Zinc in PDB 1wuo: Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A)

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A):
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A), PDB code: 1wuo was solved by Y.Yamaguchi, Y.Yamagata, M.Goto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.35 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.734, 73.016, 82.450, 85.37, 75.53, 73.62
R / Rfree (%)	21.2 / 21.8

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A) (pdb code 1wuo). 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 Metallo-Beta-Lactamase Imp-1 Mutant (D81A), PDB code: 1wuo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A)


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 Mutant (D81A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:24.0 occ:1.00 NE2 A:HIS139 2.0 22.6 1.0 ND1 A:HIS79 2.0 30.2 1.0 OXT A:ACY401 2.1 44.2 1.0 NE2 A:HIS77 2.4 23.5 1.0 O A:ACY401 2.5 36.4 1.0 C A:ACY401 2.6 41.2 1.0 CD2 A:HIS77 2.9 24.2 1.0 CE1 A:HIS79 2.9 26.4 1.0 CE1 A:HIS139 2.9 19.7 1.0 CD2 A:HIS139 3.0 24.5 1.0 CG A:HIS79 3.1 30.1 1.0 CB A:HIS79 3.5 27.7 1.0 OD1 A:CSD158 3.5 40.8 1.0 CE1 A:HIS77 3.6 30.1 1.0 SG A:CSD158 3.7 29.4 1.0 ND1 A:HIS139 4.1 23.7 1.0 NE2 A:HIS79 4.1 31.1 1.0 CH3 A:ACY401 4.1 42.8 1.0 CG A:HIS139 4.1 18.2 1.0 CG A:HIS77 4.2 22.2 1.0 CD2 A:HIS79 4.2 31.4 1.0 ND1 A:HIS77 4.5 21.4 1.0 O A:HOH438 4.5 36.5 1.0 CG2 A:THR140 4.6 24.9 1.0 CB A:CSD158 4.6 31.1 1.0 CA A:HIS79 4.9 27.4 1.0 OD2 A:CSD158 5.0 29.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A)


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 Mutant (D81A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:25.1 occ:1.00 ND1 B:HIS79 2.1 31.0 1.0 NE2 B:HIS139 2.1 17.9 1.0 OXT B:ACY402 2.2 39.9 1.0 C B:ACY402 2.3 38.9 1.0 NE2 B:HIS77 2.4 29.9 1.0 O B:ACY402 2.7 30.0 1.0 CD2 B:HIS139 2.9 19.1 1.0 CH3 B:ACY402 2.9 41.9 1.0 CE1 B:HIS79 3.0 28.4 1.0 CD2 B:HIS77 3.0 20.7 1.0 CG B:HIS79 3.2 23.6 1.0 CE1 B:HIS139 3.2 18.5 1.0 SG B:CSD158 3.3 45.0 1.0 CE1 B:HIS77 3.5 21.7 1.0 OD2 B:CSD158 3.5 51.9 1.0 CB B:HIS79 3.5 29.2 1.0 CG B:HIS139 4.1 14.6 1.0 NE2 B:HIS79 4.2 33.5 1.0 ND1 B:HIS139 4.2 19.2 1.0 CD2 B:HIS79 4.2 33.8 1.0 CG B:HIS77 4.2 21.1 1.0 ND1 B:HIS77 4.4 18.4 1.0 CB B:CSD158 4.5 43.0 1.0 OD1 B:CSD158 4.5 45.7 1.0 CG2 B:THR140 4.5 25.5 1.0 CA B:HIS79 5.0 23.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A)


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 Mutant (D81A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:24.3 occ:1.00 ND1 C:HIS79 1.9 22.8 1.0 NE2 C:HIS139 2.0 20.0 1.0 OXT C:ACY403 2.3 42.2 1.0 NE2 C:HIS77 2.3 25.4 1.0 O C:ACY403 2.7 32.6 1.0 CE1 C:HIS79 2.8 24.4 1.0 C C:ACY403 2.8 35.7 1.0 CD2 C:HIS77 2.8 23.8 1.0 CD2 C:HIS139 2.9 23.5 1.0 CG C:HIS79 3.0 20.7 1.0 CE1 C:HIS139 3.0 25.0 1.0 CB C:HIS79 3.4 24.1 1.0 CE1 C:HIS77 3.5 30.4 1.0 SG C:CSD158 3.6 29.1 1.0 OD1 C:CSD158 3.7 43.7 1.0 NE2 C:HIS79 3.9 24.3 1.0 CD2 C:HIS79 4.0 29.7 1.0 CG C:HIS139 4.1 25.0 1.0 ND1 C:HIS139 4.1 22.4 1.0 CG C:HIS77 4.1 24.7 1.0 CH3 C:ACY403 4.3 38.3 1.0 O C:HOH404 4.4 48.0 1.0 ND1 C:HIS77 4.4 20.5 1.0 CG2 C:THR140 4.4 22.9 1.0 O C:HOH445 4.5 34.9 1.0 CB C:CSD158 4.6 33.6 1.0 CA C:HIS79 4.9 22.6 1.0 OD2 C:CSD158 4.9 27.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D81A)


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 Mutant (D81A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:23.6 occ:1.00 ND1 D:HIS79 2.1 30.3 1.0 NE2 D:HIS139 2.1 14.1 1.0 NE2 D:HIS77 2.2 17.9 1.0 OXT D:ACY404 2.3 27.3 1.0 O D:ACY404 2.3 37.1 1.0 C D:ACY404 2.6 28.4 1.0 CE1 D:HIS79 2.9 31.2 1.0 CD2 D:HIS77 3.0 16.8 1.0 CD2 D:HIS139 3.0 16.6 1.0 CE1 D:HIS139 3.0 16.4 1.0 CG D:HIS79 3.1 28.1 1.0 OD1 D:CSD158 3.2 45.2 1.0 SG D:CSD158 3.4 36.0 1.0 CE1 D:HIS77 3.4 21.2 1.0 CB D:HIS79 3.5 23.5 1.0 NE2 D:HIS79 4.1 28.6 1.0 CH3 D:ACY404 4.1 37.0 1.0 ND1 D:HIS139 4.2 14.8 1.0 CG D:HIS139 4.2 15.1 1.0 CD2 D:HIS79 4.2 29.2 1.0 CG D:HIS77 4.2 17.0 1.0 O D:HOH406 4.3 29.7 1.0 CB D:CSD158 4.3 36.1 1.0 ND1 D:HIS77 4.4 16.6 1.0 O D:HOH405 4.6 53.0 1.0 CG2 D:THR140 4.6 21.7 1.0 OD2 D:CSD158 4.8 33.3 1.0 CA D:HIS79 5.0 23.4 1.0

Y.Yamaguchi, T.Kuroki, H.Yasuzawa, T.Higashi, W.Jin, A.Kawanami, Y.Yamagata, Y.Arakawa, M.Goto, H.Kurosaki. Probing the Role of Asp-120(81) of Metallo-Beta-Lactamase (Imp-1) By Site-Directed Mutagenesis, Kinetic Studies, and X-Ray Crystallography. J.Biol.Chem. V. 280 20824 2005.
ISSN: ISSN 0021-9258
PubMed: 15788415
DOI: 10.1074/JBC.M414314200