Chlorine in PDB 6p98: Oxa-48 Carbapanemase, Meropenem Complex

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

The structure of Oxa-48 Carbapanemase, Meropenem Complex, PDB code: 6p98 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)	36.57 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.132, 74.563, 97.974, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22

The structure of Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex (pdb code 6p98). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Oxa-48 Carbapanemase, Meropenem Complex, PDB code: 6p98:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:22.1 occ:1.00 NE1 A:TRP157 3.0 18.6 1.0 NZ A:LYS73 3.0 21.8 1.0 O A:HOH534 3.2 19.0 1.0 CE A:LYS73 3.6 23.6 1.0 CG A:LYS73 3.7 16.8 1.0 CB A:VAL120 3.9 23.5 0.1 CD1 A:TRP157 3.9 16.7 1.0 CG2 A:VAL120 3.9 25.9 0.8 CA A:SER70 3.9 20.7 1.0 CE2 A:TRP157 4.0 21.5 1.0 OG A:SER70 4.0 21.4 1.0 CG1 A:VAL120 4.1 25.2 0.1 CD A:LYS73 4.3 19.3 1.0 CZ2 A:TRP157 4.4 19.1 1.0 O A:ALA69 4.4 16.6 1.0 CA A:VAL120 4.5 24.1 0.1 CB A:SER70 4.5 20.6 1.0 CA A:VAL120 4.5 24.4 0.8 CB A:VAL120 4.5 22.7 0.8 CG1 A:VAL120 4.6 21.8 0.8 N A:SER70 4.6 16.9 1.0 CB A:TYR123 4.6 18.6 1.0 C62 A:KE1301 4.7 28.1 1.0 C A:ALA69 4.7 17.5 1.0 O A:SER70 4.7 16.0 1.0 C A:SER70 4.8 13.9 1.0 CD1 A:LEU158 4.8 24.0 1.0 C7 A:KE1301 4.9 21.7 1.0 CD2 A:LEU158 5.0 30.5 1.0

Chlorine binding site 2 out of 5 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:17.2 occ:1.00 NH2 A:ARG206 3.1 16.4 1.0 NH1 B:ARG206 3.2 14.3 1.0 NH1 A:ARG206 3.2 11.0 1.0 NH2 B:ARG206 3.2 17.1 1.0 O B:HOH509 3.3 32.7 1.0 CZ A:ARG206 3.6 15.4 1.0 CZ B:ARG206 3.6 16.6 1.0 CG B:GLN193 4.2 17.0 1.0 CD2 B:LEU196 4.2 20.9 1.0 CA B:GLN193 4.3 14.2 1.0 CA A:GLN193 4.3 16.0 1.0 CG A:GLN193 4.3 18.9 1.0 CD2 A:LEU196 4.4 19.1 1.0 CB A:GLN193 4.5 16.3 1.0 CB B:GLN193 4.5 16.7 1.0 CB A:LEU196 4.9 15.8 1.0 CB B:LEU196 4.9 14.1 1.0 O A:GLN193 4.9 13.6 1.0 NE A:ARG206 4.9 16.4 1.0 NE B:ARG206 5.0 17.4 1.0 O B:GLN193 5.0 16.8 1.0

Chlorine binding site 3 out of 5 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:34.7 occ:1.00 NZ B:LYS73 3.0 20.2 1.0 NE1 B:TRP157 3.1 24.4 1.0 O B:HOH483 3.2 23.7 1.0 CE B:LYS73 3.3 22.7 1.0 CG B:LYS73 3.6 22.5 1.0 CD1 B:TRP157 3.9 24.2 1.0 CA B:SER70 3.9 21.8 1.0 CG2 B:VAL120 4.0 21.9 1.0 OG B:SER70 4.0 23.9 1.0 CD B:LYS73 4.1 21.6 1.0 CE2 B:TRP157 4.1 22.7 1.0 CB B:SER70 4.4 23.5 1.0 CB B:TYR123 4.5 23.0 1.0 CA B:VAL120 4.5 21.3 1.0 CZ2 B:TRP157 4.5 22.2 1.0 CG1 B:VAL120 4.5 23.1 1.0 O B:ALA69 4.5 23.3 1.0 CB B:VAL120 4.5 22.8 1.0 N B:SER70 4.6 19.8 1.0 O B:SER70 4.7 18.9 1.0 C B:SER70 4.8 19.5 1.0 CD2 B:LEU158 4.8 28.4 1.0 C B:ALA69 4.8 22.2 1.0 CB B:LYS73 4.9 20.3 1.0 N B:LYS73 4.9 18.8 1.0 CG B:TYR123 4.9 24.9 1.0 C62 B:KE1301 5.0 34.7 1.0

Chlorine binding site 4 out of 5 in the Oxa-48 Carbapanemase, Meropenem 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, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl303 b:20.4 occ:1.00 O B:HOH514 2.3 35.0 1.0 O B:HOH505 2.5 26.2 1.0 O B:HOH507 2.5 22.4 1.0 O B:HOH413 2.6 39.3 1.0 CD B:LYS180 4.0 37.7 1.0 O B:HOH446 4.3 31.5 1.0 CE B:LYS180 4.4 35.8 1.0 CG B:LYS175 4.4 22.6 1.0 NZ B:LYS180 4.5 42.4 1.0 NH2 B:ARG174 4.8 37.4 1.0 CE B:LYS175 4.9 33.5 1.0

Chlorine binding site 5 out of 5 in the Oxa-48 Carbapanemase, Meropenem Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Oxa-48 Carbapanemase, Meropenem Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl304 b:23.3 occ:1.00 O A:HOH557 2.4 15.2 1.0 O B:HOH508 2.5 18.1 1.0 O A:HOH561 2.6 32.1 1.0 O B:HOH499 2.6 18.1 1.0 O A:HOH547 3.8 26.3 1.0 CB B:ARG186 4.0 18.6 1.0 N B:ARG186 4.2 18.2 1.0 O A:HOH533 4.2 18.3 1.0 CB A:ARG186 4.3 19.9 1.0 O B:HOH516 4.4 39.8 1.0 CA B:ARG186 4.5 19.2 1.0 CD A:ARG186 4.5 23.0 1.0 O B:HOH474 4.6 20.3 0.4 CB B:GLU185 4.6 21.8 1.0 CG A:ARG186 4.7 19.9 1.0 CD B:GLU185 4.9 27.9 1.0 C B:GLU185 5.0 17.1 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