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

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

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

Protein crystallography data

The structure of Crystal Structure of Class D Beta-Lactamase Oxa-48 with Imipenem, PDB code: 6ptu 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) 33.08 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.497, 106.656, 94.659, 90.00, 107.60, 90.00
R / Rfree (%) 16.7 / 21.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Imipenem (pdb code 6ptu). 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 Imipenem, PDB code: 6ptu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6ptu

Go back to Chlorine Binding Sites List in 6ptu
Chlorine binding site 1 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 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 Class D Beta-Lactamase Oxa-48 with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:14.3
occ:1.00
 O A:HOH564 3.1 22.0 1.0
NH2 A:ARG206 3.1 8.7 1.0
NH1 A:ARG206 3.1 10.0 1.0
O B:HOH580 3.2 19.3 1.0
NH1 B:ARG206 3.2 6.4 1.0
NH2 B:ARG206 3.3 6.3 1.0
CZ A:ARG206 3.5 9.1 1.0
CZ B:ARG206 3.7 11.2 1.0
CD2 A:LEU196 4.2 4.1 1.0
CA B:GLN193 4.2 6.7 1.0
CG B:GLN193 4.4 7.4 1.0
CD2 B:LEU196 4.4 9.5 1.0
CB B:GLN193 4.4 6.9 1.0
CA A:GLN193 4.4 8.0 1.0
CG A:GLN193 4.5 7.8 1.0
CB A:GLN193 4.6 7.1 1.0
CB B:LEU196 4.8 6.0 1.0
NE A:ARG206 4.9 7.9 1.0
CB A:LEU196 4.9 7.8 1.0
O B:GLN193 4.9 8.1 1.0
NE B:ARG206 5.0 8.2 1.0
O B:HOH431 5.0 21.0 1.0

Chlorine binding site 2 out of 6 in 6ptu

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Chlorine binding site 2 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 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 Class D Beta-Lactamase Oxa-48 with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:17.2
occ:0.90
 NE1 A:TRP157 3.0 12.4 1.0
NZ A:LYS73 3.1 12.7 1.0
O A:HOH535 3.2 13.8 1.0
CE A:LYS73 3.6 15.5 1.0
CG A:LYS73 3.7 10.5 1.0
CG2 A:VAL120 3.8 10.7 1.0
CD1 A:TRP157 3.9 11.6 1.0
CE2 A:TRP157 3.9 13.5 1.0
CA A:SER70 3.9 8.6 1.0
OG A:SER70 4.2 15.5 1.0
CZ2 A:TRP157 4.2 10.9 1.0
CD A:LYS73 4.3 16.0 1.0
CA A:VAL120 4.4 9.9 1.0
CB A:SER70 4.4 10.2 1.0
CB A:VAL120 4.5 13.6 1.0
CB A:TYR123 4.5 12.6 1.0
O A:ALA69 4.5 9.7 1.0
N A:SER70 4.6 13.1 1.0
CD2 A:LEU158 4.6 17.6 1.0
CG1 A:VAL120 4.6 12.5 1.0
C A:ALA69 4.7 12.8 1.0
C A:SER70 4.8 14.2 1.0
O A:SER70 4.8 9.5 1.0
CG A:TYR123 5.0 10.7 1.0
N A:LYS73 5.0 7.7 1.0

Chlorine binding site 3 out of 6 in 6ptu

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Chlorine binding site 3 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 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 Class D Beta-Lactamase Oxa-48 with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:18.2
occ:0.79
 NZ B:LYS73 3.0 12.9 1.0
O B:HOH547 3.0 19.1 1.0
NE1 B:TRP157 3.1 15.3 1.0
CE B:LYS73 3.4 10.9 1.0
CG B:LYS73 3.5 11.4 1.0
CG2 B:VAL120 3.7 13.1 1.0
CA B:SER70 3.9 5.6 1.0
CD1 B:TRP157 3.9 13.2 1.0
CE2 B:TRP157 4.0 13.9 1.0
CD B:LYS73 4.1 14.6 1.0
OG B:SER70 4.1 12.2 1.0
CZ2 B:TRP157 4.4 11.7 1.0
CB B:SER70 4.4 9.2 1.0
O B:ALA69 4.4 9.2 1.0
CB B:TYR123 4.5 10.7 1.0
CA B:VAL120 4.5 11.9 1.0
CB B:VAL120 4.6 14.8 1.0
N B:SER70 4.6 7.4 1.0
O B:SER70 4.7 9.6 1.0
CD2 B:LEU158 4.7 15.2 1.0
C B:ALA69 4.7 8.5 1.0
C B:SER70 4.7 9.7 1.0
CG1 B:VAL120 4.8 12.6 1.0
N B:LYS73 4.9 8.3 1.0
C62 B:ID1302 4.9 10.9 0.8
CB B:LYS73 4.9 8.5 1.0
CG B:TYR123 4.9 11.3 1.0

Chlorine binding site 4 out of 6 in 6ptu

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Chlorine binding site 4 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 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 Class D Beta-Lactamase Oxa-48 with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:16.0
occ:1.00
 O C:HOH530 3.0 21.8 1.0
NH1 C:ARG206 3.1 5.1 1.0
O D:HOH544 3.2 24.4 1.0
NH2 D:ARG206 3.2 12.7 1.0
NH1 D:ARG206 3.3 7.2 1.0
NH2 C:ARG206 3.3 12.7 1.0
CZ C:ARG206 3.6 11.5 1.0
CZ D:ARG206 3.7 12.8 1.0
CD2 C:LEU196 4.2 10.4 1.0
CA C:GLN193 4.3 11.9 1.0
CD2 D:LEU196 4.3 9.0 1.0
CG C:GLN193 4.4 8.3 1.0
CA D:GLN193 4.5 11.3 1.0
CB C:GLN193 4.5 13.0 1.0
CG D:GLN193 4.6 9.9 1.0
CB D:GLN193 4.7 9.2 1.0
O C:GLN193 4.9 10.3 1.0
CB C:LEU196 4.9 11.1 1.0
CB D:LEU196 4.9 12.5 1.0
CG C:LEU196 5.0 8.2 1.0
NE C:ARG206 5.0 10.6 1.0
NE D:ARG206 5.0 11.9 1.0

Chlorine binding site 5 out of 6 in 6ptu

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Chlorine binding site 5 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 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 Class D Beta-Lactamase Oxa-48 with Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:18.9
occ:0.69
 NZ C:LYS73 2.6 15.4 1.0
NE1 C:TRP157 3.0 18.7 1.0
O C:HOH512 3.2 14.6 1.0
CE C:LYS73 3.4 15.6 1.0
CG C:LYS73 3.6 12.1 1.0
CG2 C:VAL120 3.8 12.7 1.0
CD1 C:TRP157 3.9 18.8 1.0
CE2 C:TRP157 3.9 12.8 1.0
CA C:SER70 4.0 12.9 1.0
CD C:LYS73 4.1 16.2 1.0
OG C:SER70 4.1 15.3 1.0
CZ2 C:TRP157 4.3 13.9 1.0
CA C:VAL120 4.4 10.4 1.0
CB C:SER70 4.5 9.4 1.0
CB C:VAL120 4.5 13.6 1.0
O C:ALA69 4.5 11.9 1.0
CG1 C:VAL120 4.5 17.3 1.0
CB C:TYR123 4.6 11.0 1.0
CD2 C:LEU158 4.6 16.5 1.0
N C:SER70 4.6 10.9 1.0
C C:ALA69 4.8 9.5 1.0
O C:SER70 4.8 10.1 1.0
C C:SER70 4.9 11.6 1.0
C62 C:ID1303 4.9 17.0 0.9

Chlorine binding site 6 out of 6 in 6ptu

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


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 Imipenem within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:16.3
occ:0.82
 NZ D:LYS73 2.8 15.9 1.0
NE1 D:TRP157 3.2 14.1 1.0
O D:HOH497 3.3 12.4 1.0
CG D:LYS73 3.8 12.1 1.0
CE D:LYS73 3.8 23.0 1.0
CA D:SER70 3.9 12.7 1.0
CG2 D:VAL120 3.9 16.3 1.0
CD1 D:TRP157 4.0 12.3 1.0
OG D:SER70 4.0 15.0 1.0
CE2 D:TRP157 4.2 14.5 1.0
CD D:LYS73 4.3 22.3 1.0
CB D:SER70 4.3 12.6 1.0
CA D:VAL120 4.4 17.2 1.0
O D:ALA69 4.5 11.0 1.0
CG1 D:VAL120 4.5 18.2 1.0
CB D:VAL120 4.5 16.6 1.0
CD2 D:LEU158 4.5 12.9 1.0
CZ2 D:TRP157 4.6 17.4 1.0
N D:SER70 4.6 12.6 1.0
CB D:TYR123 4.7 15.7 1.0
O D:SER70 4.7 10.9 1.0
C D:ALA69 4.7 11.9 1.0
C D:SER70 4.8 12.7 1.0

Reference:

A.Akhtar, Y.Chen. Crystal Structure of Class D Beta-Lactamase Oxa-48 with Imipenem To Be Published.
Page generated: Mon Jul 29 13:35:19 2024

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