Chlorine in PDB 6p9c: Oxa-48 Carbapanemase, Doripenem Complex

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

The structure of Oxa-48 Carbapanemase, Doripenem Complex, PDB code: 6p9c 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)	36.51 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.604, 76.749, 101.188, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.1

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

Cadmium	(Cd)	2 atoms
Calcium	(Ca)	3 atoms

The binding sites of Chlorine atom in the Oxa-48 Carbapanemase, Doripenem Complex (pdb code 6p9c). 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, Doripenem Complex, PDB code: 6p9c:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:44.0 occ:1.00 NZ A:LYS73 2.9 40.2 1.0 NE1 A:TRP157 3.2 26.4 1.0 CE A:LYS73 3.3 41.2 1.0 O A:HOH469 3.5 28.3 1.0 CG2 A:VAL120 3.9 42.3 0.4 CG A:LYS73 3.9 21.1 1.0 CB A:TYR123 4.0 27.1 1.0 CG2 A:VAL120 4.0 41.9 0.6 CE2 A:TRP157 4.1 25.3 1.0 CAA A:4J6301 4.1 47.3 1.0 CD1 A:TRP157 4.1 21.2 1.0 OG A:SER70 4.2 29.6 1.0 CD A:LYS73 4.3 31.1 1.0 CZ2 A:TRP157 4.3 32.0 1.0 CG A:TYR123 4.4 27.7 1.0 CA A:VAL120 4.5 39.4 0.4 CA A:VAL120 4.5 39.3 0.6 CA A:SER70 4.5 23.6 1.0 CD2 A:TYR123 4.6 30.4 1.0 CB A:VAL120 4.6 40.7 0.6 CB A:VAL120 4.6 40.5 0.4 CB A:SER70 4.8 26.9 1.0 CAT A:4J6301 4.9 45.6 1.0 O A:VAL119 4.9 37.9 0.4

Chlorine binding site 2 out of 4 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:28.0 occ:1.00 NH2 A:ARG206 3.1 22.9 1.0 NH1 B:ARG206 3.1 21.6 1.0 O B:HOH482 3.2 36.3 1.0 NH2 B:ARG206 3.2 22.7 1.0 O A:HOH484 3.2 38.2 1.0 NH1 A:ARG206 3.2 23.1 1.0 CZ B:ARG206 3.6 26.8 1.0 CZ A:ARG206 3.6 24.2 1.0 CD2 A:LEU196 4.3 22.4 1.0 CA A:GLN193 4.3 19.6 1.0 CA B:GLN193 4.3 22.1 1.0 CD2 B:LEU196 4.4 22.3 1.0 CG A:GLN193 4.4 18.9 1.0 CG B:GLN193 4.4 27.2 1.0 CB A:GLN193 4.6 19.5 1.0 CB B:GLN193 4.6 22.1 1.0 CB A:LEU196 4.8 20.1 1.0 CB B:LEU196 4.9 21.7 1.0 NE B:ARG206 4.9 17.0 1.0 NE A:ARG206 4.9 20.2 1.0 O A:GLN193 4.9 21.6 1.0 CG A:LEU196 5.0 21.1 1.0 O B:GLN193 5.0 22.5 1.0

Chlorine binding site 3 out of 4 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl303 b:37.6 occ:1.00 NZ B:LYS73 3.0 29.6 1.0 NE1 B:TRP157 3.1 26.2 1.0 O B:HOH473 3.2 29.0 1.0 CE B:LYS73 3.4 31.7 1.0 CG B:LYS73 3.6 28.5 1.0 OG B:SER70 3.8 36.6 1.0 CG2 B:VAL120 3.8 31.5 1.0 CA B:SER70 3.8 29.2 1.0 CD1 B:TRP157 3.9 28.6 1.0 CE2 B:TRP157 4.0 30.0 1.0 CD B:LYS73 4.1 32.8 1.0 CB B:SER70 4.1 33.3 1.0 CZ2 B:TRP157 4.4 28.4 1.0 O B:ALA69 4.4 26.8 1.0 CB B:VAL120 4.5 28.8 1.0 CA B:VAL120 4.5 28.6 1.0 CG1 B:VAL120 4.5 30.7 1.0 N B:SER70 4.5 27.4 1.0 CB B:TYR123 4.5 25.4 1.0 C B:ALA69 4.7 28.1 1.0 CD2 B:LEU158 4.7 36.1 1.0 C B:SER70 4.8 23.9 1.0 O B:SER70 4.8 24.2 1.0 N B:LYS73 5.0 19.8 1.0 CB B:LYS73 5.0 22.5 1.0

Chlorine binding site 4 out of 4 in the Oxa-48 Carbapanemase, Doripenem 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, Doripenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl304 b:69.4 occ:1.00 CE B:LYS180 3.7 49.2 1.0 CD B:LYS180 4.1 48.3 1.0 CG B:LYS175 4.2 29.5 1.0 CE B:LYS175 4.3 35.4 1.0 NZ B:LYS180 4.7 37.1 1.0 CD B:LYS175 4.7 28.5 1.0 CB B:LYS180 4.8 28.0 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