Zinc in PDB 6c6i: Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop

All present enzymatic activity of Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop:
3.5.2.6;

The structure of Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop, PDB code: 6c6i was solved by L.Otero, E.Giannini, S.Klinke, A.Palacios, M.Mojica, R.Bonomo, L.Llarrull, A.Vila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.16 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.289, 39.250, 73.873, 90.89, 93.10, 90.02
R / Rfree (%)	20.3 / 22.9

The binding sites of Zinc atom in the Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop (pdb code 6c6i). 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 A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop, PDB code: 6c6i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop


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 A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.9 occ:1.00 ND1 A:HIS122 2.0 18.1 1.0 O A:HOH446 2.0 14.8 1.0 NE2 A:HIS189 2.0 10.8 1.0 NE2 A:HIS120 2.1 11.8 1.0 CD2 A:HIS189 3.0 11.4 1.0 CG A:HIS122 3.0 16.4 1.0 CE1 A:HIS122 3.0 17.4 1.0 CE1 A:HIS120 3.0 11.7 1.0 CD2 A:HIS120 3.1 12.3 1.0 CE1 A:HIS189 3.1 12.2 1.0 CB A:HIS122 3.3 13.0 1.0 ZN A:ZN302 3.9 17.8 1.0 OD1 A:ASP124 4.0 15.1 1.0 O A:HOH500 4.0 22.5 1.0 SG A:CYS208 4.1 14.1 1.0 NE2 A:HIS122 4.1 17.5 1.0 CD2 A:HIS122 4.1 17.9 1.0 CG A:HIS189 4.1 11.0 1.0 ND1 A:HIS120 4.2 13.0 1.0 CG A:HIS120 4.2 11.0 1.0 ND1 A:HIS189 4.2 12.3 1.0 CB A:CYS208 4.3 11.2 1.0 CG2 A:THR190 4.4 12.0 1.0 OD2 A:ASP124 4.7 19.7 1.0 CG A:ASP124 4.8 17.6 1.0 CA A:HIS122 4.8 11.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop


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 A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.8 occ:1.00 NE2 A:HIS250 2.0 15.6 1.0 OD2 A:ASP124 2.0 19.7 1.0 SG A:CYS208 2.3 14.1 1.0 O A:HOH500 2.3 22.5 1.0 O A:HOH446 2.4 14.8 1.0 CE1 A:HIS250 3.0 15.4 1.0 CD2 A:HIS250 3.0 15.9 1.0 CG A:ASP124 3.1 17.6 1.0 CB A:CYS208 3.3 11.2 1.0 OD1 A:ASP124 3.5 15.1 1.0 ZN A:ZN301 3.9 17.9 1.0 ND1 A:HIS250 4.1 16.1 1.0 CG A:HIS250 4.1 15.4 1.0 CB A:SER249 4.2 11.3 1.0 NE2 A:HIS189 4.4 10.8 1.0 CB A:ASP124 4.4 14.9 1.0 CA A:CYS208 4.5 10.5 1.0 OG A:SER249 4.6 12.0 1.0 CE1 A:HIS189 4.6 12.2 1.0 CE1 A:HIS120 4.7 11.7 1.0 NE2 A:HIS120 4.8 11.8 1.0 CE A:LYS125 4.8 20.6 1.0 CH2 A:TRP70 5.0 26.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop


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 A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.9 occ:1.00 O B:HOH410 1.9 19.9 1.0 ND1 B:HIS122 2.0 16.5 1.0 NE2 B:HIS189 2.0 14.2 1.0 NE2 B:HIS120 2.1 10.6 1.0 CD2 B:HIS189 3.0 14.3 1.0 CG B:HIS122 3.0 14.7 1.0 CE1 B:HIS122 3.0 15.9 1.0 CE1 B:HIS120 3.0 10.1 1.0 CD2 B:HIS120 3.1 11.4 1.0 CE1 B:HIS189 3.1 14.7 1.0 CB B:HIS122 3.3 11.6 1.0 ZN B:ZN302 3.9 17.7 1.0 OD1 B:ASP124 4.0 15.6 1.0 O B:HOH485 4.0 24.7 1.0 SG B:CYS208 4.0 14.3 1.0 NE2 B:HIS122 4.1 16.4 1.0 CG B:HIS189 4.1 12.5 1.0 CD2 B:HIS122 4.1 16.7 1.0 ND1 B:HIS120 4.2 12.2 1.0 CG B:HIS120 4.2 10.0 1.0 ND1 B:HIS189 4.2 14.6 1.0 CB B:CYS208 4.2 11.6 1.0 CG2 B:THR190 4.4 12.5 1.0 OD2 B:ASP124 4.7 23.2 1.0 CG B:ASP124 4.8 19.0 1.0 CA B:HIS122 4.8 10.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop


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 A Chimeric Ndm-1 Metallo-Beta-Lactamase Harboring the Imp-1 L3 Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.7 occ:1.00 NE2 B:HIS250 2.0 16.2 1.0 OD2 B:ASP124 2.1 23.2 1.0 O B:HOH485 2.2 24.7 1.0 SG B:CYS208 2.3 14.3 1.0 O B:HOH410 2.5 19.9 1.0 CE1 B:HIS250 3.0 16.2 1.0 CD2 B:HIS250 3.0 16.5 1.0 CG B:ASP124 3.1 19.0 1.0 CB B:CYS208 3.3 11.6 1.0 OD1 B:ASP124 3.6 15.6 1.0 ZN B:ZN301 3.9 17.9 1.0 ND1 B:HIS250 4.1 17.4 1.0 CG B:HIS250 4.1 16.8 1.0 CB B:SER249 4.2 12.5 1.0 CB B:ASP124 4.4 14.1 1.0 NE2 B:HIS189 4.4 14.2 1.0 CA B:CYS208 4.5 10.6 1.0 OG B:SER249 4.5 14.2 1.0 CE1 B:HIS189 4.7 14.7 1.0 CE1 B:HIS120 4.8 10.1 1.0 CE B:LYS125 4.8 26.6 1.0 NE2 B:HIS120 4.9 10.6 1.0 CH2 B:TRP70 5.0 29.3 1.0

A.R.Palacios, M.F.Mojica, E.Giannini, M.A.Taracila, C.R.Bethel, P.M.Alzari, L.H.Otero, S.Klinke, L.I.Llarrull, R.A.Bonomo, A.J.Vila. The Reaction Mechanism of Metallo-Beta-Lactamases Is Tuned By the Conformation of An Active-Site Mobile Loop. Antimicrob. Agents V. 63 2019CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 30348667
DOI: 10.1128/AAC.01754-18