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Zinc in PDB 5tx9: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole

Protein crystallography data

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole, PDB code: 5tx9 was solved by J.A.N.Alexander, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.84 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.882, 92.252, 79.381, 90.00, 100.22, 90.00
R / Rfree (%) 20.8 / 24.1

Other elements in 5tx9:

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole (pdb code 5tx9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole, PDB code: 5tx9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5tx9

Go back to Zinc Binding Sites List in 5tx9
Zinc binding site 1 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:38.5
occ:1.00
NE2 A:HIS382 2.1 51.2 1.0
OE2 A:GLU336 2.2 41.0 1.0
CE1 A:HIS382 2.6 49.5 1.0
CD A:GLU336 3.1 38.0 1.0
CD1 A:TYR334 3.3 67.8 1.0
CD2 A:HIS382 3.4 47.4 1.0
OE1 A:GLU336 3.5 41.6 1.0
CE1 A:TYR334 3.9 70.1 1.0
ND1 A:HIS382 3.9 48.2 1.0
CG A:TYR334 3.9 64.8 1.0
CB A:TYR334 4.2 52.7 1.0
CG A:HIS382 4.2 47.2 1.0
CG A:GLU336 4.4 29.6 1.0
CZ A:TYR334 4.8 73.0 1.0
CD2 A:TYR334 4.8 71.2 1.0

Zinc binding site 2 out of 4 in 5tx9

Go back to Zinc Binding Sites List in 5tx9
Zinc binding site 2 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:16.6
occ:0.38
OE2 A:GLU357 2.0 23.6 1.0
CD A:GLU357 2.9 21.2 1.0
OE1 A:GLU357 3.2 23.7 1.0
O A:HOH790 3.3 21.5 1.0
CE1 A:HIS362 3.8 16.3 1.0
NE2 A:HIS362 4.2 14.3 1.0
CG A:GLU357 4.3 20.7 1.0
O A:HOH724 4.3 26.1 1.0
ND1 A:HIS362 4.8 15.4 1.0
O A:HOH810 4.9 35.9 1.0

Zinc binding site 3 out of 4 in 5tx9

Go back to Zinc Binding Sites List in 5tx9
Zinc binding site 3 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:86.3
occ:1.00
OE2 B:GLU336 2.6 51.9 1.0
CE1 B:HIS382 2.9 61.6 1.0
CD B:GLU336 3.2 49.7 1.0
OE1 B:GLU380 3.5 49.9 1.0
NE2 B:HIS382 3.6 63.0 1.0
OE1 B:GLU336 3.7 50.2 1.0
CG B:GLU336 3.9 44.1 1.0
ND1 B:HIS382 4.0 60.3 1.0
CD B:GLU380 4.6 44.4 1.0
CB B:GLU336 4.8 35.9 1.0
CB B:GLU380 4.9 27.8 1.0
CD2 B:HIS382 4.9 62.1 1.0

Zinc binding site 4 out of 4 in 5tx9

Go back to Zinc Binding Sites List in 5tx9
Zinc binding site 4 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:23.9
occ:0.36
OE2 B:GLU357 1.9 24.3 1.0
CD B:GLU357 2.7 20.0 1.0
OE1 B:GLU357 2.8 20.2 1.0
O B:HOH800 3.1 21.1 1.0
CE1 B:HIS362 4.1 15.4 1.0
CG B:GLU357 4.1 23.1 1.0
O B:HOH685 4.3 24.0 1.0
O B:HOH811 4.5 26.3 1.0
NE2 B:HIS362 4.6 15.5 1.0
ND1 B:HIS362 5.0 15.1 1.0

Reference:

J.A.N.Alexander, S.S.Chatterjee, S.M.Hamilton, L.D.Eltis, H.F.Chambers, N.C.J.Strynadka. Structural and Kinetic Analysis of Penicillin-Binding Protein 4 (PBP4)-Mediated Antibiotic Resistance Instaphylococcus Aureus. J. Biol. Chem. 2018.
ISSN: ESSN 1083-351X
PubMed: 30366985
DOI: 10.1074/JBC.RA118.004952
Page generated: Wed Dec 16 10:57:30 2020

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