Chlorine 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:

Zinc	(Zn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Ndm-12 Metallo-Beta-Lactamase in Complex with Hydrolyzed Ampicillin, PDB code: 6ol8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl303 b:33.6 occ:1.00 N A:PRO56 3.4 27.6 1.0 C A:ALA55 3.5 28.4 1.0 CD A:PRO56 3.5 28.5 1.0 CA A:ALA55 3.5 27.5 1.0 N A:ALA55 3.9 28.1 1.0 O A:ALA55 4.1 27.2 1.0 CA A:PRO56 4.2 27.5 1.0 C A:LEU54 4.3 28.2 1.0 O A:LEU54 4.3 29.6 1.0 CG A:GLN53 4.4 32.1 1.0 CG A:PRO56 4.5 28.8 1.0 CD A:GLN53 4.5 32.4 1.0 NE2 A:GLN53 4.6 37.9 1.0 CB A:ALA55 4.9 28.2 1.0 O A:HOH459 4.9 31.9 1.0 OE1 A:GLN53 5.0 40.6 1.0

Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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:Cl304 b:35.0 occ:1.00 N A:LYS242 3.0 33.7 1.0 C A:PHE240 3.2 27.5 1.0 CA A:PHE240 3.4 27.4 1.0 N A:PRO241 3.4 28.4 1.0 CB A:LYS242 3.5 45.2 1.0 CD A:PRO241 3.5 29.0 1.0 CA A:LYS242 3.5 39.0 1.0 N A:ALA243 3.6 29.2 1.0 O A:PHE240 3.7 30.1 1.0 C A:LYS242 3.8 36.0 1.0 CB A:PHE240 4.1 28.2 1.0 C A:PRO241 4.1 31.9 1.0 CG A:PRO241 4.3 28.8 1.0 CG A:LYS242 4.3 54.6 1.0 CA A:PRO241 4.3 30.1 1.0 O A:HOH473 4.6 40.9 1.0 N A:PHE240 4.6 27.7 1.0 CD1 A:PHE240 4.6 28.2 1.0 CA A:ALA243 4.7 29.7 1.0 O A:ALA239 4.7 31.7 1.0 CB A:ALA243 4.7 27.4 1.0 O A:LYS242 4.8 43.7 1.0 O A:HOH508 4.8 31.3 1.0 CG A:PHE240 4.9 28.7 1.0 CB A:PRO241 5.0 31.5 1.0

Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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 A:Cl305 b:45.4 occ:1.00 ND2 A:ASN166 3.2 31.8 1.0 CB B:ARG85 3.8 39.7 1.0 CB A:ASN166 3.9 29.8 1.0 CG B:PRO112 4.0 38.2 1.0 CG A:ASN166 4.0 29.9 1.0 CB B:ALA114 4.2 35.7 1.0 CB B:PRO112 4.3 36.7 1.0 CD B:ARG85 4.4 39.7 1.0 CA B:ALA114 4.5 35.9 1.0 O B:HOH498 4.7 31.8 1.0 CG B:ARG85 4.7 36.4 1.0 O A:HOH497 4.8 23.2 1.0 CA B:ARG85 4.8 36.5 1.0 O A:HOH522 4.9 39.6 1.0 N B:ALA114 4.9 35.6 1.0

Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl 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 A:Cl306 b:54.3 occ:0.70 CE1 A:HIS261 3.8 35.1 1.0 ND1 A:HIS261 4.0 37.2 1.0 NH2 A:ARG264 4.0 62.6 1.0 CG A:MET265 4.1 39.8 1.0 CE A:LYS268 4.3 77.3 1.0 NE A:ARG264 4.3 52.0 1.0 N A:MET265 4.3 33.1 1.0 CB A:ARG264 4.4 38.7 1.0 CZ A:ARG264 4.5 54.7 1.0 C A:ARG264 4.6 34.5 1.0 CA A:MET265 4.6 36.2 1.0 NE2 A:HIS261 4.8 33.1 1.0 O A:HIS261 4.9 34.8 1.0 O A:ARG264 4.9 34.0 1.0 CB A:MET265 5.0 38.1 1.0

Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl303 b:41.4 occ:1.00 O B:HOH500 3.0 39.0 1.0 N B:ASN57 3.2 35.1 1.0 ND2 B:ASN57 3.5 36.2 1.0 CB B:ASN57 3.5 34.0 1.0 CB B:ALA55 3.7 36.3 1.0 CD B:PRO56 3.8 46.3 1.0 N B:PRO56 3.8 43.9 1.0 CA B:ASN57 3.8 37.5 1.0 CB B:PRO56 3.9 42.6 1.0 CG2 B:THR201 3.9 40.9 1.0 CG B:ASN57 4.0 38.1 1.0 C B:PRO56 4.1 40.9 1.0 CA B:PRO56 4.2 41.4 1.0 C B:ALA55 4.2 37.2 1.0 CG B:PRO56 4.2 45.8 1.0 C B:ASN57 4.4 34.8 1.0 CG2 B:VAL58 4.4 34.0 1.0 CA B:ALA55 4.5 37.5 1.0 N B:VAL58 4.5 36.6 1.0 O B:ALA55 4.8 42.2 1.0 CB B:THR201 4.9 41.5 1.0

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.