOH436 1.9 32.1 1.0
OD2 B:ASP81 2.0 49.2 1.0
NE2 B:HIS197 2.2 50.1 1.0
SG B:CYS158 2.4 46.2 1.0
CG B:ASP81 2.9 42.3 1.0
CD2 B:HIS197 3.0 46.3 1.0
CE1 B:HIS197 3.1 41.4 1.0
O B:HOH432 3.2 50.1 1.0
OD1 B:ASP81 3.2 43.7 1.0
CB B:CYS158 3.4 40.9 1.0
ZN B:ZN301 3.4 42.9 1.0
NE2 B:HIS77 4.1 45.9 1.0
NE2 B:HIS139 4.2 59.9 1.0
CG B:HIS197 4.2 47.6 1.0
ND1 B:HIS197 4.2 46.9 1.0
CE1 B:HIS77 4.2 43.6 1.0
CB B:ASP81 4.3 38.0 1.0
CB B:SER196 4.3 42.4 1.0
CD B:LYS33 4.5 38.3 1.0
CE B:LYS33 4.5 39.4 1.0
OG B:SER196 4.5 44.5 1.0
CA B:CYS158 4.6 42.9 1.0
CE1 B:HIS139 4.8 55.7 1.0
CD2 B:HIS139 5.0 59.5 1.0
ND1 B:HIS79 5.0 30.5 1.0

Zinc binding site 5 out of 8 in 7xhw

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Zinc binding site 5 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:51.7
occ:1.00
 ND1 C:HIS79 2.0 37.8 1.0
NE2 C:HIS139 2.0 40.2 1.0
NE2 C:HIS77 2.3 56.9 1.0
O C:HOH404 2.3 59.8 1.0
CE1 C:HIS79 3.0 43.9 1.0
CE1 C:HIS139 3.0 48.3 1.0
CD2 C:HIS139 3.0 45.9 1.0
CD2 C:HIS77 3.1 56.8 1.0
CG C:HIS79 3.1 40.4 1.0
ZN C:ZN302 3.2 62.2 1.0
CE1 C:HIS77 3.3 58.1 1.0
CB C:HIS79 3.5 44.0 1.0
OD1 C:ASP81 3.6 53.4 1.0
CB C:CYS158 3.9 45.7 1.0
SG C:CYS158 3.9 50.8 1.0
ND1 C:HIS139 4.1 46.9 1.0
NE2 C:HIS79 4.1 40.1 1.0
CG C:HIS139 4.1 46.3 1.0
CD2 C:HIS79 4.2 40.6 1.0
CG C:HIS77 4.3 57.2 1.0
ND1 C:HIS77 4.3 55.0 1.0
OD2 C:ASP81 4.4 50.8 1.0
CG C:ASP81 4.4 55.0 1.0
CG2 C:THR140 4.7 47.8 1.0
CA C:HIS79 4.9 48.1 1.0

Zinc binding site 6 out of 8 in 7xhw

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Zinc binding site 6 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:62.2
occ:1.00
 O C:HOH404 2.0 59.8 1.0
OD2 C:ASP81 2.1 50.8 1.0
SG C:CYS158 2.3 50.8 1.0
NE2 C:HIS197 2.5 75.4 1.0
CG C:ASP81 3.0 55.0 1.0
ZN C:ZN301 3.2 51.7 1.0
CB C:CYS158 3.2 45.7 1.0
CD2 C:HIS197 3.2 67.4 1.0
OD1 C:ASP81 3.3 53.4 1.0
CE1 C:HIS197 3.5 65.2 1.0
NE2 C:HIS77 4.0 56.9 1.0
CE1 C:HIS77 4.1 58.1 1.0
NE2 C:HIS139 4.2 40.2 1.0
CG C:HIS197 4.3 71.3 1.0
CB C:SER196 4.4 49.8 1.0
CE C:LYS33 4.4 56.5 1.0
CB C:ASP81 4.4 51.9 1.0
CA C:CYS158 4.4 47.8 1.0
ND1 C:HIS197 4.4 70.3 1.0
CD C:LYS33 4.5 55.5 1.0
OG C:SER196 4.6 49.5 1.0
CE1 C:HIS139 4.8 48.3 1.0
CD2 C:HIS139 4.9 45.9 1.0
ND1 C:HIS79 5.0 37.8 1.0

Zinc binding site 7 out of 8 in 7xhw

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Zinc binding site 7 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:40.4
occ:1.00
 ND1 D:HIS79 1.8 37.8 1.0
NE2 D:HIS139 2.0 34.5 1.0
NE2 D:HIS77 2.2 33.5 1.0
CE1 D:HIS79 2.8 41.3 1.0
CE1 D:HIS139 2.9 34.6 1.0
CG D:HIS79 2.9 42.1 1.0
CD2 D:HIS77 3.0 38.2 1.0
CD2 D:HIS139 3.1 32.8 1.0
CE1 D:HIS77 3.3 32.7 1.0
CB D:HIS79 3.3 43.5 1.0
ZN D:ZN302 3.3 52.2 1.0
OD1 D:ASP81 3.9 40.5 1.0
NE2 D:HIS79 3.9 39.8 1.0
SG D:CYS158 3.9 41.3 1.0
CB D:CYS158 3.9 38.9 1.0
CD2 D:HIS79 4.0 39.0 1.0
O D:HOH411 4.0 44.9 1.0
ND1 D:HIS139 4.0 37.5 1.0
CG D:HIS139 4.2 34.1 1.0
OD2 D:ASP81 4.2 38.4 1.0
CG D:HIS77 4.3 39.0 1.0
ND1 D:HIS77 4.3 36.8 1.0
CG D:ASP81 4.4 40.6 1.0
CG2 D:THR140 4.7 36.0 1.0
CA D:HIS79 4.8 43.8 1.0

Zinc binding site 8 out of 8 in 7xhw

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Zinc binding site 8 out of 8 in the Crystal Structure of 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 Metallo-Beta-Lactamase Imp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:52.2
occ:1.00
 OD2 D:ASP81 2.0 38.4 1.0
SG D:CYS158 2.2 41.3 1.0
NE2 D:HIS197 2.4 49.7 1.0
CG D:ASP81 3.0 40.6 1.0
CD2 D:HIS197 3.1 46.6 1.0
O D:HOH411 3.2 44.9 1.0
CB D:CYS158 3.3 38.9 1.0
ZN D:ZN301 3.3 40.4 1.0
OD1 D:ASP81 3.4 40.5 1.0
CE1 D:HIS197 3.4 48.0 1.0
NE2 D:HIS77 4.0 33.5 1.0
CE1 D:HIS77 4.1 32.7 1.0
CE D:LYS33 4.2 46.7 1.0
CG D:HIS197 4.3 47.8 1.0
CB D:SER196 4.3 43.3 1.0
CB D:ASP81 4.3 41.7 1.0
NE2 D:HIS139 4.4 34.5 1.0
CD D:LYS33 4.4 47.5 1.0
ND1 D:HIS197 4.4 46.9 1.0
CA D:CYS158 4.5 38.0 1.0
OG D:SER196 4.5 45.5 1.0
CE1 D:HIS139 4.8 34.6 1.0
ND1 D:HIS79 4.9 37.8 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 15:06:14 2024

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