Atomistry » Fluorine » PDB 2y1x-2z5z » 2y2l
Atomistry »
  Fluorine »
    PDB 2y1x-2z5z »
      2y2l »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy