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Sodium in PDB 5txi: Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole

Protein crystallography data

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole, PDB code: 5txi 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) 46.15 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.904, 92.293, 79.519, 90.00, 100.01, 90.00
R / Rfree (%) 17.1 / 20.2

Other elements in 5txi:

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 5txi

Go back to Sodium Binding Sites List in 5txi
Sodium binding site 1 out of 4 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:32.5
occ:1.00
O A:HOH520 2.2 30.8 1.0
OD1 A:ASP313 2.3 27.2 1.0
CG A:ASP313 3.2 28.1 1.0
OD2 A:ASP313 3.5 29.6 1.0
OE1 A:GLU309 3.9 27.1 1.0
O A:HOH656 4.0 22.2 1.0
O A:GLU309 4.4 18.0 1.0
CB A:ASP313 4.6 19.9 1.0
N A:ASP313 4.7 15.4 1.0
NH1 A:ARG276 4.8 18.3 1.0
CA A:ASP313 4.8 16.8 1.0

Sodium binding site 2 out of 4 in 5txi

Go back to Sodium Binding Sites List in 5txi
Sodium binding site 2 out of 4 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:29.6
occ:1.00
OD2 A:ASP364 2.0 39.1 1.0
O A:HOH733 2.1 32.0 1.0
CG A:ASP364 2.9 29.6 1.0
OD1 A:ASP364 3.1 30.9 1.0
O A:HOH558 4.0 35.7 1.0
CE A:LYS353 4.2 46.0 1.0
CB A:ASP364 4.3 24.2 1.0
CA A:TYR365 4.4 18.5 1.0
C A:ASP364 4.4 18.4 1.0
N A:TYR365 4.4 19.1 1.0
O A:ASP364 4.5 21.2 1.0
C A:TYR365 4.6 17.7 1.0
N A:PRO366 4.8 19.1 1.0
CD A:PRO366 4.9 19.1 1.0
CA A:ASP364 5.0 20.3 1.0

Sodium binding site 3 out of 4 in 5txi

Go back to Sodium Binding Sites List in 5txi
Sodium binding site 3 out of 4 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:10.2
occ:1.00
O B:HOH518 2.1 21.6 1.0
O B:HOH700 2.1 36.8 1.0
O B:HOH701 2.1 28.5 1.0
O B:HOH612 2.1 36.8 1.0
OD1 B:ASP313 2.1 24.0 1.0
O B:HOH758 2.3 31.5 1.0
CG B:ASP313 3.1 23.1 1.0
OD2 B:ASP313 3.4 23.5 1.0
OE1 B:GLU309 3.9 24.8 1.0
O B:HOH697 4.2 18.2 1.0
O B:HOH635 4.2 37.1 1.0
O B:GLU309 4.3 15.8 1.0
CB B:ASP313 4.4 20.1 1.0
N B:ASP313 4.6 14.7 1.0
CA B:ASP313 4.6 14.7 1.0
NH1 B:ARG276 4.8 15.0 1.0
C B:PHE312 4.9 18.2 1.0
CB B:PHE312 4.9 13.4 1.0

Sodium binding site 4 out of 4 in 5txi

Go back to Sodium Binding Sites List in 5txi
Sodium binding site 4 out of 4 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:18.6
occ:1.00
OD2 B:ASP364 2.0 34.6 1.0
O B:HOH760 2.1 24.6 1.0
O B:HOH759 2.3 22.2 1.0
CG B:ASP364 2.9 28.1 1.0
OD1 B:ASP364 3.2 28.9 1.0
O B:HOH638 4.1 29.4 1.0
CA B:TYR365 4.3 15.9 1.0
CB B:ASP364 4.3 18.8 1.0
N B:TYR365 4.4 17.0 1.0
CE B:LYS353 4.4 38.9 1.0
C B:ASP364 4.5 21.3 1.0
C B:TYR365 4.5 16.7 1.0
O B:ASP364 4.6 19.7 1.0
N B:PRO366 4.8 17.5 1.0
CD B:PRO366 4.9 19.7 1.0
O B:TYR365 5.0 16.3 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: Tue Dec 15 11:38:50 2020

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