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Fluorine in PDB 2y2j: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4)

Enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4):
2.4.1.129;

Protein crystallography data

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4), PDB code: 2y2j was solved by C.Contreras-Martel, A.Amoroso, E.C.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.J.Schofield, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.98 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.960, 149.037, 97.283, 90.00, 90.00, 90.00
R / Rfree (%) 18.37 / 22.07

Other elements in 2y2j:

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4) also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 15 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4) (pdb code 2y2j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4), PDB code: 2y2j:

Fluorine binding site 1 out of 1 in 2y2j

Go back to Fluorine Binding Sites List in 2y2j
Fluorine binding site 1 out of 1 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:52.6
occ:1.00
 F9 A:ZA41000 0.0 52.6 1.0
C8 A:ZA41000 1.3 39.0 1.0
C11 A:ZA41000 2.3 51.5 1.0
C7 A:ZA41000 2.4 47.2 1.0
CB A:ALA459 2.9 23.9 1.0
C5 A:ZA41000 2.9 40.4 1.0
CA A:ALA459 3.0 28.9 1.0
O A:THR654 3.0 32.8 1.0
N4 A:ZA41000 3.0 33.7 1.0
O A:MET556 3.2 35.1 1.0
CA A:THR655 3.4 39.0 1.0
O1 A:ZA41000 3.6 35.6 1.0
C12 A:ZA41000 3.6 45.9 1.0
C14 A:ZA41000 3.7 48.0 1.0
C A:ALA459 3.7 28.5 1.0
C A:THR654 3.7 36.9 1.0
N A:SER460 3.8 25.2 1.0
N A:THR655 4.0 36.7 1.0
O6 A:ZA41000 4.0 46.8 1.0
CG2 A:THR655 4.0 35.0 1.0
C13 A:ZA41000 4.1 51.8 1.0
C3 A:ZA41000 4.1 37.2 1.0
N A:ALA459 4.2 26.6 1.0
CB A:THR655 4.2 38.1 1.0
C A:THR655 4.3 46.9 1.0
C A:MET556 4.4 37.6 1.0
B A:ZA41000 4.4 36.5 1.0
N A:GLY656 4.5 33.1 1.0
O A:ALA459 4.7 28.5 1.0
OG A:SER457 4.7 34.2 1.0
OG A:SER460 4.7 36.7 1.0
O A:HOH2142 4.7 43.8 1.0
N A:THR654 4.8 27.7 1.0
CA A:GLY557 4.9 37.1 1.0
CA A:THR654 5.0 33.1 1.0

Reference:

C.Contreras-Martel, A.Amoroso, E.C.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.J.Schofield, A.Dessen. Structure-Guided Design of Cell Wall Biosynthesis Inhibitors That Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa). Acs Chem.Biol V. 6 943 2011.
ISSN: ISSN 1554-8929
PubMed: 21732689
DOI: 10.1021/CB2001846
Page generated: Mon Jul 14 14:56:55 2025

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