Zinc in PDB 2bmi: Metallo-Beta-Lactamase

All present enzymatic activity of Metallo-Beta-Lactamase:
3.5.2.6;

The structure of Metallo-Beta-Lactamase, PDB code: 2bmi was solved by A.Carfi, E.Duee, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.256, 94.920, 111.420, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.2

The structure of Metallo-Beta-Lactamase also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Metallo-Beta-Lactamase (pdb code 2bmi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Metallo-Beta-Lactamase, PDB code: 2bmi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the 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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn271 b:12.1 occ:1.00 O A:HOH276 1.8 6.8 1.0 NE2 A:HIS145 2.1 9.3 1.0 ND1 A:HIS84 2.1 7.5 1.0 NE2 A:HIS82 2.1 10.0 1.0 CD2 A:HIS145 3.0 10.2 1.0 CG A:HIS84 3.0 4.5 1.0 CE1 A:HIS82 3.0 7.8 1.0 CE1 A:HIS84 3.1 7.9 1.0 CE1 A:HIS145 3.1 11.4 1.0 CD2 A:HIS82 3.2 5.2 1.0 CB A:HIS84 3.3 6.1 1.0 ZN A:ZN272 3.4 10.0 1.0 O A:HOH410 3.5 25.2 1.0 O A:HOH492 3.9 9.7 1.0 OD1 A:ASP86 3.9 7.6 1.0 CG A:HIS145 4.2 11.9 1.0 CD2 A:HIS84 4.2 2.0 1.0 ND1 A:HIS82 4.2 7.8 1.0 SG A:CYS164 4.2 8.2 1.0 NE2 A:HIS84 4.2 4.2 1.0 ND1 A:HIS145 4.2 10.5 1.0 OD2 A:ASP86 4.3 6.1 1.0 CB A:CYS164 4.3 9.9 1.0 CG A:HIS82 4.3 7.8 1.0 CG A:ASP86 4.5 8.2 1.0 CA A:HIS84 4.8 9.0 1.0

Zinc binding site 2 out of 4 in the 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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn272 b:10.0 occ:1.00 O A:HOH276 1.9 6.8 1.0 NE2 A:HIS206 2.0 3.3 1.0 OD2 A:ASP86 2.2 6.1 1.0 O A:HOH492 2.2 9.7 1.0 SG A:CYS164 2.4 8.2 1.0 CD2 A:HIS206 3.0 2.4 1.0 CE1 A:HIS206 3.0 3.6 1.0 CG A:ASP86 3.2 8.2 1.0 ZN A:ZN271 3.4 12.1 1.0 CB A:CYS164 3.5 9.9 1.0 OD1 A:ASP86 3.6 7.6 1.0 O A:HOH410 3.9 25.2 1.0 NE2 A:HIS145 4.0 9.3 1.0 O A:HOH493 4.0 9.0 1.0 ND1 A:HIS206 4.2 2.8 1.0 CG A:HIS206 4.2 3.4 1.0 CE1 A:HIS145 4.2 11.4 1.0 O A:HOH288 4.5 4.1 1.0 CB A:ASP86 4.5 7.8 1.0 CE1 A:HIS82 4.5 7.8 1.0 NE2 A:HIS82 4.6 10.0 1.0 CA A:CYS164 4.7 9.3 1.0 CD2 A:HIS145 4.8 10.2 1.0

Zinc binding site 3 out of 4 in the 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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn271 b:11.2 occ:1.00 O B:HOH278 1.9 8.0 1.0 ND1 B:HIS84 2.1 8.4 1.0 NE2 B:HIS145 2.1 12.2 1.0 NE2 B:HIS82 2.1 5.8 1.0 CE1 B:HIS82 3.0 6.3 1.0 CD2 B:HIS145 3.0 8.5 1.0 CG B:HIS84 3.0 8.6 1.0 CE1 B:HIS84 3.1 7.0 1.0 CE1 B:HIS145 3.1 12.8 1.0 CD2 B:HIS82 3.2 7.7 1.0 CB B:HIS84 3.3 9.4 1.0 ZN B:ZN272 3.5 12.2 1.0 O B:HOH406 3.6 15.6 1.0 O B:HOH474 3.8 11.5 1.0 OD1 B:ASP86 4.0 8.8 1.0 ND1 B:HIS82 4.2 5.0 1.0 CG B:HIS145 4.2 8.7 1.0 CD2 B:HIS84 4.2 6.6 1.0 NE2 B:HIS84 4.2 9.2 1.0 ND1 B:HIS145 4.2 8.9 1.0 SG B:CYS164 4.2 8.9 1.0 OD2 B:ASP86 4.2 8.3 1.0 CB B:CYS164 4.3 5.8 1.0 CG B:HIS82 4.3 5.6 1.0 CG B:ASP86 4.6 9.4 1.0 CA B:HIS84 4.8 10.2 1.0

Zinc binding site 4 out of 4 in the 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 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn272 b:12.2 occ:1.00 O B:HOH278 1.9 8.0 1.0 NE2 B:HIS206 2.1 8.6 1.0 OD2 B:ASP86 2.1 8.3 1.0 O B:HOH474 2.2 11.5 1.0 SG B:CYS164 2.4 8.9 1.0 CD2 B:HIS206 3.0 9.6 1.0 CE1 B:HIS206 3.2 8.0 1.0 CG B:ASP86 3.2 9.4 1.0 ZN B:ZN271 3.5 11.2 1.0 CB B:CYS164 3.5 5.8 1.0 OD1 B:ASP86 3.6 8.8 1.0 O B:HOH475 4.0 8.1 1.0 CG B:HIS206 4.2 7.1 1.0 O B:HOH406 4.2 15.6 1.0 ND1 B:HIS206 4.2 7.2 1.0 NE2 B:HIS145 4.3 12.2 1.0 CB B:ASP86 4.5 6.7 1.0 CE1 B:HIS145 4.5 12.8 1.0 CE1 B:HIS82 4.5 6.3 1.0 O B:HOH291 4.5 6.3 1.0 NE2 B:HIS82 4.6 5.8 1.0 CA B:CYS164 4.7 9.0 1.0 O B:GLY205 4.9 8.7 1.0 CD2 B:HIS145 5.0 8.5 1.0

A.Carfi, E.Duee, R.Paul-Soto, M.Galleni, J.M.Frere, O.Dideberg. X-Ray Structure of the Znii Beta-Lactamase From Bacteroides Fragilis in An Orthorhombic Crystal Form. Acta Crystallogr.,Sect.D V. 54 45 1998.
ISSN: ISSN 0907-4449
PubMed: 9761816
DOI: 10.1107/S090744499700927X