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Chlorine in PDB 6pqi: Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime

Enzymatic activity of Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime

All present enzymatic activity of Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime, PDB code: 6pqi was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.64 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.732, 107.005, 96.196, 90.00, 104.17, 90.00
R / Rfree (%) 18.2 / 21.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime (pdb code 6pqi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime, PDB code: 6pqi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6pqi

Go back to Chlorine Binding Sites List in 6pqi
Chlorine binding site 1 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime


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 Class D Beta-Lactamase Oxa-48 with Cefotaxime within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:33.6
occ:0.99
 NH2 A:ARG206 3.1 29.7 1.0
NH1 A:ARG206 3.2 26.9 1.0
NH1 B:ARG206 3.2 34.5 1.0
NH2 B:ARG206 3.2 31.1 1.0
CZ A:ARG206 3.6 35.9 1.0
CZ B:ARG206 3.6 30.5 1.0
CA B:GLN193 4.3 30.8 1.0
CD2 B:LEU196 4.3 29.0 1.0
CD2 A:LEU196 4.3 27.9 1.0
CA A:GLN193 4.3 30.8 1.0
CG B:GLN193 4.3 38.4 1.0
CG A:GLN193 4.4 27.7 1.0
CB B:GLN193 4.5 35.5 1.0
CB A:GLN193 4.5 32.3 1.0
O B:GLN193 4.9 30.0 1.0
NE A:ARG206 4.9 23.6 1.0
CB B:LEU196 4.9 28.5 1.0
CB A:LEU196 4.9 27.8 1.0
O A:GLN193 4.9 30.8 1.0
NE B:ARG206 4.9 28.2 1.0
CD1 A:LEU196 5.0 26.8 1.0
CG A:LEU196 5.0 31.9 1.0

Chlorine binding site 2 out of 6 in 6pqi

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Chlorine binding site 2 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime


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 Class D Beta-Lactamase Oxa-48 with Cefotaxime within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:43.1
occ:0.89
 NZ A:LYS73 2.9 33.4 1.0
NE1 A:TRP157 3.0 34.1 1.0
O A:HOH450 3.3 33.3 1.0
CE A:LYS73 3.5 43.2 1.0
CG A:LYS73 3.6 29.7 1.0
CG2 A:VAL120 3.8 33.7 1.0
CD1 A:TRP157 3.9 37.7 1.0
CE2 A:TRP157 3.9 37.6 1.0
CA A:SER70 4.0 28.3 1.0
OG A:SER70 4.1 42.3 1.0
CD A:LYS73 4.1 39.7 1.0
CZ2 A:TRP157 4.3 40.0 1.0
CA A:VAL120 4.3 34.1 1.0
CB A:VAL120 4.4 40.3 1.0
O A:ALA69 4.4 32.6 1.0
CG1 A:VAL120 4.4 43.8 1.0
CB A:TYR123 4.5 36.2 1.0
CB A:SER70 4.5 35.9 1.0
N A:SER70 4.7 31.4 1.0
CD2 A:LEU158 4.7 41.1 1.0
C A:ALA69 4.8 34.6 1.0
C8 A:CEF301 4.8 42.7 0.8
O A:SER70 4.8 29.0 1.0
C A:SER70 4.9 33.0 1.0
CG A:TYR123 5.0 37.0 1.0
CB A:LYS73 5.0 32.9 1.0
O A:VAL120 5.0 33.2 1.0

Chlorine binding site 3 out of 6 in 6pqi

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Chlorine binding site 3 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime


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 Class D Beta-Lactamase Oxa-48 with Cefotaxime within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:40.5
occ:0.68
 NZ B:LYS73 2.5 42.3 1.0
NE1 B:TRP157 2.9 46.9 1.0
O B:HOH464 3.3 44.4 1.0
CE B:LYS73 3.5 35.6 1.0
CG2 B:VAL120 3.6 39.1 1.0
CD1 B:TRP157 3.7 59.6 1.0
CG B:LYS73 3.7 34.3 1.0
CA B:SER70 3.8 35.9 1.0
CE2 B:TRP157 3.9 49.4 1.0
OG B:SER70 3.9 41.4 1.0
O B:ALA69 4.2 32.6 1.0
CD B:LYS73 4.2 38.5 1.0
CD2 B:LEU158 4.3 57.5 1.0
CB B:VAL120 4.3 43.2 1.0
CG1 B:VAL120 4.3 42.4 1.0
CB B:SER70 4.4 35.4 1.0
CZ2 B:TRP157 4.4 59.6 1.0
C8 B:CEF301 4.4 46.6 0.9
CA B:VAL120 4.4 35.9 1.0
N B:SER70 4.4 28.7 1.0
C B:ALA69 4.5 32.3 1.0
C B:SER70 4.7 33.6 1.0
O B:SER70 4.7 30.6 1.0
CB B:TYR123 4.8 35.0 1.0
CG B:TRP157 4.9 48.8 1.0

Chlorine binding site 4 out of 6 in 6pqi

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Chlorine binding site 4 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime


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 Class D Beta-Lactamase Oxa-48 with Cefotaxime within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:43.9
occ:0.89
 NZ C:LYS73 2.9 37.1 1.0
NE1 C:TRP157 2.9 33.7 1.0
O C:HOH462 3.2 36.9 1.0
CE C:LYS73 3.5 38.8 1.0
CG C:LYS73 3.7 35.1 1.0
CD1 C:TRP157 3.7 36.5 1.0
CG2 C:VAL120 3.8 40.6 1.0
CE2 C:TRP157 3.9 39.2 1.0
CA C:SER70 4.0 34.2 1.0
OG C:SER70 4.1 42.7 1.0
CD C:LYS73 4.2 37.4 1.0
CZ2 C:TRP157 4.3 40.6 1.0
CG1 C:VAL120 4.3 40.8 1.0
CA C:VAL120 4.3 35.2 1.0
O C:ALA69 4.4 31.4 1.0
CB C:VAL120 4.4 41.6 1.0
CD2 C:LEU158 4.4 44.7 1.0
CB C:SER70 4.5 36.8 1.0
CB C:TYR123 4.6 35.4 1.0
N C:SER70 4.6 32.1 1.0
C C:ALA69 4.7 35.0 1.0
C8 C:CEF301 4.8 48.9 0.8
O C:SER70 4.8 32.2 1.0
C C:SER70 4.9 30.4 1.0
CG C:TRP157 4.9 34.9 1.0
CD2 C:TRP157 5.0 36.1 1.0

Chlorine binding site 5 out of 6 in 6pqi

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Chlorine binding site 5 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime


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 Class D Beta-Lactamase Oxa-48 with Cefotaxime within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:28.8
occ:0.82
 NH1 D:ARG206 3.1 27.6 1.0
NH2 D:ARG206 3.1 27.9 1.0
CZ D:ARG206 3.6 29.4 1.0
CD2 D:LEU196 4.2 24.1 1.0
CG D:GLN193 4.3 34.5 1.0
CA D:GLN193 4.3 31.5 1.0
CB D:GLN193 4.5 34.1 1.0
O D:HOH431 4.9 41.8 1.0
CB D:LEU196 4.9 28.2 1.0
NE D:ARG206 4.9 32.3 1.0
O D:GLN193 4.9 29.1 1.0
CG D:LEU196 5.0 26.4 1.0

Chlorine binding site 6 out of 6 in 6pqi

Go back to Chlorine Binding Sites List in 6pqi
Chlorine binding site 6 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:43.0
occ:0.73
 NZ D:LYS73 2.8 39.1 1.0
NE1 D:TRP157 2.9 43.0 1.0
O D:HOH439 3.1 40.0 1.0
CE D:LYS73 3.4 35.9 1.0
CG D:LYS73 3.6 30.6 1.0
CD1 D:TRP157 3.7 51.5 1.0
CG2 D:VAL120 3.8 36.6 1.0
CA D:SER70 3.9 32.5 1.0
OG D:SER70 3.9 35.2 1.0
CE2 D:TRP157 3.9 49.3 1.0
CD D:LYS73 4.1 38.8 1.0
CG1 D:VAL120 4.2 33.5 1.0
O D:ALA69 4.2 30.8 1.0
CB D:SER70 4.3 26.6 1.0
CB D:VAL120 4.4 41.0 1.0
CZ2 D:TRP157 4.4 58.9 1.0
CA D:VAL120 4.4 28.5 1.0
CD2 D:LEU158 4.5 51.1 1.0
N D:SER70 4.5 29.3 1.0
C D:ALA69 4.6 31.8 1.0
C8 D:CEF301 4.7 43.8 0.9
CB D:TYR123 4.7 40.0 1.0
C D:SER70 4.8 30.1 1.0
O D:SER70 4.8 29.4 1.0
CG D:TRP157 4.9 47.5 1.0
CB D:LYS73 5.0 30.1 1.0

Reference:

A.Akhtar, Y.Chen. Crystal Structure of Class D Beta-Lactamase Oxa-48 with Cefotaxime To Be Published.
Page generated: Mon Jul 29 13:30:03 2024

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