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Fluorine in PDB 2y2l: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06)

Enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06):
2.4.1.129;

Protein crystallography data

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06), PDB code: 2y2l 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) 44.92 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.055, 101.628, 145.557, 90.00, 90.00, 90.00
R / Rfree (%) 18.981 / 25.614

Other elements in 2y2l:

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06) also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 33 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06) (pdb code 2y2l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06), PDB code: 2y2l:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2y2l

Go back to Fluorine Binding Sites List in 2y2l
Fluorine binding site 1 out of 4 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06)


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 (E06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:80.8
occ:1.00
 F15 A:E061000 0.0 80.8 1.0
C14 A:E061000 1.3 47.5 1.0
C7 A:E061000 2.4 58.8 1.0
C13 A:E061000 2.4 48.8 1.0
O A:HOH2081 2.7 49.2 1.0
O6 A:E061000 2.8 48.1 1.0
C5 A:E061000 2.8 48.4 1.0
CB A:MET556 3.0 41.3 1.0
CE A:MET556 3.4 28.4 1.0
CG A:MET556 3.4 39.4 1.0
C8 A:E061000 3.6 44.3 1.0
C12 A:E061000 3.7 51.4 1.0
ND2 A:ASN518 4.0 34.9 1.0
N4 A:E061000 4.0 44.4 1.0
SD A:MET556 4.1 48.4 1.0
CG A:ASN518 4.1 38.0 1.0
C11 A:E061000 4.2 56.5 1.0
OD1 A:ASN518 4.2 31.7 1.0
O A:MET556 4.4 39.8 1.0
CA A:MET556 4.4 35.0 1.0
CB A:SER553 4.5 36.3 1.0
C A:MET556 4.6 36.2 1.0
F9 A:E061000 4.8 55.9 1.0
O A:SER553 5.0 33.6 1.0

Fluorine binding site 2 out of 4 in 2y2l

Go back to Fluorine Binding Sites List in 2y2l
Fluorine binding site 2 out of 4 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06)


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 (E06) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:55.9
occ:1.00
 F9 A:E061000 0.0 55.9 1.0
C8 A:E061000 1.3 44.3 1.0
C11 A:E061000 2.4 56.5 1.0
C7 A:E061000 2.4 58.8 1.0
C5 A:E061000 2.9 48.4 1.0
CB A:ALA459 3.0 27.5 1.0
O A:THR654 3.0 36.7 1.0
CA A:ALA459 3.1 28.6 1.0
N4 A:E061000 3.2 44.4 1.0
O A:MET556 3.3 39.8 1.0
CA A:THR655 3.4 35.2 1.0
C14 A:E061000 3.6 47.5 1.0
C12 A:E061000 3.6 51.4 1.0
C A:THR654 3.8 34.2 1.0
O1 A:E061000 3.8 32.7 1.0
O6 A:E061000 3.9 48.1 1.0
N A:THR655 4.0 37.5 1.0
C A:ALA459 4.0 34.3 1.0
C13 A:E061000 4.1 48.8 1.0
CG2 A:THR655 4.1 28.8 1.0
C A:THR655 4.2 44.6 1.0
O A:HOH2181 4.2 46.8 1.0
N A:SER460 4.2 31.3 1.0
N A:GLY656 4.2 47.1 1.0
CB A:THR655 4.3 32.0 1.0
C3 A:E061000 4.3 45.3 1.0
N A:ALA459 4.3 33.1 1.0
C16 A:E061000 4.4 39.8 1.0
C A:MET556 4.5 36.2 1.0
B A:E061000 4.6 43.4 1.0
OG A:SER457 4.7 31.1 1.0
F15 A:E061000 4.8 80.8 1.0
N A:THR654 5.0 29.4 1.0
O A:ALA459 5.0 31.4 1.0
O A:THR655 5.0 37.5 1.0

Fluorine binding site 3 out of 4 in 2y2l

Go back to Fluorine Binding Sites List in 2y2l
Fluorine binding site 3 out of 4 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:68.7
occ:1.00
 F15 B:E061000 0.0 68.7 1.0
C14 B:E061000 1.3 52.3 1.0
C7 B:E061000 2.3 59.6 1.0
O B:HOH2074 2.4 57.3 1.0
C13 B:E061000 2.4 49.8 1.0
C5 B:E061000 2.7 52.1 1.0
O6 B:E061000 2.8 46.4 1.0
CB B:MET556 3.2 48.3 1.0
CE B:MET556 3.5 35.9 1.0
C8 B:E061000 3.6 53.3 1.0
C12 B:E061000 3.7 45.1 1.0
CG B:MET556 3.8 40.2 1.0
N4 B:E061000 3.9 34.8 1.0
OD1 B:ASN518 4.0 44.0 1.0
C11 B:E061000 4.1 44.6 1.0
CG B:ASN518 4.2 41.3 1.0
ND2 B:ASN518 4.3 28.1 1.0
SD B:MET556 4.4 52.0 1.0
CA B:MET556 4.5 36.9 1.0
CB B:SER553 4.6 36.2 1.0
O B:MET556 4.6 34.1 1.0
F9 B:E061000 4.7 47.3 1.0
C B:MET556 4.7 40.3 1.0

Fluorine binding site 4 out of 4 in 2y2l

Go back to Fluorine Binding Sites List in 2y2l
Fluorine binding site 4 out of 4 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E06) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:47.3
occ:1.00
 F9 B:E061000 0.0 47.3 1.0
C8 B:E061000 1.3 53.3 1.0
C7 B:E061000 2.4 59.6 1.0
C11 B:E061000 2.4 44.6 1.0
C5 B:E061000 2.9 52.1 1.0
CB B:ALA459 3.0 23.1 1.0
O B:THR654 3.0 30.4 1.0
N4 B:E061000 3.1 34.8 1.0
CA B:ALA459 3.3 30.4 1.0
O B:MET556 3.3 34.1 1.0
CA B:THR655 3.5 34.5 1.0
C14 B:E061000 3.6 52.3 1.0
C12 B:E061000 3.6 45.1 1.0
C B:THR654 3.8 33.7 1.0
O1 B:E061000 3.8 30.2 1.0
O6 B:E061000 3.8 46.4 1.0
N B:THR655 4.0 34.8 1.0
C B:ALA459 4.0 35.8 1.0
C13 B:E061000 4.1 49.8 1.0
N B:SER460 4.1 29.3 1.0
CG2 B:THR655 4.2 27.1 1.0
C3 B:E061000 4.3 37.5 1.0
C B:THR655 4.3 39.4 1.0
CB B:THR655 4.3 31.8 1.0
N B:GLY656 4.4 36.7 1.0
N B:ALA459 4.4 30.5 1.0
O B:HOH2177 4.4 38.6 1.0
C B:MET556 4.5 40.3 1.0
C16 B:E061000 4.5 32.1 1.0
B B:E061000 4.6 39.8 1.0
F15 B:E061000 4.7 68.7 1.0
OG B:SER457 4.7 32.6 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: Wed Jul 31 16:48:42 2024

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