Chlorine in PDB 6p99: Oxa-48 Carbapanemase, Ertapenem Complex

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

The structure of Oxa-48 Carbapanemase, Ertapenem Complex, PDB code: 6p99 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)	38.41 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.883, 76.822, 101.247, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.7

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

Cadmium	(Cd)	3 atoms
Calcium	(Ca)	3 atoms

The binding sites of Chlorine atom in the Oxa-48 Carbapanemase, Ertapenem Complex (pdb code 6p99). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Oxa-48 Carbapanemase, Ertapenem Complex, PDB code: 6p99:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Oxa-48 Carbapanemase, Ertapenem 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, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:55.5 occ:1.00 NZ A:LYS73 2.3 40.8 1.0 NE1 A:TRP157 2.9 36.9 1.0 O A:HOH627 3.2 33.6 1.0 CE A:LYS73 3.4 39.3 1.0 OG A:SER70 3.6 49.4 1.0 CG2 A:VAL120 3.7 47.8 1.0 CG A:LYS73 3.7 36.9 1.0 CD1 A:TRP157 3.8 36.7 1.0 CE2 A:TRP157 3.8 36.3 1.0 CD A:LYS73 4.0 39.7 1.0 CZ2 A:TRP157 4.1 41.4 1.0 CA A:SER70 4.2 34.6 1.0 CA A:VAL120 4.3 42.3 1.0 CB A:TYR123 4.3 40.1 1.0 CB A:VAL120 4.3 48.0 1.0 CG1 A:VAL120 4.4 43.1 1.0 CB A:SER70 4.4 39.1 1.0 CG A:TYR123 4.8 36.4 1.0 CD2 A:LEU158 4.8 44.4 1.0 O A:VAL120 4.9 45.1 1.0 CG A:TRP157 5.0 41.5 1.0 N A:SER70 5.0 30.0 1.0 O A:ALA69 5.0 36.4 1.0 CD2 A:TRP157 5.0 40.3 1.0

Chlorine binding site 2 out of 3 in the Oxa-48 Carbapanemase, Ertapenem 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, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:41.9 occ:1.00 NH1 B:ARG206 3.1 30.8 1.0 NH1 A:ARG206 3.3 33.8 1.0 NH2 A:ARG206 3.4 30.5 1.0 NH2 B:ARG206 3.4 30.1 1.0 CZ B:ARG206 3.7 37.1 1.0 CZ A:ARG206 3.8 36.6 1.0 CA A:GLN193 4.2 34.4 1.0 CA B:GLN193 4.2 38.5 1.0 CD2 B:LEU196 4.3 32.9 1.0 CG A:GLN193 4.3 27.8 1.0 CB A:GLN193 4.4 28.6 1.0 CB B:GLN193 4.4 37.4 1.0 CG B:GLN193 4.4 34.4 1.0 CD2 A:LEU196 4.6 31.6 1.0 O B:GLN193 4.8 37.5 1.0 O A:GLN193 4.8 34.0 1.0 CB B:LEU196 4.9 37.7 1.0 CB A:LEU196 4.9 27.8 1.0

Chlorine binding site 3 out of 3 in the Oxa-48 Carbapanemase, Ertapenem 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, Ertapenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:54.0 occ:1.00 NZ B:LYS73 2.9 48.7 1.0 NE1 B:TRP157 3.0 36.9 1.0 CE B:LYS73 3.3 44.8 1.0 CG2 B:VAL120 3.6 45.3 1.0 CG B:LYS73 3.8 40.1 1.0 CD1 B:TRP157 4.0 42.5 1.0 CE2 B:TRP157 4.0 40.8 1.0 CA B:SER70 4.1 45.0 1.0 CG1 B:VAL120 4.1 39.3 1.0 CD B:LYS73 4.1 47.2 1.0 CB B:VAL120 4.2 40.9 1.0 CA B:VAL120 4.2 39.2 1.0 CZ2 B:TRP157 4.3 37.8 1.0 CB B:SER70 4.5 52.8 1.0 CB B:TYR123 4.6 43.6 1.0 O B:ALA69 4.6 44.2 1.0 OG B:SER70 4.6 58.9 1.0 N B:SER70 4.7 45.8 1.0 CD2 B:LEU158 4.9 49.1 1.0 O B:SER70 4.9 45.2 1.0 C B:ALA69 4.9 45.9 1.0 C B:SER70 4.9 44.3 1.0 CD1 B:LEU158 5.0 47.8 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