Zinc in PDB 6ol8: Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin

The structure of Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin, PDB code: 6ol8 was solved by J.E.Raczynska, B.Imiolczyk, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.65 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.469, 76.449, 130.906, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.7

The structure of Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin (pdb code 6ol8). 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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin, PDB code: 6ol8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin


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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:28.1 occ:1.00 O A:HOH411 1.8 15.2 1.0 ND1 A:HIS122 1.9 28.2 1.0 NE2 A:HIS189 2.0 27.2 1.0 NE2 A:HIS120 2.1 30.1 1.0 OXT A:ZZ7308 2.2 34.9 0.9 CE1 A:HIS122 2.9 29.1 1.0 CG A:HIS122 2.9 27.6 1.0 CD2 A:HIS189 2.9 30.1 1.0 CE1 A:HIS189 3.0 26.9 1.0 CD2 A:HIS120 3.0 29.8 1.0 CE1 A:HIS120 3.1 27.4 1.0 C15 A:ZZ7308 3.1 36.1 0.9 CB A:HIS122 3.3 28.0 1.0 C14 A:ZZ7308 3.7 39.1 0.9 N3 A:ZZ7308 3.9 39.9 0.9 O4 A:ZZ7308 3.9 39.5 0.9 OD1 A:ASP124 4.0 26.4 1.0 NE2 A:HIS122 4.0 27.2 1.0 CD2 A:HIS122 4.0 26.3 1.0 ND1 A:HIS189 4.1 26.8 1.0 CG A:HIS189 4.1 28.2 1.0 CG2 A:THR190 4.2 22.4 1.0 CG A:HIS120 4.2 27.8 1.0 ND1 A:HIS120 4.2 26.9 1.0 SG A:CYS208 4.3 26.4 1.0 CB A:CYS208 4.3 26.4 1.0 ZN A:ZN302 4.4 30.4 1.0 C13 A:ZZ7308 4.4 40.5 0.9 C12 A:ZZ7308 4.7 36.7 0.9 O A:HOH480 4.7 38.5 1.0 CA A:HIS122 4.8 26.7 1.0 O1 A:ZZ7308 4.8 37.1 0.9 OD2 A:ASP124 4.8 26.5 1.0 CG A:ASP124 4.8 26.4 1.0 C2 A:ZZ7308 4.9 38.5 0.9

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin


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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.4 occ:1.00 NE2 A:HIS250 1.9 24.3 1.0 OD2 A:ASP124 2.0 26.5 1.0 O1 A:ZZ7308 2.1 37.1 0.9 N3 A:ZZ7308 2.2 39.9 0.9 SG A:CYS208 2.4 26.4 1.0 O A:HOH411 2.8 15.2 1.0 C2 A:ZZ7308 2.8 38.5 0.9 CD2 A:HIS250 2.9 29.1 1.0 CE1 A:HIS250 2.9 26.0 1.0 C12 A:ZZ7308 3.0 36.7 0.9 CG A:ASP124 3.1 26.4 1.0 C13 A:ZZ7308 3.2 40.5 0.9 CB A:CYS208 3.3 26.4 1.0 C16 A:ZZ7308 3.4 30.4 0.9 OD1 A:ASP124 3.7 26.4 1.0 C6 A:ZZ7308 3.8 39.9 0.9 CG A:HIS250 4.0 28.1 1.0 ND1 A:HIS250 4.0 26.1 1.0 CB A:SER249 4.1 26.6 1.0 OXT A:ZZ7308 4.1 34.9 0.9 O2 A:ZZ7308 4.1 27.4 0.9 C14 A:ZZ7308 4.3 39.1 0.9 CB A:ASP124 4.3 24.5 1.0 ZN A:ZN301 4.4 28.1 1.0 CA A:CYS208 4.4 26.5 1.0 S1 A:ZZ7308 4.4 42.8 0.9 NE2 A:HIS189 4.6 27.2 1.0 OG A:SER249 4.6 22.7 1.0 CE1 A:HIS189 4.7 26.9 1.0 C15 A:ZZ7308 4.7 36.1 0.9

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin


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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:29.8 occ:1.00 NE2 B:HIS189 1.8 32.5 1.0 O B:HOH407 1.9 21.4 1.0 ND1 B:HIS122 1.9 27.3 1.0 NE2 B:HIS120 2.2 30.6 1.0 OXT B:ZZ7305 2.2 40.7 0.9 CE1 B:HIS122 2.8 27.8 1.0 CE1 B:HIS189 2.9 29.7 1.0 CD2 B:HIS189 2.9 30.0 1.0 CG B:HIS122 2.9 26.1 1.0 CD2 B:HIS120 3.1 27.5 1.0 C15 B:ZZ7305 3.2 38.9 0.9 CE1 B:HIS120 3.2 29.5 1.0 CB B:HIS122 3.2 24.9 1.0 C14 B:ZZ7305 3.8 36.8 0.9 N3 B:ZZ7305 3.8 36.2 0.9 OD1 B:ASP124 3.9 28.5 1.0 ND1 B:HIS189 4.0 28.6 1.0 O4 B:ZZ7305 4.0 33.8 0.9 NE2 B:HIS122 4.0 25.6 1.0 CG B:HIS189 4.0 29.4 1.0 CD2 B:HIS122 4.0 25.8 1.0 SG B:CYS208 4.1 34.0 1.0 CG2 B:THR190 4.1 26.2 1.0 ZN B:ZN302 4.2 31.5 1.0 CB B:CYS208 4.2 32.8 1.0 CG B:HIS120 4.3 26.1 1.0 ND1 B:HIS120 4.3 26.6 1.0 C13 B:ZZ7305 4.4 41.3 0.9 C12 B:ZZ7305 4.6 28.9 0.9 OD2 B:ASP124 4.7 40.0 1.0 CA B:HIS122 4.7 26.0 1.0 CG B:ASP124 4.7 29.5 1.0 O B:HOH419 4.8 34.3 1.0 O1 B:ZZ7305 4.8 30.0 0.9 C2 B:ZZ7305 4.8 29.3 0.9

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin


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 Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:31.5 occ:1.00 NE2 B:HIS250 1.9 32.5 1.0 OD2 B:ASP124 2.0 40.0 1.0 O1 B:ZZ7305 2.1 30.0 0.9 N3 B:ZZ7305 2.2 36.2 0.9 SG B:CYS208 2.3 34.0 1.0 O B:HOH407 2.7 21.4 1.0 C2 B:ZZ7305 2.8 29.3 0.9 CD2 B:HIS250 2.9 31.3 1.0 CE1 B:HIS250 2.9 33.2 1.0 C12 B:ZZ7305 3.0 28.9 0.9 CG B:ASP124 3.1 29.5 1.0 C13 B:ZZ7305 3.3 41.3 0.9 CB B:CYS208 3.3 32.8 1.0 C16 B:ZZ7305 3.6 28.0 0.9 OD1 B:ASP124 3.6 28.5 1.0 C6 B:ZZ7305 3.8 31.0 0.9 OXT B:ZZ7305 3.9 40.7 0.9 ND1 B:HIS250 4.0 28.9 1.0 CG B:HIS250 4.0 30.8 1.0 O2 B:ZZ7305 4.1 25.5 0.9 CB B:SER249 4.1 29.9 1.0 ZN B:ZN301 4.2 29.8 1.0 C14 B:ZZ7305 4.3 36.8 0.9 CB B:ASP124 4.3 29.4 1.0 S1 B:ZZ7305 4.4 40.2 0.9 CA B:CYS208 4.4 31.4 1.0 NE2 B:HIS189 4.5 32.5 1.0 CE1 B:HIS189 4.5 29.7 1.0 OG B:SER249 4.5 27.2 1.0 C15 B:ZZ7305 4.6 38.9 0.9

J.E.Raczynska, J.Sliwiak, M.Komorowska, J.Czyrko, B.Imiolczyk, K.Brzezinski, M.Jaskolski. Flexible Loop of New Delhi Metall-Beta-Lactamase Modulates Its Activity Towards Different Substrates To Be Published.