Chlorine in PDB 6p97: Oxa-48 Carbapanemase, Imipenem Complex

All present enzymatic activity of Oxa-48 Carbapanemase, Imipenem Complex:
3.5.2.6;

The structure of Oxa-48 Carbapanemase, Imipenem Complex, PDB code: 6p97 was solved by C.A.Smith, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.11 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.131, 76.210, 101.130, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.3

The structure of Oxa-48 Carbapanemase, Imipenem Complex also contains other interesting chemical elements:

Cadmium	(Cd)	2 atoms
Calcium	(Ca)	5 atoms

The binding sites of Chlorine atom in the Oxa-48 Carbapanemase, Imipenem Complex (pdb code 6p97). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Oxa-48 Carbapanemase, Imipenem Complex, PDB code: 6p97:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Oxa-48 Carbapanemase, Imipenem Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Oxa-48 Carbapanemase, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:29.5 occ:1.00 NZ A:LYS73 2.9 22.8 1.0 NE1 A:TRP157 3.1 20.4 1.0 O A:HOH543 3.1 21.1 1.0 CE A:LYS73 3.5 25.4 1.0 CG A:LYS73 3.6 19.1 1.0 CG2 A:VAL120 3.8 24.3 1.0 CE2 A:TRP157 3.9 18.9 1.0 CD1 A:TRP157 4.0 20.8 1.0 CB A:TYR123 4.1 23.2 1.0 OG A:SER70 4.2 31.4 1.0 CA A:VAL120 4.2 23.2 1.0 CD A:LYS73 4.2 22.5 1.0 CA A:SER70 4.2 19.9 1.0 CZ2 A:TRP157 4.2 20.5 1.0 CG1 A:VAL120 4.3 25.4 1.0 CB A:VAL120 4.3 26.6 1.0 CB A:SER70 4.5 25.2 1.0 CG A:TYR123 4.6 22.8 1.0 O A:VAL120 4.8 22.9 1.0 O A:ALA69 4.9 18.5 1.0 N A:SER70 4.9 19.1 1.0 CD2 A:LEU158 4.9 28.8 1.0 CB A:LYS73 5.0 17.6 1.0

Chlorine binding site 2 out of 4 in the Oxa-48 Carbapanemase, Imipenem Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Oxa-48 Carbapanemase, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:21.9 occ:1.00 O A:HOH580 3.1 36.3 1.0 O B:HOH548 3.1 33.6 1.0 NH1 A:ARG206 3.2 16.5 1.0 NH1 B:ARG206 3.2 17.5 1.0 NH2 B:ARG206 3.2 18.7 1.0 NH2 A:ARG206 3.2 17.7 1.0 CZ B:ARG206 3.6 21.2 1.0 CZ A:ARG206 3.6 21.2 1.0 CD2 B:LEU196 4.2 21.2 1.0 CA A:GLN193 4.2 18.6 1.0 CA B:GLN193 4.3 20.3 1.0 CD2 A:LEU196 4.3 19.1 1.0 CG A:GLN193 4.4 17.4 1.0 CG B:GLN193 4.4 22.1 1.0 CB A:GLN193 4.5 16.1 1.0 CB B:GLN193 4.5 21.7 1.0 O A:GLN193 4.8 18.5 1.0 CB A:LEU196 4.9 15.8 1.0 CB B:LEU196 4.9 15.5 1.0 NE B:ARG206 4.9 18.9 1.0 O B:GLN193 4.9 20.1 1.0 NE A:ARG206 5.0 20.0 1.0 CG B:LEU196 5.0 20.0 1.0

Chlorine binding site 3 out of 4 in the Oxa-48 Carbapanemase, Imipenem Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Oxa-48 Carbapanemase, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:32.3 occ:1.00 NZ B:LYS73 3.0 26.9 1.0 NE1 B:TRP157 3.0 23.8 1.0 O B:HOH507 3.1 23.9 1.0 CE B:LYS73 3.5 25.9 1.0 CG B:LYS73 3.6 25.6 1.0 CG2 B:VAL120 3.9 28.7 1.0 CE2 B:TRP157 3.9 24.5 1.0 CD1 B:TRP157 4.0 25.6 1.0 CB B:TYR123 4.1 21.8 1.0 CG1 B:VAL120 4.1 29.0 1.0 CA B:VAL120 4.1 24.3 1.0 CA B:SER70 4.2 24.3 1.0 CD B:LYS73 4.2 24.5 1.0 CZ2 B:TRP157 4.2 23.3 1.0 CB B:VAL120 4.3 27.0 1.0 OG B:SER70 4.3 40.6 1.0 CB B:SER70 4.5 33.5 1.0 CG B:TYR123 4.7 24.5 1.0 O B:VAL120 4.7 23.3 1.0 O B:ALA69 4.8 26.1 1.0 N B:SER70 4.9 24.4 1.0 CD2 B:LEU158 4.9 32.0 1.0 C B:VAL120 5.0 24.2 1.0 CB B:LYS73 5.0 20.2 1.0

Chlorine binding site 4 out of 4 in the Oxa-48 Carbapanemase, Imipenem Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Oxa-48 Carbapanemase, Imipenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl303 b:23.6 occ:1.00 O B:HOH562 2.4 33.3 1.0 O B:HOH557 2.5 41.0 1.0 O B:HOH556 2.6 27.8 1.0 O B:HOH513 3.7 33.3 1.0 CG B:LYS175 4.1 24.5 1.0 CE B:LYS175 4.3 33.7 1.0 CD B:LYS175 4.8 26.6 1.0 NZ B:LYS175 4.8 31.2 1.0 CD B:LYS180 5.0 51.4 1.0

C.A.Smith, N.K.Stewart, M.Toth, S.B.Vakulenko. Structural Insights Into the Mechanism of Carbapenemase Activity of the Oxa-48 Beta-Lactamase. Antimicrob.Agents Chemother. V. 63 2019.
ISSN: ESSN 1098-6596
PubMed: 31358584
DOI: 10.1128/AAC.01202-19