Zinc in PDB 4uam: 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site

The structure of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site, PDB code: 4uam was solved by T.J.Carruthers, P.D.Carr, C.J.Jackson, G.Otting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.93 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.990, 75.910, 82.360, 83.45, 75.30, 74.01
R / Rfree (%)	16.2 / 18.2

The structure of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site (pdb code 4uam). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site, PDB code: 4uam:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.8 occ:0.44 OD1 A:CSD158 2.0 20.6 0.3 OD2 A:ASP81 2.1 19.1 1.0 OD2 A:CSD158 2.1 22.7 0.3 NE2 A:HIS197 2.1 27.7 1.0 OHB A:FLC303 2.2 30.2 0.9 OG2 A:FLC303 2.3 28.1 0.9 SG A:CSD158 2.3 21.7 0.4 SG A:CSD158 2.4 22.0 0.3 SG A:CSD158 2.4 21.9 0.3 OB2 A:FLC303 2.5 17.8 0.9 HOB A:FLC303 2.7 36.2 0.9 CE1 A:HIS197 3.0 24.1 1.0 HE1 A:HIS197 3.1 28.9 1.0 CB A:FLC303 3.1 30.6 0.9 CBC A:FLC303 3.2 23.8 0.9 OD2 A:CSD158 3.2 21.1 0.3 CD2 A:HIS197 3.2 28.1 1.0 CG A:ASP81 3.2 19.0 1.0 OD1 A:CSD158 3.3 21.7 0.3 CGC A:FLC303 3.4 29.9 0.9 HD2 A:HIS197 3.5 33.7 1.0 CG A:FLC303 3.8 25.2 0.9 FE A:FE301 3.8 18.5 0.8 OD1 A:ASP81 3.8 18.0 1.0 CB A:CSD158 3.8 22.2 0.3 HB3 A:CSD158 3.8 26.6 0.4 CB A:CSD158 3.8 22.2 0.4 CB A:CSD158 3.8 21.8 0.3 HB2 A:CSD158 3.9 26.6 0.3 HB3 A:SER196 3.9 28.9 1.0 HB2 A:CSD158 4.0 26.2 0.3 HD3 A:LYS33 4.0 17.5 1.0 OA2 A:FLC303 4.0 53.0 0.9 HG1 A:FLC303 4.0 30.3 0.9 ND1 A:HIS197 4.2 23.7 1.0 HE1 A:HIS77 4.2 22.4 1.0 HB2 A:SER196 4.3 28.9 1.0 CG A:HIS197 4.3 27.3 1.0 OB1 A:FLC303 4.3 25.0 0.9 HE2 A:LYS33 4.4 17.6 1.0 HB2 A:CSD158 4.4 26.6 0.4 HB3 A:CSD158 4.4 26.6 0.3 CB A:ASP81 4.4 15.1 1.0 HB3 A:CSD158 4.4 26.2 0.3 HG A:SER196 4.4 31.7 1.0 CA A:FLC303 4.5 47.4 0.9 HB2 A:ASP81 4.5 18.1 1.0 OG1 A:FLC303 4.5 31.1 0.9 CB A:SER196 4.5 24.1 1.0 HB3 A:ASP81 4.5 18.1 1.0 HZ1 A:LYS161 4.6 37.6 1.0 NE2 A:HIS77 4.6 16.1 1.0 NE2 A:HIS139 4.6 17.1 1.0 HG2 A:FLC303 4.6 30.3 0.9 HA A:CSD158 4.7 24.6 0.4 CAC A:FLC303 4.7 56.6 0.9 CE1 A:HIS77 4.7 18.7 1.0 HA A:CSD158 4.7 24.6 0.3 HA A:CSD158 4.7 24.7 0.3 HE3 A:LYS33 4.7 17.6 1.0 CD A:LYS33 4.8 14.6 1.0 OG A:SER196 4.8 26.4 1.0 HE1 A:HIS139 4.8 19.2 1.0 HA2 A:FLC303 4.8 56.9 0.9 CE A:LYS33 4.8 14.7 1.0 CA A:CSD158 4.9 20.5 0.4 HD1 A:HIS197 4.9 28.5 1.0 CA A:CSD158 4.9 20.6 0.3 CA A:CSD158 4.9 20.5 0.3 CE1 A:HIS139 5.0 16.0 1.0 HE2 A:LYS161 5.0 32.3 1.0

Zinc binding site 2 out of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:19.7 occ:0.44 OD1 B:CSD158 1.9 24.5 0.3 OD2 B:CSD158 2.0 26.8 0.3 OD2 B:ASP81 2.1 25.9 1.0 NE2 B:HIS197 2.1 27.6 1.0 OHB B:FLC303 2.2 35.2 0.9 SG B:CSD158 2.3 24.4 0.4 OG1 B:FLC303 2.4 30.5 0.9 SG B:CSD158 2.4 24.6 0.3 SG B:CSD158 2.5 24.7 0.3 OB1 B:FLC303 2.5 18.1 0.9 HOB B:FLC303 2.8 42.2 0.9 CE1 B:HIS197 3.0 24.4 1.0 CD2 B:HIS197 3.1 33.7 1.0 CB B:FLC303 3.2 36.3 0.9 HE1 B:HIS197 3.2 29.3 1.0 CBC B:FLC303 3.2 27.8 0.9 CG B:ASP81 3.2 23.1 1.0 OD2 B:CSD158 3.3 24.2 0.3 HD2 B:HIS197 3.3 40.5 1.0 OD1 B:CSD158 3.4 24.4 0.3 CGC B:FLC303 3.4 31.2 0.9 CB B:CSD158 3.8 24.4 0.3 CB B:CSD158 3.8 24.2 0.3 CG B:FLC303 3.8 29.0 0.9 HB2 B:CSD158 3.8 29.3 0.3 OD1 B:ASP81 3.8 20.9 1.0 HB3 B:SER196 3.8 33.9 1.0 CB B:CSD158 3.8 24.4 0.4 HB3 B:CSD158 3.8 29.3 0.4 HB2 B:CSD158 3.8 29.0 0.3 FE B:FE301 3.8 20.3 0.8 HD3 B:LYS33 3.9 21.4 1.0 HG2 B:FLC303 4.0 34.8 0.9 HG B:SER196 4.1 34.0 1.0 ND1 B:HIS197 4.2 29.1 1.0 OA1 B:FLC303 4.2 47.2 0.9 HE1 B:HIS77 4.2 25.1 1.0 HB2 B:SER196 4.2 33.9 1.0 CG B:HIS197 4.2 35.4 1.0 HE2 B:LYS33 4.4 21.2 1.0 HB2 B:CSD158 4.4 29.3 0.4 OB2 B:FLC303 4.4 25.2 0.9 HB3 B:CSD158 4.4 29.3 0.3 HB3 B:CSD158 4.4 29.0 0.3 CB B:SER196 4.4 28.3 1.0 CB B:ASP81 4.4 19.2 1.0 HB2 B:ASP81 4.4 23.1 1.0 CA B:FLC303 4.5 49.6 0.9 OG2 B:FLC303 4.5 30.9 0.9 HB3 B:ASP81 4.5 23.1 1.0 HA B:CSD158 4.6 26.8 0.4 NE2 B:HIS77 4.6 20.3 1.0 HZ3 B:LYS161 4.6 43.5 1.0 HA B:CSD158 4.7 26.8 0.3 HA B:CSD158 4.7 26.8 0.3 HG1 B:FLC303 4.7 34.8 0.9 NE2 B:HIS139 4.7 17.6 1.0 HE3 B:LYS33 4.7 21.2 1.0 OG B:SER196 4.7 28.4 1.0 CE1 B:HIS77 4.7 21.0 1.0 CD B:LYS33 4.7 17.9 1.0 CAC B:FLC303 4.8 52.4 0.9 CE B:LYS33 4.8 17.7 1.0 HA2 B:FLC303 4.8 59.5 0.9 CA B:CSD158 4.8 22.4 0.4 CA B:CSD158 4.9 22.3 0.3 CA B:CSD158 4.9 22.4 0.3 HE1 B:HIS139 4.9 22.7 1.0 HD1 B:HIS197 4.9 34.9 1.0 HE2 B:LYS161 4.9 34.5 1.0

Zinc binding site 3 out of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:18.7 occ:0.44 OD1 C:CSD158 1.8 21.7 0.3 OD2 C:ASP81 2.0 19.7 1.0 NE2 C:HIS197 2.1 24.9 1.0 OD2 C:CSD158 2.2 25.1 0.3 OHB C:FLC303 2.3 35.8 0.9 OG2 C:FLC303 2.3 26.9 0.9 SG C:CSD158 2.3 19.9 0.4 SG C:CSD158 2.4 22.2 0.3 SG C:CSD158 2.5 21.7 0.3 OB2 C:FLC303 2.6 20.6 0.9 HOB C:FLC303 2.9 42.9 0.9 CE1 C:HIS197 3.0 24.5 1.0 HE1 C:HIS197 3.1 29.4 1.0 CB C:FLC303 3.1 33.7 0.9 CBC C:FLC303 3.2 24.2 0.9 CG C:ASP81 3.2 20.4 1.0 CD2 C:HIS197 3.2 27.8 1.0 OD1 C:CSD158 3.2 20.4 0.3 CGC C:FLC303 3.3 30.4 0.9 OD2 C:CSD158 3.4 20.8 0.3 HD2 C:HIS197 3.5 33.3 1.0 CG C:FLC303 3.7 26.5 0.9 OD1 C:ASP81 3.7 17.6 1.0 CB C:CSD158 3.8 18.0 0.3 CB C:CSD158 3.8 18.4 0.3 HB3 C:SER196 3.8 31.2 1.0 HB2 C:CSD158 3.8 21.6 0.3 FE C:FE301 3.8 19.7 0.8 HB3 C:CSD158 3.9 22.2 0.4 CB C:CSD158 3.9 18.5 0.4 HD3 C:LYS33 3.9 18.5 1.0 HG2 C:FLC303 3.9 31.8 0.9 HB2 C:CSD158 3.9 22.0 0.3 HE1 C:HIS77 4.1 19.0 1.0 ND1 C:HIS197 4.2 25.8 1.0 HB2 C:SER196 4.2 31.2 1.0 OB1 C:FLC303 4.3 20.1 0.9 CG C:HIS197 4.3 31.6 1.0 OA2 C:FLC303 4.3 43.7 0.9 HG C:SER196 4.3 32.2 1.0 HE2 C:LYS33 4.3 19.0 1.0 CB C:ASP81 4.3 16.4 1.0 HB3 C:CSD158 4.4 22.0 0.3 HB3 C:CSD158 4.4 21.6 0.3 HB2 C:ASP81 4.4 19.7 1.0 HB2 C:CSD158 4.4 22.2 0.4 CB C:SER196 4.4 26.0 1.0 OG1 C:FLC303 4.4 28.5 0.9 HB3 C:ASP81 4.5 19.7 1.0 CA C:FLC303 4.5 48.1 0.9 HG1 C:FLC303 4.6 31.8 0.9 HA C:CSD158 4.6 20.4 0.4 NE2 C:HIS77 4.6 16.1 1.0 CE1 C:HIS77 4.6 15.9 1.0 HE3 C:LYS33 4.7 19.0 1.0 NE2 C:HIS139 4.7 18.8 1.0 OG C:SER196 4.7 26.8 1.0 HA C:CSD158 4.7 20.5 0.3 CD C:LYS33 4.7 15.4 1.0 HZ2 C:LYS161 4.7 37.6 1.0 HA C:CSD158 4.7 20.6 0.3 CAC C:FLC303 4.8 50.8 0.9 CE C:LYS33 4.8 15.8 1.0 HE1 C:HIS139 4.9 21.2 1.0 HA1 C:FLC303 4.9 57.8 0.9 CA C:CSD158 4.9 17.0 0.4 CA C:CSD158 4.9 17.1 0.3 CA C:CSD158 4.9 17.2 0.3 HD1 C:HIS197 4.9 31.0 1.0

Zinc binding site 4 out of 4 in the 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.8 Angstrom Crystal Structure of Imp-1 Metallo-Beta-Lactamase with A Mixed Iron-Zinc Center in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:21.6 occ:0.44 OD1 D:CSD158 1.9 23.5 0.3 OD2 D:CSD158 2.0 25.4 0.3 OD2 D:ASP81 2.0 18.1 1.0 NE2 D:HIS197 2.1 32.1 1.0 OHB D:FLC303 2.2 30.8 0.9 SG D:CSD158 2.3 21.9 0.4 SG D:CSD158 2.3 23.4 0.3 OG1 D:FLC303 2.4 30.1 0.9 SG D:CSD158 2.5 22.6 0.3 OB1 D:FLC303 2.6 19.6 0.9 HOB D:FLC303 2.8 36.9 0.9 CE1 D:HIS197 3.0 29.6 1.0 HE1 D:HIS197 3.1 35.6 1.0 OD2 D:CSD158 3.1 20.8 0.3 CB D:FLC303 3.1 32.8 0.9 CBC D:FLC303 3.1 25.0 0.9 CG D:ASP81 3.2 17.0 1.0 CD2 D:HIS197 3.2 31.8 1.0 OD1 D:CSD158 3.4 21.4 0.3 CGC D:FLC303 3.4 32.1 0.9 HD2 D:HIS197 3.5 38.2 1.0 CG D:FLC303 3.7 32.2 0.9 OD1 D:ASP81 3.8 18.5 1.0 CB D:CSD158 3.8 20.3 0.3 FE D:FE301 3.8 19.9 0.8 HB2 D:CSD158 3.8 24.4 0.3 HB3 D:CSD158 3.8 25.1 0.4 CB D:CSD158 3.8 19.7 0.3 CB D:CSD158 3.8 20.9 0.4 HD3 D:LYS33 3.8 22.1 1.0 HB3 D:SER196 3.9 34.5 1.0 HB2 D:CSD158 3.9 23.7 0.3 HG1 D:FLC303 4.0 38.6 0.9 HE1 D:HIS77 4.1 22.2 1.0 HG D:SER196 4.2 31.9 1.0 ND1 D:HIS197 4.2 28.8 1.0 HB2 D:SER196 4.2 34.5 1.0 OB2 D:FLC303 4.3 19.0 0.9 HE2 D:LYS33 4.3 22.5 1.0 CG D:HIS197 4.3 31.5 1.0 HB2 D:CSD158 4.4 25.1 0.4 CB D:ASP81 4.4 14.0 1.0 HB3 D:CSD158 4.4 23.7 0.3 HB3 D:CSD158 4.4 24.4 0.3 HB2 D:ASP81 4.4 16.8 1.0 CB D:SER196 4.4 28.7 1.0 CA D:FLC303 4.5 46.6 0.9 OG2 D:FLC303 4.5 30.1 0.9 HB3 D:ASP81 4.5 16.8 1.0 HZ1 D:LYS161 4.5 41.5 1.0 NE2 D:HIS77 4.6 16.3 1.0 NE2 D:HIS139 4.6 17.9 1.0 OA1 D:FLC303 4.6 50.4 0.9 HG2 D:FLC303 4.6 38.6 0.9 HE3 D:LYS33 4.6 22.5 1.0 HA D:CSD158 4.7 23.1 0.4 CE1 D:HIS77 4.7 18.5 1.0 CAC D:FLC303 4.7 56.8 0.9 CD D:LYS33 4.7 18.4 1.0 HA D:CSD158 4.7 23.1 0.3 HA D:CSD158 4.7 23.0 0.3 OG D:SER196 4.7 26.6 1.0 HE1 D:HIS139 4.7 20.9 1.0 CE D:LYS33 4.7 18.8 1.0 HA1 D:FLC303 4.8 56.0 0.9 CA D:CSD158 4.9 19.3 0.4 CA D:CSD158 4.9 19.3 0.3 CA D:CSD158 4.9 19.2 0.3 CE1 D:HIS139 4.9 17.4 1.0 HD1 D:HIS197 4.9 34.5 1.0

T.J.Carruthers, P.D.Carr, C.T.Loh, C.J.Jackson, G.Otting. Iron(III) Located in the Dinuclear Metallo-Beta-Lactamase Imp-1 By Pseudocontact Shifts. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25320022
DOI: 10.1002/ANIE.201408693