Zinc in PDB 3i13: Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8

All present enzymatic activity of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8:
3.5.2.6;

The structure of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8, PDB code: 3i13 was solved by J.M.Gonzalez, A.Buschiazzo, A.J.Vila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.55 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.111, 61.410, 69.483, 90.00, 93.06, 90.00
R / Rfree (%)	15.9 / 21.7

The binding sites of Zinc atom in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8 (pdb code 3i13). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8, PDB code: 3i13:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn228 b:30.9 occ:1.00 ND1 A:HIS88 2.0 20.6 1.0 NE2 A:HIS149 2.0 21.8 1.0 O A:HOH306 2.1 23.5 1.0 NE2 A:HIS86 2.1 17.6 1.0 O A:HOH321 2.8 35.7 1.0 CD2 A:HIS149 2.9 16.4 1.0 CG A:HIS88 3.0 22.2 1.0 CE1 A:HIS88 3.0 18.3 1.0 CE1 A:HIS86 3.0 18.4 1.0 CD2 A:HIS86 3.1 22.5 1.0 CE1 A:HIS149 3.1 24.3 1.0 CB A:HIS88 3.3 23.5 1.0 ZN A:ZN229 3.7 37.4 0.5 OD1 A:ASP90 4.0 39.1 1.0 NE2 A:HIS88 4.1 21.2 1.0 CD2 A:HIS88 4.1 23.0 1.0 ND1 A:HIS86 4.1 19.3 1.0 CG A:HIS149 4.1 19.0 1.0 ND1 A:HIS149 4.2 16.1 1.0 CG A:HIS86 4.2 16.7 1.0 CG2 A:THR150 4.2 18.4 1.0 CB A:CYS168 4.3 20.1 0.5 O A:HOH393 4.4 29.4 0.5 CB A:CYS168 4.4 20.6 0.5 SG A:CYS168 4.5 18.8 0.5 SG A:CYS168 4.5 18.2 0.5 OD2 A:ASP90 4.5 40.1 1.0 CG A:ASP90 4.7 34.8 1.0 CA A:HIS88 4.8 24.5 1.0

Zinc binding site 2 out of 2 in the Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacillus Cereus Zn-Dependent Metallo-Beta-Lactamase at pH 5.8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn229 b:37.4 occ:0.50 SG A:CYS168 1.8 18.8 0.5 O A:HOH306 2.2 23.5 1.0 O A:HOH393 2.2 29.4 0.5 SG A:CYS168 2.3 18.2 0.5 OD2 A:ASP90 2.4 40.1 1.0 NE2 A:HIS210 2.5 35.1 1.0 CB A:CYS168 3.2 20.6 0.5 CB A:CYS168 3.2 20.1 0.5 CD2 A:HIS210 3.3 34.2 1.0 CG A:ASP90 3.5 34.8 1.0 CE1 A:HIS210 3.5 32.6 1.0 ZN A:ZN228 3.7 30.9 1.0 OD1 A:ASP90 3.8 39.1 1.0 NE2 A:HIS149 4.1 21.8 1.0 CE1 A:HIS86 4.2 18.4 1.0 NH1 A:ARG91 4.2 34.5 1.0 NE A:ARG91 4.2 29.8 1.0 O A:HOH321 4.3 35.7 1.0 NE2 A:HIS86 4.4 17.6 1.0 CA A:CYS168 4.4 19.0 0.5 CE1 A:HIS149 4.4 24.3 1.0 CA A:CYS168 4.5 19.5 0.5 CG A:HIS210 4.5 28.4 1.0 ND1 A:HIS210 4.6 33.7 1.0 CZ A:ARG91 4.7 32.6 1.0 O A:HOH402 4.7 36.4 1.0 CB A:ASP90 4.7 31.5 1.0 CD2 A:HIS149 4.8 16.4 1.0 N A:CYS168 4.9 20.1 0.5 O A:HOH303 4.9 50.8 1.0

J.M.Gonzalez, A.Buschiazzo, A.J.Vila. Evidence of Adaptability in Metal Coordination Geometry and Active-Site Loop Conformation Among B1 Metallo-Beta-Lactamases . Biochemistry V. 49 7930 2010.
ISSN: ISSN 0006-2960
PubMed: 20677753
DOI: 10.1021/BI100894R