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

Enzymatic activity of Oxa-48 Carbapanemase, Imipenem Complex

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

Protein crystallography data

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

Other elements in 6p97:

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

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

Chlorine Binding Sites:

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 6p97

Go back to Chlorine Binding Sites List in 6p97
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 6p97

Go back to Chlorine Binding Sites List in 6p97
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 6p97

Go back to Chlorine Binding Sites List in 6p97
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 6p97

Go back to Chlorine Binding Sites List in 6p97
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

Reference:

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
Page generated: Mon Jul 29 13:15:50 2024

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