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Chlorine in PDB 5eph: Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem

Enzymatic activity of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem

All present enzymatic activity of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem, PDB code: 5eph was solved by C.Pozzi, M.Benvenuti, F.De Luca, J.D.Docquier, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.68 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.980, 95.860, 103.420, 90.00, 91.97, 90.00
R / Rfree (%) 16.4 / 20.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem (pdb code 5eph). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem, PDB code: 5eph:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5eph

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Chlorine binding site 1 out of 5 in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:13.7
occ:1.00
 OG1 A:THR63 3.1 9.6 1.0
ND2 A:ASN237 3.2 12.2 1.0
N A:THR63 3.2 10.2 1.0
N A:SER62 3.2 12.8 1.0
N A:CYS61 3.5 15.7 1.0
CG2 A:THR63 3.7 10.9 1.0
SG A:CYS231 3.7 19.0 1.0
C A:MET60 3.8 19.5 1.0
CB A:THR63 3.8 10.2 1.0
CA A:GLY229 3.9 12.6 1.0
CA A:SER62 3.9 12.5 1.0
O A:ALA59 3.9 17.9 1.0
CB A:SER62 4.0 13.7 1.0
CB A:ASN237 4.0 10.4 1.0
CA A:MET60 4.0 17.5 1.0
C A:SER62 4.0 11.3 1.0
CG A:ASN237 4.1 10.5 1.0
CE2 A:TYR255 4.1 9.8 1.0
CA A:THR63 4.1 10.1 1.0
C A:CYS61 4.2 14.6 1.0
CA A:CYS61 4.3 15.8 1.0
O A:MET60 4.4 26.8 1.0
SG A:CYS61 4.4 17.6 1.0
N A:GLY229 4.5 12.7 1.0
OG A:SER62 4.6 14.6 1.0
C A:GLY229 4.6 13.5 1.0
CD2 A:TYR255 4.7 9.2 1.0
C A:ALA59 4.8 16.6 1.0
N A:MET60 4.8 17.1 1.0
O A:THR228 4.8 11.2 1.0
CB A:CYS61 4.9 15.7 1.0
OH A:TYR255 4.9 12.1 1.0
CZ A:TYR255 5.0 9.7 1.0

Chlorine binding site 2 out of 5 in 5eph

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Chlorine binding site 2 out of 5 in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:23.8
occ:1.00
 OG A:SER43 3.0 13.2 1.0
ND2 A:ASN45 3.2 20.6 1.0
O B:HOH545 3.3 38.1 1.0
O A:HOH474 3.3 37.5 1.0
CB A:SER43 3.3 13.1 1.0
NZ B:LYS197 3.4 17.1 0.5
N A:ASN45 3.6 15.6 1.0
CB A:ASN45 3.6 18.6 1.0
OD1 A:ASN47 3.8 14.5 1.0
CE1 B:TYR194 3.9 17.0 1.0
CG A:ASN45 3.9 20.3 1.0
N A:GLU44 4.0 13.5 1.0
CD1 B:TYR194 4.1 15.3 1.0
CE B:LYS197 4.2 16.7 0.5
CA A:ASN45 4.2 16.3 1.0
NZ B:LYS197 4.2 12.2 0.5
CB A:GLU44 4.3 18.3 1.0
O A:HOH412 4.4 17.8 1.0
C A:SER43 4.5 13.1 1.0
C A:GLU44 4.5 16.1 1.0
CA A:GLU44 4.5 16.4 1.0
O B:HOH408 4.5 32.3 1.0
CA A:SER43 4.6 12.3 1.0
O B:HOH558 4.9 23.1 1.0
CG A:ASN47 4.9 12.9 1.0
CD B:LYS197 4.9 12.1 0.5

Chlorine binding site 3 out of 5 in 5eph

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Chlorine binding site 3 out of 5 in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:16.6
occ:1.00
 OG1 B:THR63 3.1 12.2 1.0
N B:THR63 3.2 13.4 1.0
N B:SER62 3.2 16.6 1.0
ND2 B:ASN237 3.3 13.4 1.0
N B:CYS61 3.4 18.2 1.0
CG2 B:THR63 3.7 12.7 1.0
CB B:THR63 3.8 12.5 1.0
SG B:CYS231 3.8 22.8 1.0
CA B:SER62 3.9 15.7 1.0
CB B:SER62 3.9 16.2 1.0
CA B:GLY229 4.0 13.2 1.0
C B:SER62 4.0 14.1 1.0
CA B:MET60 4.0 17.6 1.0
C B:MET60 4.0 19.2 1.0
CA B:THR63 4.0 12.5 1.0
CB B:ASN237 4.1 11.7 1.0
O B:ALA59 4.1 19.4 1.0
CG B:ASN237 4.1 13.4 1.0
C B:CYS61 4.2 18.4 1.0
CE2 B:TYR255 4.2 12.3 1.0
CA B:CYS61 4.3 18.4 1.0
SG B:CYS61 4.4 23.9 1.0
OG B:SER62 4.5 15.1 1.0
N B:GLY229 4.5 11.8 1.0
C B:GLY229 4.6 14.0 1.0
CG B:MET60 4.8 17.9 1.0
CB B:CYS61 4.9 22.3 1.0
C B:ALA59 4.9 16.9 1.0
N B:MET60 5.0 17.5 1.0
CD2 B:TYR255 5.0 11.7 1.0
OH B:TYR255 5.0 12.3 1.0
O B:THR228 5.0 13.1 1.0
CB B:MET60 5.0 19.1 1.0

Chlorine binding site 4 out of 5 in 5eph

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Chlorine binding site 4 out of 5 in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:15.7
occ:1.00
 OG1 C:THR63 3.0 11.6 1.0
N C:THR63 3.2 12.7 1.0
ND2 C:ASN237 3.2 14.3 1.0
N C:SER62 3.2 14.0 1.0
N C:CYS61 3.5 18.6 1.0
C C:MET60 3.6 19.4 1.0
CG2 C:THR63 3.6 11.7 1.0
CA C:MET60 3.6 19.8 1.0
CB C:THR63 3.7 11.9 1.0
SG C:CYS231 3.8 20.5 1.0
CA C:GLY229 3.8 12.9 1.0
CA C:SER62 3.9 11.8 1.0
CB C:SER62 3.9 12.6 1.0
CB C:ASN237 4.0 12.2 1.0
O C:ALA59 4.0 16.4 1.0
C C:SER62 4.0 12.6 1.0
CA C:THR63 4.0 12.6 1.0
CG C:ASN237 4.1 13.6 1.0
CE2 C:TYR255 4.2 14.5 1.0
C C:CYS61 4.2 14.5 1.0
O C:MET60 4.2 23.0 1.0
N C:GLY229 4.4 12.5 1.0
CA C:CYS61 4.4 17.1 1.0
CB C:MET60 4.4 20.0 1.0
SG C:CYS61 4.4 20.6 1.0
OG C:SER62 4.5 12.7 1.0
C C:GLY229 4.5 13.8 1.0
N C:MET60 4.7 17.6 1.0
O C:THR228 4.7 12.1 1.0
C C:ALA59 4.8 18.2 1.0
CD2 C:TYR255 4.9 15.8 1.0
C C:THR228 4.9 13.3 1.0
CB C:CYS61 4.9 18.0 1.0
O C:GLY229 5.0 13.2 1.0
OH C:TYR255 5.0 14.7 1.0

Chlorine binding site 5 out of 5 in 5eph

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Chlorine binding site 5 out of 5 in the Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Extended-Spectrum Beta-Lactamase Bel-1 in Complex with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:20.1
occ:1.00
 OG1 D:THR63 3.1 17.9 1.0
N D:THR63 3.2 17.1 1.0
ND2 D:ASN237 3.2 15.1 1.0
N D:SER62 3.2 18.3 1.0
N D:CYS61 3.4 22.5 1.0
CG2 D:THR63 3.6 16.3 1.0
C D:MET60 3.7 26.6 1.0
CB D:THR63 3.7 17.4 1.0
CA D:GLY229 3.8 15.3 1.0
CA D:MET60 3.8 25.3 1.0
SG D:CYS231 3.9 23.3 1.0
CB D:SER62 3.9 19.5 1.0
CA D:SER62 3.9 18.1 1.0
CB D:ASN237 3.9 14.7 1.0
C D:SER62 4.0 15.8 1.0
CA D:THR63 4.0 16.9 1.0
CG D:ASN237 4.0 14.8 1.0
O D:ALA59 4.1 27.9 1.0
C D:CYS61 4.2 18.9 1.0
CE2 D:TYR255 4.2 16.8 1.0
CA D:CYS61 4.3 21.8 1.0
SG D:CYS61 4.4 24.5 1.0
N D:GLY229 4.4 14.2 1.0
OG D:SER62 4.5 17.8 1.0
O D:MET60 4.5 32.5 1.0
C D:GLY229 4.5 17.2 1.0
N D:MET60 4.8 21.1 1.0
O D:THR228 4.8 15.1 1.0
C D:ALA59 4.8 24.8 1.0
CB D:CYS61 4.9 23.3 1.0
CD2 D:TYR255 4.9 16.8 1.0
C D:THR228 4.9 13.6 1.0
OH D:TYR255 4.9 19.0 1.0
CB D:MET60 5.0 27.2 1.0
CG D:MET60 5.0 27.6 1.0
O D:GLY229 5.0 15.6 1.0

Reference:

C.Pozzi, F.De Luca, M.Benvenuti, L.Poirel, P.Nordmann, G.M.Rossolini, S.Mangani, J.D.Docquier. Crystal Structure of the Pseudomonas Aeruginosa Bel-1 Extended-Spectrum Beta-Lactamase and Its Complexes with Moxalactam and Imipenem. Antimicrob.Agents Chemother. V. 60 7189 2016.
ISSN: ESSN 1098-6596
PubMed: 27671060
DOI: 10.1128/AAC.00936-16
Page generated: Fri Jul 26 07:26:15 2024

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