Zinc in PDB 5b3r: Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa:
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa, PDB code: 5b3r was solved by A.Shimizu-Ibuka, Y.Ishii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.550, 87.380, 105.750, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.2

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa (pdb code 5b3r). 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-18 From Pseudomonas Aeruginosa, PDB code: 5b3r:
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-18 From Pseudomonas Aeruginosa


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-18 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:26.4 occ:1.00 ND1 A:HIS97 2.0 24.4 1.0 O5 A:CIT2003 2.0 27.2 1.0 NE2 A:HIS157 2.1 32.0 1.0 NE2 A:HIS95 2.2 22.2 1.0 C6 A:CIT2003 2.7 30.0 1.0 O6 A:CIT2003 2.7 27.9 1.0 CE1 A:HIS97 3.0 25.2 1.0 CG A:HIS97 3.0 24.4 1.0 CD2 A:HIS95 3.0 21.8 1.0 CD2 A:HIS157 3.1 31.0 1.0 CE1 A:HIS157 3.2 31.0 1.0 CB A:HIS97 3.3 25.2 1.0 CE1 A:HIS95 3.4 24.6 1.0 ZN A:ZN2002 3.6 18.4 0.5 OD1 A:ASP99 3.7 25.6 1.0 SG A:CYS176 3.9 27.2 1.0 NE2 A:HIS97 4.1 25.3 1.0 O4 A:CIT2003 4.1 33.2 1.0 CB A:CYS176 4.1 26.4 1.0 CD2 A:HIS97 4.1 24.4 1.0 C3 A:CIT2003 4.2 30.9 1.0 CG A:HIS95 4.2 22.0 1.0 CG A:HIS157 4.2 31.0 1.0 ND1 A:HIS157 4.3 30.7 1.0 OD2 A:ASP99 4.4 25.8 1.0 ND1 A:HIS95 4.4 23.6 1.0 CG A:ASP99 4.5 26.4 1.0 C5 A:CIT2003 4.5 32.8 1.0 CG2 A:THR158 4.7 27.3 1.0 O7 A:CIT2003 4.7 31.2 1.0 CA A:HIS97 4.8 25.6 1.0 C4 A:CIT2003 4.9 32.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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-18 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:18.4 occ:0.50 NE2 A:HIS215 1.9 21.0 1.0 O5 A:CIT2003 2.0 27.2 1.0 O4 A:CIT2003 2.1 33.2 1.0 OD2 A:ASP99 2.2 25.8 1.0 O7 A:CIT2003 2.2 31.2 1.0 SG A:CYS176 2.3 27.2 1.0 CE1 A:HIS215 2.7 25.0 1.0 C6 A:CIT2003 2.7 30.0 1.0 C3 A:CIT2003 2.9 30.9 1.0 CD2 A:HIS215 3.0 25.1 1.0 C5 A:CIT2003 3.1 32.8 1.0 CG A:ASP99 3.3 26.4 1.0 C4 A:CIT2003 3.4 32.0 1.0 CB A:CYS176 3.5 26.4 1.0 ZN A:ZN2001 3.6 26.4 1.0 OD1 A:ASP99 3.7 25.6 1.0 O6 A:CIT2003 3.9 27.9 1.0 ND1 A:HIS215 3.9 24.0 1.0 CG A:HIS215 4.0 24.2 1.0 O3 A:CIT2003 4.3 29.2 1.0 C2 A:CIT2003 4.3 34.5 1.0 O1 A:CIT2003 4.3 38.5 1.0 NE2 A:HIS157 4.3 32.0 1.0 CB A:SER214 4.4 25.2 1.0 NE2 A:HIS95 4.4 22.2 1.0 CA A:CYS176 4.5 25.6 1.0 CE1 A:HIS95 4.6 24.6 1.0 CB A:ASP99 4.6 25.6 1.0 C1 A:CIT2003 4.7 36.9 1.0 OG A:SER214 4.7 27.0 1.0 CE1 A:HIS157 4.7 31.0 1.0 CD A:LYS51 4.8 21.1 1.0 CE A:LYS51 4.9 21.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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-18 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:22.2 occ:1.00 O5 B:CIT2003 1.9 25.6 1.0 ND1 B:HIS97 2.0 20.5 1.0 NE2 B:HIS157 2.0 24.1 1.0 NE2 B:HIS95 2.2 20.6 1.0 C6 B:CIT2003 2.7 25.9 1.0 O6 B:CIT2003 2.8 23.3 1.0 CE1 B:HIS97 3.0 21.7 1.0 CD2 B:HIS95 3.0 19.6 1.0 CE1 B:HIS157 3.0 24.6 1.0 CG B:HIS97 3.1 20.6 1.0 CD2 B:HIS157 3.1 23.6 1.0 CE1 B:HIS95 3.3 21.2 1.0 CB B:HIS97 3.4 20.2 1.0 OD1 B:ASP99 3.8 23.5 1.0 SG B:CYS176 4.0 21.1 1.0 NE2 B:HIS97 4.1 21.1 1.0 O3 B:CIT2003 4.1 21.6 1.0 CB B:CYS176 4.1 19.3 1.0 ZN B:ZN2002 4.1 29.4 1.0 ND1 B:HIS157 4.1 24.0 1.0 C3 B:CIT2003 4.1 25.4 1.0 CD2 B:HIS97 4.1 20.9 1.0 CG B:HIS157 4.2 24.1 1.0 CG B:HIS95 4.2 19.4 1.0 ND1 B:HIS95 4.3 20.1 1.0 C5 B:CIT2003 4.5 23.6 1.0 O7 B:CIT2003 4.6 25.4 1.0 CG B:ASP99 4.6 22.8 1.0 CG2 B:THR158 4.6 21.9 1.0 OD2 B:ASP99 4.7 24.7 1.0 CA B:HIS97 4.8 20.9 1.0 C4 B:CIT2003 4.9 24.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Metallo-Beta-Lactamase Imp-18 From Pseudomonas Aeruginosa


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-18 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:29.4 occ:1.00 NE2 B:HIS215 2.1 23.3 1.0 O3 B:CIT2003 2.1 21.6 1.0 O7 B:CIT2003 2.1 25.4 1.0 SG B:CYS176 2.3 21.1 1.0 OD2 B:ASP99 2.7 24.7 1.0 O5 B:CIT2003 2.7 25.6 1.0 C3 B:CIT2003 2.9 25.4 1.0 CE1 B:HIS215 3.0 23.9 1.0 C5 B:CIT2003 3.0 23.6 1.0 CD2 B:HIS215 3.1 24.2 1.0 C6 B:CIT2003 3.1 25.9 1.0 C4 B:CIT2003 3.2 24.3 1.0 CB B:CYS176 3.4 19.3 1.0 CG B:ASP99 3.7 22.8 1.0 OD1 B:ASP99 4.1 23.5 1.0 ZN B:ZN2001 4.1 22.2 1.0 ND1 B:HIS215 4.1 24.9 1.0 CB B:SER214 4.2 22.2 1.0 O4 B:CIT2003 4.2 24.2 1.0 CG B:HIS215 4.2 24.3 1.0 O2 B:CIT2003 4.3 32.1 1.0 O6 B:CIT2003 4.3 23.3 1.0 C2 B:CIT2003 4.3 28.4 1.0 CA B:CYS176 4.4 20.6 1.0 OG B:SER214 4.6 22.9 1.0 NE2 B:HIS157 4.6 24.1 1.0 CE B:LYS179 4.7 22.4 1.0 CE1 B:HIS157 4.8 24.6 1.0 NZ B:LYS179 4.8 22.0 1.0 C1 B:CIT2003 4.8 30.5 1.0 NE2 B:HIS95 4.9 20.6 1.0 CD B:LYS51 4.9 20.0 1.0 CB B:ASP99 5.0 22.8 1.0

T.Furuyama, H.Nonomura, Y.Ishii, N.D.Hanson, A.Shimizu-Ibuka. Structural and Mutagenic Analysis of Metallo-Beta-Lactamase Imp-18 Antimicrob. Agents V. 60 5521 2016CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 27381398
DOI: 10.1128/AAC.00985-16