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Zinc in PDB 3wxc: Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor

Enzymatic activity of Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor, PDB code: 3wxc was solved by J.Saito, T.Watanabe, M.Yamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.994, 52.795, 198.384, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 27.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor (pdb code 3wxc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor, PDB code: 3wxc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3wxc

Go back to Zinc Binding Sites List in 3wxc
Zinc binding site 1 out of 4 in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor


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 Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:31.2
occ:1.00
 ND1 A:HIS79 1.9 31.3 1.0
NE2 A:HIS139 2.0 33.7 1.0
O8 A:C93303 2.1 33.1 1.0
NE2 A:HIS77 2.2 29.0 1.0
O9 A:C93303 2.6 35.6 1.0
C7 A:C93303 2.7 35.1 1.0
CE1 A:HIS139 2.8 34.5 1.0
CE1 A:HIS79 2.9 32.1 1.0
CG A:HIS79 2.9 32.6 1.0
CD2 A:HIS77 3.1 30.1 1.0
CD2 A:HIS139 3.1 33.1 1.0
CE1 A:HIS77 3.3 29.1 1.0
CB A:HIS79 3.3 32.5 1.0
ZN A:ZN302 3.5 29.4 1.0
NE2 A:HIS79 4.0 32.5 1.0
SG A:CYS158 4.0 30.7 1.0
ND1 A:HIS139 4.0 33.2 1.0
O11 A:C93303 4.0 32.7 1.0
CD2 A:HIS79 4.0 32.3 1.0
CB A:CYS158 4.1 30.9 1.0
OD1 A:ASP81 4.1 28.9 1.0
CG A:HIS139 4.1 34.3 1.0
C2 A:C93303 4.2 33.9 1.0
CG A:HIS77 4.3 31.8 1.0
ND1 A:HIS77 4.3 30.7 1.0
CG2 A:THR140 4.4 35.2 1.0
OD2 A:ASP81 4.7 29.9 1.0
N13 A:C93303 4.7 35.7 1.0
CA A:HIS79 4.7 32.7 1.0
CG A:ASP81 4.8 30.1 1.0
C10 A:C93303 4.9 32.9 1.0
C3 A:C93303 5.0 34.8 1.0

Zinc binding site 2 out of 4 in 3wxc

Go back to Zinc Binding Sites List in 3wxc
Zinc binding site 2 out of 4 in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor


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 Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:29.4
occ:1.00
 O8 A:C93303 2.0 33.1 1.0
OD2 A:ASP81 2.1 29.9 1.0
NE2 A:HIS197 2.2 30.4 1.0
SG A:CYS158 2.3 30.7 1.0
C7 A:C93303 3.0 35.1 1.0
CG A:ASP81 3.1 30.1 1.0
CD2 A:HIS197 3.1 30.2 1.0
CE1 A:HIS197 3.1 30.9 1.0
O11 A:C93303 3.2 32.7 1.0
OD1 A:ASP81 3.3 28.9 1.0
C2 A:C93303 3.4 33.9 1.0
CB A:CYS158 3.5 30.9 1.0
ZN A:ZN301 3.5 31.2 1.0
C1 A:C93303 3.8 33.5 1.0
C10 A:C93303 3.9 32.9 1.0
O9 A:C93303 4.1 35.6 1.0
CE1 A:HIS77 4.2 29.1 1.0
C3 A:C93303 4.2 34.8 1.0
NE2 A:HIS77 4.2 29.0 1.0
ND1 A:HIS197 4.2 30.4 1.0
CG A:HIS197 4.2 31.8 1.0
CB A:SER196 4.4 31.0 1.0
NE2 A:HIS139 4.4 33.7 1.0
CD A:LYS33 4.4 30.0 1.0
CB A:ASP81 4.4 31.1 1.0
N13 A:C93303 4.5 35.7 1.0
CE A:LYS33 4.5 29.1 1.0
CA A:CYS158 4.6 30.8 1.0
OG A:SER196 4.7 31.2 1.0
CE1 A:HIS139 4.8 34.5 1.0
C6 A:C93303 4.8 33.1 1.0
C18 A:C93303 4.8 35.7 1.0

Zinc binding site 3 out of 4 in 3wxc

Go back to Zinc Binding Sites List in 3wxc
Zinc binding site 3 out of 4 in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor


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 Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:25.5
occ:1.00
 ND1 B:HIS79 2.0 21.6 1.0
NE2 B:HIS77 2.0 19.9 1.0
NE2 B:HIS139 2.1 19.9 1.0
O8 B:C93303 2.1 21.5 1.0
O9 B:C93303 2.7 28.8 1.0
C7 B:C93303 2.7 28.2 1.0
CD2 B:HIS77 2.9 20.7 1.0
CE1 B:HIS79 2.9 23.2 1.0
CD2 B:HIS139 3.0 20.9 1.0
CG B:HIS79 3.0 24.2 1.0
CE1 B:HIS139 3.1 22.4 1.0
CE1 B:HIS77 3.1 19.6 1.0
CB B:HIS79 3.4 24.0 1.0
ZN B:ZN302 3.6 22.8 1.0
CB B:CYS158 4.0 22.9 1.0
OD1 B:ASP81 4.0 23.6 1.0
SG B:CYS158 4.1 25.2 1.0
NE2 B:HIS79 4.1 22.3 1.0
CG B:HIS77 4.1 20.9 1.0
CD2 B:HIS79 4.1 23.4 1.0
ND1 B:HIS77 4.2 19.6 1.0
CG B:HIS139 4.2 23.7 1.0
ND1 B:HIS139 4.2 24.0 1.0
C2 B:C93303 4.2 28.7 1.0
O11 B:C93303 4.2 29.4 1.0
CG2 B:THR140 4.3 21.5 1.0
OD2 B:ASP81 4.5 22.8 1.0
N13 B:C93303 4.6 27.4 1.0
CG B:ASP81 4.7 23.1 1.0
CA B:HIS79 4.8 24.0 1.0
C3 B:C93303 5.0 29.1 1.0
ND2 B:ASN167 5.0 28.6 1.0

Zinc binding site 4 out of 4 in 3wxc

Go back to Zinc Binding Sites List in 3wxc
Zinc binding site 4 out of 4 in the Crystal Structure of Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor


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 Imp-1 Metallo-Beta-Lactamase Complexed with A 3- Aminophtalic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:22.8
occ:1.00
 NE2 B:HIS197 2.0 21.5 1.0
OD2 B:ASP81 2.0 22.8 1.0
O8 B:C93303 2.1 21.5 1.0
SG B:CYS158 2.3 25.2 1.0
CE1 B:HIS197 2.9 21.6 1.0
CD2 B:HIS197 2.9 22.8 1.0
CG B:ASP81 3.0 23.1 1.0
C7 B:C93303 3.1 28.2 1.0
CB B:CYS158 3.3 22.9 1.0
OD1 B:ASP81 3.4 23.6 1.0
O11 B:C93303 3.4 29.4 1.0
C2 B:C93303 3.4 28.7 1.0
ZN B:ZN301 3.6 25.5 1.0
C1 B:C93303 3.9 29.4 1.0
ND1 B:HIS197 4.0 22.7 1.0
CG B:HIS197 4.0 24.6 1.0
CE1 B:HIS77 4.1 19.6 1.0
C10 B:C93303 4.1 29.8 1.0
C3 B:C93303 4.1 29.1 1.0
NE2 B:HIS77 4.2 19.9 1.0
O9 B:C93303 4.2 28.8 1.0
N13 B:C93303 4.3 27.4 1.0
CB B:SER196 4.4 23.7 1.0
CB B:ASP81 4.4 23.3 1.0
NE2 B:HIS139 4.4 19.9 1.0
CA B:CYS158 4.5 23.4 1.0
CD B:LYS33 4.5 24.0 1.0
C18 B:C93303 4.6 29.3 1.0
CE B:LYS33 4.6 21.4 1.0
OG B:SER196 4.7 20.9 1.0
CE1 B:HIS139 4.9 22.4 1.0
C6 B:C93303 4.9 29.5 1.0

Reference:

Y.Hiraiwa, J.Saito, T.Watanabe, M.Yamada, A.Morinaka, T.Fukushima, T.Kudo. X-Ray Crystallographic Analysis of Imp-1 Metallo-Beta-Lactamase Complexed with A 3-Aminophthalic Acid Derivative, Structure-Based Drug Design, and Synthesis of 3,6-Disubstituted Phthalic Acid Derivative Inhibitors Bioorg.Med.Chem.Lett. V. 24 4891 2014.
ISSN: ISSN 0960-894X
PubMed: 25246278
DOI: 10.1016/J.BMCL.2014.08.039
Page generated: Sat Oct 26 18:23:21 2024

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