Chlorine in PDB 6p96: Oxa-48 Carbapanemase, Apo Form

All present enzymatic activity of Oxa-48 Carbapanemase, Apo Form:
3.5.2.6;

The structure of Oxa-48 Carbapanemase, Apo Form, PDB code: 6p96 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 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.746, 76.827, 100.044, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.9

The structure of Oxa-48 Carbapanemase, Apo Form 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, Apo Form (pdb code 6p96). 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, Apo Form, PDB code: 6p96:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Oxa-48 Carbapanemase, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:25.6 occ:1.00 NZ A:LYS73 2.9 26.0 1.0 O A:HOH517 3.0 22.4 1.0 NE1 A:TRP157 3.2 21.5 1.0 CE A:LYS73 3.4 21.7 1.0 CG A:LYS73 3.6 19.0 1.0 CB A:TYR123 3.7 21.9 1.0 CG2 A:VAL120 3.8 22.7 1.0 OG A:SER70 3.9 26.4 1.0 CE2 A:TRP157 3.9 20.6 1.0 CA A:VAL120 3.9 19.2 1.0 CZ2 A:TRP157 4.1 21.6 1.0 CD A:LYS73 4.1 19.4 1.0 CG1 A:VAL120 4.1 22.6 1.0 CB A:VAL120 4.1 21.1 1.0 CD1 A:TRP157 4.1 21.8 1.0 CG A:TYR123 4.3 24.3 1.0 O A:VAL120 4.5 22.6 1.0 CA A:SER70 4.5 20.4 1.0 CB A:SER70 4.7 25.2 1.0 C A:VAL120 4.7 24.9 1.0 N A:VAL120 4.7 19.7 1.0 CD1 A:TYR123 4.9 23.2 1.0 CB A:LYS73 5.0 20.1 1.0 CD2 A:TYR123 5.0 22.8 1.0

Chlorine binding site 2 out of 4 in the Oxa-48 Carbapanemase, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:20.0 occ:1.00 NH1 B:ARG206 3.1 16.4 1.0 O A:HOH572 3.2 28.5 1.0 O B:HOH565 3.2 31.2 1.0 NH2 A:ARG206 3.2 18.2 1.0 NH1 A:ARG206 3.2 16.3 1.0 NH2 B:ARG206 3.3 16.9 1.0 CZ B:ARG206 3.6 16.9 1.0 CZ A:ARG206 3.7 18.7 1.0 CD2 A:LEU196 4.2 19.6 1.0 CA B:GLN193 4.3 18.1 1.0 CD2 B:LEU196 4.3 19.3 1.0 CA A:GLN193 4.3 18.9 1.0 CG A:GLN193 4.4 17.4 1.0 CG B:GLN193 4.4 18.1 1.0 CB B:GLN193 4.5 19.5 1.0 CB A:GLN193 4.6 16.6 1.0 CB B:LEU196 4.9 18.6 1.0 CB A:LEU196 4.9 16.8 1.0 O B:GLN193 4.9 20.2 1.0 O A:GLN193 4.9 17.7 1.0 NE B:ARG206 4.9 16.5 1.0 CG A:LEU196 5.0 18.1 1.0 NE A:ARG206 5.0 17.9 1.0 CG B:LEU196 5.0 17.6 1.0 O B:HOH460 5.0 40.2 1.0

Chlorine binding site 3 out of 4 in the Oxa-48 Carbapanemase, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:25.6 occ:1.00 O B:HOH543 3.0 22.8 1.0 NZ B:LYS73 3.1 24.6 1.0 NE1 B:TRP157 3.1 21.1 1.0 CE B:LYS73 3.6 22.1 1.0 CG B:LYS73 3.7 19.8 1.0 CG2 B:VAL120 3.8 23.0 1.0 CB B:TYR123 3.8 20.6 1.0 OG B:SER70 3.9 29.6 1.0 CE2 B:TRP157 3.9 20.2 1.0 CA B:VAL120 3.9 21.7 1.0 CD1 B:TRP157 4.1 22.4 1.0 CG1 B:VAL120 4.1 25.5 1.0 CZ2 B:TRP157 4.1 22.3 1.0 CB B:VAL120 4.1 25.3 1.0 CD B:LYS73 4.3 21.4 1.0 CA B:SER70 4.4 23.0 1.0 O B:VAL120 4.5 20.5 1.0 CG B:TYR123 4.5 21.6 1.0 CB B:SER70 4.7 23.3 1.0 C B:VAL120 4.7 23.0 1.0 N B:VAL120 4.8 21.9 1.0 O B:ALA69 5.0 21.6 1.0

Chlorine binding site 4 out of 4 in the Oxa-48 Carbapanemase, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:43.2 occ:1.00 O B:HOH568 2.4 49.1 1.0 O B:HOH575 2.4 43.0 1.0 O B:HOH572 2.6 40.8 1.0 O B:HOH570 2.9 31.9 1.0 O B:HOH473 4.3 27.9 1.0 CE B:LYS175 4.3 29.0 1.0 CG B:LYS175 4.3 26.4 1.0 NZ B:LYS180 4.5 50.0 1.0 CD B:LYS175 4.8 27.5 1.0 NZ B:LYS175 4.8 29.0 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