Zinc in PDB 7ev5: Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase

The structure of Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase, PDB code: 7ev5 was solved by S.X.Au, N.D.Muhd Noor, H.Matsumura, R.N.Z.R.A.Rahman, Y.M.Normi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.26 / 1.44
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.356, 55.356, 143.094, 90, 90, 90
R / Rfree (%)	18.4 / 20.9

The structure of Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase also contains other interesting chemical elements:

Iodine

(I)

11 atoms

The binding sites of Zinc atom in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase (pdb code 7ev5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase, PDB code: 7ev5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bleg-1 B3 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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.1 occ:1.00 O A:HOH422 1.9 11.6 1.0 NE2 A:HIS131 2.1 8.7 1.0 NE2 A:HIS54 2.1 8.6 1.0 ND1 A:HIS56 2.1 9.8 1.0 OD2 A:ASP150 2.6 9.5 1.0 CD2 A:HIS54 3.0 8.8 1.0 CE1 A:HIS131 3.0 10.2 1.0 CE1 A:HIS56 3.0 9.2 1.0 CD2 A:HIS131 3.1 8.8 1.0 CE1 A:HIS54 3.1 8.6 1.0 CG A:HIS56 3.1 9.8 1.0 ZN A:ZN302 3.3 11.6 1.0 CB A:HIS56 3.5 9.1 1.0 CG A:ASP150 3.6 9.3 1.0 NE2 A:HIS59 3.9 7.9 1.0 CB A:ASP150 4.0 9.5 1.0 O A:HOH533 4.1 18.1 1.0 CD2 A:HIS59 4.1 9.2 1.0 ND1 A:HIS131 4.2 10.6 1.0 CG A:HIS54 4.2 7.0 1.0 NE2 A:HIS56 4.2 11.5 1.0 ND1 A:HIS54 4.2 8.8 1.0 CG A:HIS131 4.2 9.7 1.0 CD2 A:HIS56 4.3 12.5 1.0 OD1 A:ASP58 4.3 12.3 1.0 OD1 A:ASP150 4.6 10.0 1.0 CE1 A:HIS59 4.8 8.5 1.0 OD2 A:ASP58 4.8 10.1 1.0 CA A:HIS56 4.9 9.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bleg-1 B3 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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.6 occ:1.00 O A:HOH422 2.0 11.6 1.0 NE2 A:HIS191 2.0 10.6 1.0 OD2 A:ASP150 2.0 9.5 1.0 NE2 A:HIS59 2.1 7.9 1.0 OD2 A:ASP58 2.3 10.1 1.0 CD2 A:HIS59 3.0 9.2 1.0 CE1 A:HIS191 3.0 12.2 1.0 CG A:ASP150 3.0 9.3 1.0 CD2 A:HIS191 3.0 10.7 1.0 CE1 A:HIS59 3.1 8.5 1.0 OD1 A:ASP150 3.3 10.0 1.0 CG A:ASP58 3.3 8.8 1.0 ZN A:ZN301 3.3 11.1 1.0 O A:HOH533 3.5 18.1 1.0 OD1 A:ASP58 3.5 12.3 1.0 ND1 A:HIS191 4.1 11.8 1.0 NE2 A:HIS54 4.1 8.6 1.0 CG A:HIS59 4.2 8.6 1.0 CG A:HIS191 4.2 11.5 1.0 ND1 A:HIS59 4.2 8.2 1.0 CE1 A:HIS54 4.2 8.6 1.0 CB A:ASP150 4.4 9.5 1.0 OG1 A:THR12 4.4 12.5 1.0 CG2 A:THR12 4.4 11.4 1.0 CB A:ASP58 4.7 10.1 1.0 NE2 A:HIS131 4.7 8.7 1.0 O A:HOH596 5.0 25.5 1.0

S.X.Au, N.S.Dzulkifly, N.D.Muhd Noor, H.Matsumura, R.N.Z.R.A.Rahman, Y.M.Normi. Dual Activity Bleg-1 From Bacillus Lehensis G1 Revealed Structural Resemblance to B3 Metallo-Beta-Lactamase and Glyoxalase II: An Insight Into Its Enzyme Promiscuity and Evolutionary Divergence Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22179377