Zinc in PDB 4wd6: Crystal Structure of Dim-1 Metallo-Beta-Lactamase

The structure of Crystal Structure of Dim-1 Metallo-Beta-Lactamase, PDB code: 4wd6 was solved by M.P.S.Booth, M.Kosmopoulou, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.55 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.719, 47.856, 185.216, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 27.4

The binding sites of Zinc atom in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase (pdb code 4wd6). 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 Dim-1 Metallo-Beta-Lactamase, PDB code: 4wd6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase


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 Dim-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:42.6 occ:1.00 O A:HOH424 1.8 34.3 1.0 ND1 A:HIS79 2.0 46.4 1.0 NE2 A:HIS139 2.1 47.6 1.0 NE2 A:HIS77 2.3 31.6 1.0 O A:HOH441 2.5 44.3 1.0 CE1 A:HIS139 2.9 51.6 1.0 CE1 A:HIS79 3.0 48.0 1.0 CG A:HIS79 3.1 42.8 1.0 CD2 A:HIS77 3.1 31.4 1.0 CD2 A:HIS139 3.3 45.4 1.0 CE1 A:HIS77 3.4 30.8 1.0 CB A:HIS79 3.4 41.5 1.0 ZN A:ZN302 4.0 48.0 1.0 OD1 A:ASP81 4.0 43.9 1.0 ND1 A:HIS139 4.1 49.4 1.0 NE2 A:HIS79 4.1 45.7 1.0 CD2 A:HIS79 4.2 46.8 1.0 CG A:HIS139 4.3 45.7 1.0 O A:HOH428 4.3 49.5 1.0 CG A:HIS77 4.3 31.2 1.0 ND1 A:HIS77 4.4 31.2 1.0 CB A:CYS158 4.7 35.4 1.0 SG A:CYS158 4.8 40.4 1.0 CA A:HIS79 4.9 41.7 1.0 CG2 A:THR140 4.9 42.4 1.0 CG A:ASP81 4.9 42.4 1.0 OD2 A:ASP81 5.0 41.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase


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 Dim-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:48.0 occ:1.00 SG A:CYS158 2.2 40.4 1.0 NE2 A:HIS200 2.2 37.2 1.0 OD2 A:ASP81 2.3 41.2 1.0 O A:HOH424 2.4 34.3 1.0 CD2 A:HIS200 3.1 33.7 1.0 CG A:ASP81 3.2 42.4 1.0 CE1 A:HIS200 3.2 36.1 1.0 CB A:CYS158 3.3 35.4 1.0 OD1 A:ASP81 3.5 43.9 1.0 ZN A:ZN301 4.0 42.6 1.0 CE1 A:HIS77 4.1 30.8 1.0 NH2 A:ARG82 4.1 36.9 1.0 NE A:ARG82 4.2 35.6 1.0 O A:HOH428 4.2 49.5 1.0 NE2 A:HIS77 4.3 31.6 1.0 CG A:HIS200 4.3 34.4 1.0 ND1 A:HIS200 4.3 36.3 1.0 O A:HOH441 4.4 44.3 1.0 CB A:ASP81 4.5 45.2 1.0 CA A:CYS158 4.6 31.6 1.0 CZ A:ARG82 4.6 35.6 1.0 NE2 A:HIS139 4.8 47.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase


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 Dim-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:50.7 occ:1.00 O B:HOH433 1.9 39.8 1.0 NE2 B:HIS77 2.2 46.0 1.0 NE2 B:HIS139 2.3 53.6 1.0 ND1 B:HIS79 2.3 60.4 1.0 O B:HOH434 2.4 46.1 1.0 CE1 B:HIS77 3.0 42.7 1.0 CD2 B:HIS139 3.1 49.0 1.0 CG B:HIS79 3.3 60.9 1.0 CE1 B:HIS79 3.3 60.4 1.0 CD2 B:HIS77 3.3 46.2 1.0 CE1 B:HIS139 3.4 50.6 1.0 CB B:HIS79 3.5 56.7 1.0 ZN B:ZN302 4.0 57.2 1.0 ND1 B:HIS77 4.2 41.7 1.0 OD1 B:ASP81 4.2 59.8 1.0 CG B:HIS139 4.3 47.3 1.0 CG B:HIS77 4.3 43.1 1.0 ND1 B:HIS139 4.4 51.3 1.0 NE2 B:HIS79 4.4 62.5 1.0 CD2 B:HIS79 4.4 62.8 1.0 O B:HOH424 4.7 36.2 1.0 SG B:CYS158 4.8 44.4 1.0 CG2 B:THR140 4.8 48.9 1.0 CB B:CYS158 4.9 39.7 1.0 CG B:ASP81 4.9 59.0 1.0 CA B:HIS79 4.9 55.1 1.0 OD2 B:ASP81 5.0 53.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dim-1 Metallo-Beta-Lactamase


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 Dim-1 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:57.2 occ:1.00 SG B:CYS158 2.1 44.4 1.0 NE2 B:HIS200 2.1 51.1 1.0 O B:HOH433 2.4 39.8 1.0 O B:HOH424 2.4 36.2 1.0 OD2 B:ASP81 2.6 53.1 1.0 CD2 B:HIS200 3.0 49.4 1.0 CE1 B:HIS200 3.1 49.4 1.0 CB B:CYS158 3.1 39.7 1.0 CG B:ASP81 3.6 59.0 1.0 OD1 B:ASP81 3.9 59.8 1.0 ZN B:ZN301 4.0 50.7 1.0 CE1 B:HIS77 4.1 42.7 1.0 O B:HOH436 4.2 62.9 1.0 NH2 B:ARG82 4.2 49.8 1.0 CG B:HIS200 4.2 45.9 1.0 ND1 B:HIS200 4.2 49.8 1.0 O B:HOH434 4.3 46.1 1.0 NE B:ARG82 4.4 46.7 1.0 CA B:CYS158 4.4 36.6 1.0 NE2 B:HIS139 4.5 53.6 1.0 O B:HOH429 4.6 43.1 1.0 CE1 B:HIS139 4.7 50.6 1.0 NE2 B:HIS77 4.7 46.0 1.0 CZ B:ARG82 4.7 47.4 1.0 CB B:ASP81 4.9 59.9 1.0

M.P.S.Booth, M.Kosmopoulou, L.Poirel, P.Nordmann, J.Spencer. Crystal Structure of Dim-1 Metallo-Beta-Lactamase To Be Published.