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Chlorine in PDB 5df8: Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone

Enzymatic activity of Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone

All present enzymatic activity of Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone:
2.4.1.129;

Protein crystallography data

The structure of Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone, PDB code: 5df8 was solved by J.Ren, J.E.Nettleship, A.Males, D.I.Stuart, R.J.Owens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.21 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.218, 74.374, 82.448, 71.69, 86.06, 85.88
R / Rfree (%) 22.6 / 26.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone (pdb code 5df8). 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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone, PDB code: 5df8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5df8

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Chlorine binding site 1 out of 6 in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone


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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:34.5
occ:1.00
 N A:VAL388 3.0 14.4 1.0
NE A:ARG387 3.6 14.5 1.0
CA A:ARG387 3.6 13.5 1.0
C A:ARG387 3.8 14.2 1.0
CD A:ARG387 3.8 13.2 1.0
CB B:LEU240 3.8 16.9 1.0
CB A:VAL388 3.9 22.7 1.0
CB A:ARG387 3.9 13.8 1.0
CA A:VAL388 3.9 17.3 1.0
N A:GLY389 4.2 15.6 1.0
CD2 B:LEU240 4.2 21.1 1.0
O B:LEU240 4.3 12.9 1.0
CG A:ARG387 4.4 14.6 1.0
CG B:LEU240 4.5 18.7 1.0
CG2 A:VAL388 4.5 19.4 1.0
C A:VAL388 4.6 16.9 1.0
C B:LEU240 4.6 14.5 1.0
CA B:LEU240 4.6 15.8 1.0
O A:GLU386 4.7 18.9 1.0
CD1 B:LEU240 4.7 16.1 1.0
CZ A:ARG387 4.8 14.2 1.0
N A:ARG387 4.9 13.6 1.0
O A:HOH885 5.0 24.0 1.0

Chlorine binding site 2 out of 6 in 5df8

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Chlorine binding site 2 out of 6 in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone


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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:48.7
occ:1.00
 N A:MET436 3.4 16.4 1.0
OG1 A:THR437 3.4 17.9 1.0
OG A:SER435 3.6 15.5 1.0
N A:THR437 3.9 16.2 1.0
CA A:SER435 3.9 16.4 1.0
CG A:MET436 3.9 29.4 1.0
CG2 A:THR437 4.1 18.4 1.0
C A:SER435 4.1 17.9 1.0
CB A:THR437 4.2 18.2 1.0
CA A:MET436 4.3 15.7 1.0
CB A:SER435 4.3 15.8 1.0
CD2 A:LEU381 4.3 22.7 1.0
C A:MET436 4.4 16.9 1.0
CB A:MET436 4.6 19.8 1.0
CA A:THR437 4.7 16.7 1.0
O A:LEU434 4.9 15.9 1.0

Chlorine binding site 3 out of 6 in 5df8

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Chlorine binding site 3 out of 6 in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone


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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:33.2
occ:1.00
 NH1 A:ARG504 3.3 13.6 1.0
N A:VAL491 3.3 16.0 1.0
O A:HOH913 3.4 34.6 1.0
NH2 A:ARG504 3.5 15.9 1.0
O A:HOH848 3.6 30.6 1.0
CA A:LYS490 3.7 21.0 1.0
CE A:LYS490 3.7 29.8 1.0
CB A:LYS490 3.8 20.3 1.0
CZ A:ARG504 3.9 13.9 1.0
C A:LYS490 4.0 18.5 1.0
CG A:LYS490 4.0 19.7 1.0
CB A:VAL491 4.1 17.4 1.0
O A:HOH924 4.1 51.8 1.0
CA A:VAL491 4.3 17.0 1.0
CG2 A:VAL491 4.3 15.0 1.0
O A:HOH744 4.5 8.9 1.0
CD A:LYS490 4.5 25.8 1.0
O A:VAL491 4.8 17.3 1.0
NZ A:LYS490 4.9 33.4 1.0
O A:HOH1003 4.9 34.0 1.0

Chlorine binding site 4 out of 6 in 5df8

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Chlorine binding site 4 out of 6 in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone


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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:38.4
occ:1.00
 NE2 B:GLN265 3.2 13.7 1.0
CG2 B:THR267 3.4 11.2 1.0
CE1 B:HIS232 3.5 21.0 1.0
CD B:ARG236 3.6 29.2 1.0
O B:HOH910 3.6 25.9 1.0
NE2 B:HIS232 3.6 21.0 1.0
NE B:ARG236 3.7 39.6 1.0
OE1 B:GLN265 3.9 16.1 1.0
O B:HOH716 3.9 17.1 1.0
O B:HOH948 3.9 53.3 1.0
CD B:GLN265 4.0 18.1 1.0
CG B:GLU159 4.2 24.5 1.0
CG B:ARG236 4.3 18.7 1.0
O B:HOH858 4.6 23.8 1.0
ND1 B:HIS232 4.7 21.9 1.0
CB B:ARG236 4.8 16.3 1.0
CB B:THR267 4.9 11.5 1.0
CZ B:ARG236 4.9 44.9 1.0
CD2 B:HIS232 4.9 18.9 1.0

Chlorine binding site 5 out of 6 in 5df8

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Chlorine binding site 5 out of 6 in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone


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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl606

b:31.2
occ:1.00
 NH1 B:ARG504 3.3 13.2 1.0
O B:HOH817 3.3 21.3 1.0
N B:VAL491 3.3 21.4 1.0
CG2 B:VAL491 3.8 21.1 1.0
NH2 B:ARG504 3.8 14.6 1.0
CB B:VAL491 3.9 23.8 1.0
CA B:LYS490 4.0 21.3 1.0
CZ B:ARG504 4.0 14.8 1.0
CB B:LYS490 4.1 21.7 1.0
CE B:LYS490 4.1 28.4 1.0
C B:LYS490 4.2 20.9 1.0
CA B:VAL491 4.2 21.7 1.0
O B:HOH914 4.4 38.5 1.0
CG B:LYS490 4.5 20.2 1.0
O B:HOH748 4.5 13.6 1.0
O B:VAL491 4.7 21.1 1.0
O B:HOH944 4.8 51.9 1.0
CD B:LYS490 5.0 23.9 1.0
C B:VAL491 5.0 23.5 1.0

Chlorine binding site 6 out of 6 in 5df8

Go back to Chlorine Binding Sites List in 5df8
Chlorine binding site 6 out of 6 in the Crystal Structure of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone


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 Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa in Complex with Cefoperazone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:51.2
occ:1.00
 N B:ASN501 3.3 39.2 1.0
NE B:ARG499 3.7 36.8 1.0
CB B:ARG499 3.8 29.9 1.0
CB B:ASN501 3.8 42.5 1.0
CA B:ASN501 3.8 41.6 1.0
N B:GLU500 3.9 34.0 1.0
NH1 B:ARG499 3.9 27.3 1.0
N B:ALA502 3.9 33.9 1.0
C B:ASN501 4.0 34.4 1.0
CG B:GLU500 4.2 68.4 1.0
CZ B:ARG499 4.3 35.4 1.0
C B:GLU500 4.4 43.0 1.0
CA B:ARG499 4.5 28.0 1.0
C B:ARG499 4.5 28.3 1.0
CB B:ALA502 4.5 22.3 1.0
CG B:ARG499 4.6 34.0 1.0
CA B:GLU500 4.6 45.7 1.0
ND2 B:ASN501 4.6 58.7 1.0
O B:ASN501 4.7 34.4 1.0
CD B:ARG499 4.7 33.0 1.0
CG B:ASN501 4.8 55.3 1.0
CA B:ALA502 4.8 26.2 1.0
CB B:GLU500 5.0 55.8 1.0

Reference:

J.Ren, J.E.Nettleship, A.Males, D.I.Stuart, R.J.Owens. Crystal Structures of Penicillin-Binding Protein 3 in Complexes with Azlocillin and Cefoperazone in Both Acylated and Deacylated Forms. Febs Lett. V. 590 288 2016.
ISSN: ISSN 0014-5793
PubMed: 26823174
DOI: 10.1002/1873-3468.12054
Page generated: Fri Jul 26 06:40:28 2024

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