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Fluorine in PDB 2y68: Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase

Enzymatic activity of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase

All present enzymatic activity of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase:
6.3.2.9;

Protein crystallography data

The structure of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase, PDB code: 2y68 was solved by T.Tomasic, N.Zidar, R.Sink, A.Kovac, D.Patin, D.Blanot, C.Contreras-Martel, A.Dessen, M.Muller-Premru, A.Zega, S.Gobec, L.Peterlin-Masic, D.Kikelj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.35 / 1.49
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 65.544, 65.544, 134.959, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.4

Other elements in 2y68:

The structure of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase (pdb code 2y68). 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 Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase, PDB code: 2y68:

Fluorine binding site 1 out of 1 in 2y68

Go back to Fluorine Binding Sites List in 2y68
Fluorine binding site 1 out of 1 in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:32.5
occ:1.00
 FAS A:T04500 0.0 32.5 1.0
CAS A:T04500 1.4 28.8 1.0
CAR A:T04500 2.3 31.4 1.0
CAT A:T04500 2.4 29.4 1.0
CAU A:T04500 3.0 29.3 1.0
O A:HOH2193 3.0 27.1 1.0
O A:HOH2234 3.0 26.6 1.0
CE2 A:PHE161 3.2 29.0 1.0
OBC A:T04500 3.2 30.7 1.0
CD2 A:PHE161 3.2 24.0 1.0
CE1 A:HIS183 3.4 16.2 1.0
O A:HOH2165 3.4 33.9 1.0
CAP A:T04500 3.6 34.1 1.0
NE2 A:HIS183 3.7 19.1 1.0
CAQ A:T04500 3.7 24.8 1.0
N A:T04500 4.1 26.4 1.0
CAO A:T04500 4.1 28.0 1.0
CB A:SER159 4.2 15.0 1.0
ND1 A:HIS183 4.2 17.4 1.0
CZ A:PHE161 4.3 21.0 1.0
OXT A:T04500 4.3 26.0 1.0
CG A:PHE161 4.4 13.5 1.0
CD2 A:HIS183 4.6 18.2 1.0
OG A:SER159 4.7 14.2 1.0
O A:HOH2163 4.8 40.4 1.0
CA A:T04500 4.8 31.3 1.0
C A:T04500 4.9 26.6 1.0
O A:HOH2166 4.9 34.5 1.0
CG A:HIS183 4.9 15.4 1.0
O A:HOH2441 4.9 45.2 1.0

Reference:

T.Tomasic, N.Zidar, R.Sink, A.Kovac, D.Blanot, C.Contreras-Martel, A.Dessen, M.Muller-Premru, A.Zega, S.Gobec, D.Kikelj, L.P.Masic. Structure-Based Design of A New Series of D-Glutamic Acid Based Inhibitors of Bacterial Udp-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase (Murd). J. Med. Chem. V. 54 4600 2011.
ISSN: ISSN 1520-4804
PubMed: 21591605
DOI: 10.1021/JM2002525
Page generated: Mon Jul 14 14:57:57 2025

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