Fluorine in PDB 2y2k: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5):
2.4.1.129;

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5), PDB code: 2y2k was solved by C.Contreras-Martel, A.Amoroso, E.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.Schofield, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.55 / 2.09
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	98.309, 149.908, 97.578, 90.00, 90.00, 90.00
R / Rfree (%)	20.178 / 26.252

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5) also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	17 atoms

The binding sites of Fluorine atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5) (pdb code 2y2k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5), PDB code: 2y2k:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5)


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 (ZA5) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:61.8 occ:1.00 F15 A:ZA51000 0.0 61.8 1.0 C14 A:ZA51000 1.3 54.0 1.0 C7 A:ZA51000 2.3 53.6 1.0 C13 A:ZA51000 2.4 49.3 1.0 O6 A:ZA51000 2.6 61.7 1.0 C5 A:ZA51000 2.7 47.0 1.0 CB A:MET556 3.4 44.0 1.0 CE A:MET556 3.5 28.8 1.0 C8 A:ZA51000 3.6 56.9 1.0 CG A:MET556 3.6 41.7 1.0 C12 A:ZA51000 3.7 45.3 1.0 ND2 A:ASN518 3.8 39.0 1.0 N4 A:ZA51000 3.8 36.0 1.0 CG A:ASN518 3.9 34.1 1.0 OD1 A:ASN518 4.1 32.0 1.0 C11 A:ZA51000 4.2 60.1 1.0 SD A:MET556 4.4 48.1 1.0 O A:MET556 4.6 38.0 1.0 O A:HOH2079 4.6 38.1 1.0 F9 A:ZA51000 4.7 53.4 1.0 CB A:ASN518 4.8 29.8 1.0 C3 A:ZA51000 4.8 33.6 1.0 CA A:MET556 4.8 42.4 1.0 CB A:SER553 5.0 31.5 1.0

Fluorine binding site 2 out of 2 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA5) within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:53.4 occ:1.00 F9 A:ZA51000 0.0 53.4 1.0 C8 A:ZA51000 1.4 56.9 1.0 C11 A:ZA51000 2.4 60.1 1.0 C7 A:ZA51000 2.4 53.6 1.0 O A:THR654 2.8 30.1 1.0 CB A:ALA459 2.8 22.1 1.0 C5 A:ZA51000 2.9 47.0 1.0 N4 A:ZA51000 3.0 36.0 1.0 CA A:ALA459 3.2 28.9 1.0 O A:MET556 3.3 38.0 1.0 CA A:THR655 3.4 44.7 1.0 C A:THR654 3.6 39.0 1.0 O1 A:ZA51000 3.6 39.5 1.0 C12 A:ZA51000 3.6 45.3 1.0 C14 A:ZA51000 3.7 54.0 1.0 O6 A:ZA51000 3.9 61.7 1.0 N A:THR655 3.9 39.9 1.0 C A:ALA459 4.0 29.5 1.0 N A:SER460 4.0 29.9 1.0 C13 A:ZA51000 4.1 49.3 1.0 C3 A:ZA51000 4.1 33.6 1.0 C A:THR655 4.1 60.2 1.0 CG2 A:THR655 4.1 41.8 1.0 CB A:THR655 4.2 39.8 1.0 N A:GLY656 4.4 45.9 1.0 N A:ALA459 4.4 28.1 1.0 B A:ZA51000 4.4 49.5 1.0 C A:MET556 4.6 41.7 1.0 N A:THR654 4.7 29.7 1.0 F15 A:ZA51000 4.7 61.8 1.0 CA A:THR654 4.8 30.3 1.0 OG A:SER457 4.8 36.4 1.0 OG A:SER460 4.9 44.6 1.0 O A:THR655 4.9 41.0 1.0

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