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Chlorine in PDB 6pt1: Crystal Structure of Class D Beta-Lactamase Oxa-48 with Meropenem

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

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

Protein crystallography data

The structure of Crystal Structure of Class D Beta-Lactamase Oxa-48 with Meropenem, PDB code: 6pt1 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) 30.99 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.797, 106.512, 95.835, 90.00, 104.66, 90.00
R / Rfree (%) 18.7 / 23.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Meropenem (pdb code 6pt1). 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 Meropenem, PDB code: 6pt1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6pt1

Go back to Chlorine Binding Sites List in 6pt1
Chlorine binding site 1 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Meropenem


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:23.5
occ:1.00
 NH1 B:ARG206 3.1 19.9 1.0
NH2 A:ARG206 3.1 17.9 1.0
NH1 A:ARG206 3.2 18.3 1.0
NH2 B:ARG206 3.2 18.1 1.0
CZ B:ARG206 3.6 19.7 1.0
CZ A:ARG206 3.6 23.6 1.0
CD2 B:LEU196 4.2 18.1 1.0
CD2 A:LEU196 4.2 17.6 1.0
CG B:GLN193 4.3 25.5 1.0
CA B:GLN193 4.3 20.1 1.0
CA A:GLN193 4.4 18.6 1.0
CB B:GLN193 4.5 23.1 1.0
CG A:GLN193 4.5 24.4 1.0
CB A:GLN193 4.7 23.2 1.0
CB B:LEU196 4.7 22.0 1.0
CB A:LEU196 4.8 21.3 1.0
O B:HOH468 4.9 35.9 1.0
O B:GLN193 4.9 20.1 1.0
O A:HOH467 4.9 36.8 1.0
NE B:ARG206 4.9 22.0 1.0
NE A:ARG206 4.9 18.4 1.0
CG B:LEU196 4.9 19.8 1.0
CG A:LEU196 4.9 18.9 1.0
O A:GLN193 5.0 21.0 1.0

Chlorine binding site 2 out of 6 in 6pt1

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


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:35.1
occ:0.79
 NE1 A:TRP157 2.9 25.6 1.0
NZ A:LYS73 3.1 34.8 1.0
O A:HOH482 3.4 27.3 1.0
CE A:LYS73 3.5 36.2 1.0
CG A:LYS73 3.7 25.4 1.0
CD1 A:TRP157 3.8 26.9 1.0
CG2 A:VAL120 3.9 33.1 1.0
CE2 A:TRP157 3.9 29.8 1.0
CA A:SER70 3.9 27.1 1.0
OG A:SER70 4.2 29.9 1.0
CD A:LYS73 4.2 28.9 1.0
CZ2 A:TRP157 4.3 31.6 1.0
CA A:VAL120 4.4 32.3 1.0
CG1 A:VAL120 4.4 37.8 1.0
O A:ALA69 4.4 23.5 1.0
CB A:SER70 4.5 24.6 1.0
CB A:VAL120 4.5 34.3 1.0
CB A:TYR123 4.5 28.9 1.0
N A:SER70 4.6 21.5 1.0
CD2 A:LEU158 4.6 26.7 1.0
C A:ALA69 4.7 24.4 1.0
O A:SER70 4.7 24.4 1.0
C A:SER70 4.8 23.6 1.0
C9 A:MER303 4.9 34.5 0.9
C7 A:MER303 5.0 37.3 0.9
CG A:TRP157 5.0 22.5 1.0

Chlorine binding site 3 out of 6 in 6pt1

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


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

b:42.3
occ:0.44
 NZ B:LYS73 2.4 36.0 1.0
NE1 B:TRP157 2.6 57.4 1.0
O B:HOH462 3.0 46.2 1.0
CD1 B:TRP157 3.2 61.6 1.0
CE B:LYS73 3.3 31.7 1.0
CG B:LYS73 3.5 25.3 1.0
CE2 B:TRP157 3.7 63.0 1.0
CD B:LYS73 4.0 28.2 1.0
CA B:SER70 4.0 27.9 1.0
CG2 B:VAL120 4.1 30.6 1.0
O B:ALA69 4.2 21.9 1.0
CZ2 B:TRP157 4.3 59.5 1.0
CG B:TRP157 4.4 60.6 1.0
OG B:SER70 4.5 27.1 1.0
CD1 B:LEU158 4.6 63.1 1.0
C B:ALA69 4.6 24.3 1.0
N B:SER70 4.6 22.5 1.0
CB B:SER70 4.6 25.1 1.0
CB B:TYR123 4.7 29.0 1.0
CD2 B:TRP157 4.7 65.4 1.0
N B:LYS73 4.7 20.6 1.0
O B:SER70 4.7 22.8 1.0
C B:SER70 4.8 25.1 1.0
C9 B:MER302 4.9 35.4 0.8
CB B:LYS73 4.9 21.6 1.0
CA B:VAL120 5.0 25.7 1.0
CB B:VAL120 5.0 34.4 1.0

Chlorine binding site 4 out of 6 in 6pt1

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


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:23.4
occ:1.00
 NH1 C:ARG206 3.2 15.7 1.0
O C:HOH523 3.2 37.6 1.0
NH1 D:ARG206 3.2 17.5 1.0
NH2 C:ARG206 3.2 18.5 1.0
NH2 D:ARG206 3.2 20.1 1.0
CZ C:ARG206 3.6 21.8 1.0
CZ D:ARG206 3.6 19.0 1.0
CD2 D:LEU196 4.1 17.9 1.0
CG D:GLN193 4.2 24.1 1.0
CA D:GLN193 4.3 19.0 1.0
CD2 C:LEU196 4.3 13.8 1.0
CA C:GLN193 4.4 19.1 1.0
CG C:GLN193 4.5 23.7 1.0
CB D:GLN193 4.5 23.0 1.0
CB C:GLN193 4.6 22.9 1.0
O D:HOH494 4.7 34.4 1.0
CB C:LEU196 4.8 19.4 1.0
CB D:LEU196 4.8 21.5 1.0
O D:GLN193 4.9 20.2 1.0
CG D:LEU196 4.9 18.8 1.0
NE C:ARG206 4.9 20.7 1.0
NE D:ARG206 4.9 22.9 1.0
CG C:LEU196 5.0 18.8 1.0
O C:GLN193 5.0 19.7 1.0

Chlorine binding site 5 out of 6 in 6pt1

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


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 Meropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:38.8
occ:1.00
 NE1 C:TRP157 3.0 26.6 1.0
NZ C:LYS73 3.1 29.3 1.0
O C:HOH513 3.2 27.4 1.0
CE C:LYS73 3.5 34.1 1.0
CG C:LYS73 3.7 24.6 1.0
CG2 C:VAL120 3.8 30.4 1.0
CD1 C:TRP157 3.8 26.8 1.0
CA C:SER70 3.9 23.3 1.0
CE2 C:TRP157 4.0 28.4 1.0
OG C:SER70 4.1 27.1 1.0
CD C:LYS73 4.2 30.4 1.0
CB C:SER70 4.4 24.5 1.0
CZ2 C:TRP157 4.4 34.0 1.0
CA C:VAL120 4.4 28.9 1.0
O C:ALA69 4.4 23.3 1.0
CB C:TYR123 4.4 27.3 1.0
CB C:VAL120 4.5 33.8 1.0
CD2 C:LEU158 4.5 26.6 1.0
N C:SER70 4.6 21.9 1.0
C9 C:MER303 4.6 31.3 0.9
CG1 C:VAL120 4.6 32.1 1.0
C C:ALA69 4.7 23.7 1.0
O C:SER70 4.8 21.9 1.0
C C:SER70 4.9 24.9 1.0
CG C:TYR123 5.0 25.6 1.0

Chlorine binding site 6 out of 6 in 6pt1

Go back to Chlorine Binding Sites List in 6pt1
Chlorine binding site 6 out of 6 in the Crystal Structure of Class D Beta-Lactamase Oxa-48 with Meropenem


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

b:70.8
occ:1.00
 NZ D:LYS73 2.4 37.4 1.0
NE1 D:TRP157 2.5 58.7 1.0
CE D:LYS73 3.3 35.5 1.0
CE2 D:TRP157 3.3 65.6 1.0
CD1 D:TRP157 3.5 66.5 1.0
CG2 D:VAL120 3.5 35.7 1.0
CZ2 D:TRP157 3.7 64.7 1.0
CG D:LYS73 3.8 26.8 1.0
CD D:LYS73 4.1 29.1 1.0
CA D:SER70 4.2 29.1 1.0
OG D:SER70 4.3 27.5 1.0
CB D:VAL120 4.4 40.3 1.0
CA D:VAL120 4.5 27.0 1.0
C9 D:MER302 4.5 36.6 0.9
O D:ALA69 4.5 21.4 1.0
CD2 D:TRP157 4.5 68.0 1.0
CG D:TRP157 4.6 65.8 1.0
CG1 D:VAL120 4.6 38.1 1.0
CD2 D:LEU158 4.6 66.4 1.0
CB D:SER70 4.7 25.4 1.0
CB D:TYR123 4.7 32.5 1.0
N D:SER70 4.8 20.9 1.0
C D:ALA69 4.8 23.9 1.0
C7 D:MER302 4.8 39.0 0.9

Reference:

A.Akhtar, Y.Chen. Crystal Structure of Class D Beta-Lactamase Oxa-48 with Meropenem To Be Published.
Page generated: Mon Jul 29 13:34:52 2024

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