Fluorine in PDB 2vvt: Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor

All present enzymatic activity of Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor:
5.1.1.3;

The structure of Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor, PDB code: 2vvt was solved by B.Geng, G.Breault, J.Comita-Prevoir, R.Petrichko, C.Eyermann, T.Lundqvist, P.Doig, E.Gorseth, B.Noonan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.65 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.402, 69.432, 165.120, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.4

The binding sites of Fluorine atom in the Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor (pdb code 2vvt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor, PDB code: 2vvt:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1269 b:23.6 occ:1.00 F31 A:I241269 0.0 23.6 1.0 C26 A:I241269 1.3 20.4 1.0 C25 A:I241269 2.3 19.4 1.0 C27 A:I241269 2.4 21.6 1.0 C24 A:I241269 2.7 19.0 1.0 N9 A:I241269 3.0 18.2 1.0 C8 A:I241269 3.1 19.8 1.0 OD1 A:ASN155 3.3 34.2 1.0 O A:HOH2199 3.5 36.0 1.0 C30 A:I241269 3.6 18.4 1.0 ND2 A:ASN155 3.6 26.0 1.0 C28 A:I241269 3.6 20.4 1.0 CG A:ASN155 3.8 27.7 1.0 C5 A:I241269 4.1 18.9 1.0 C29 A:I241269 4.1 19.0 1.0 N7 A:I241269 4.1 17.9 1.0 CG1 A:ILE250 4.3 22.8 1.0 C6 A:I241269 4.6 18.0 1.0 F32 A:I241269 4.7 21.8 1.0 N1 A:I241269 4.9 16.6 1.0 CD1 A:ILE250 5.0 25.3 1.0

Fluorine binding site 2 out of 4 in the Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1269 b:21.8 occ:1.00 F32 A:I241269 0.0 21.8 1.0 C30 A:I241269 1.4 18.4 1.0 C25 A:I241269 2.3 19.4 1.0 C29 A:I241269 2.4 19.0 1.0 C24 A:I241269 2.8 19.0 1.0 N1 A:I241269 3.3 16.6 1.0 CG1 A:VAL152 3.4 12.7 1.0 C20 A:I241269 3.6 16.5 1.0 CG A:LEU190 3.6 12.6 1.0 C26 A:I241269 3.6 20.4 1.0 C28 A:I241269 3.6 20.4 1.0 N9 A:I241269 3.7 18.2 1.0 C21 A:I241269 3.7 17.1 1.0 CE2 A:TYR157 3.7 18.4 1.0 C22 A:I241269 3.8 17.4 1.0 C5 A:I241269 3.8 18.9 1.0 CD1 A:LEU190 3.9 15.4 1.0 C27 A:I241269 4.1 21.6 1.0 O A:VAL152 4.2 14.5 1.0 CZ A:TYR157 4.3 20.6 1.0 CD2 A:TYR157 4.3 18.7 1.0 C2 A:I241269 4.4 17.8 1.0 OH A:TYR157 4.4 23.5 1.0 CD2 A:LEU190 4.4 11.1 1.0 C23 A:I241269 4.5 17.2 1.0 CB A:LEU190 4.6 10.6 1.0 O11 A:I241269 4.6 16.8 1.0 F31 A:I241269 4.7 23.6 1.0 CB A:VAL152 4.8 12.8 1.0 C A:VAL152 4.9 14.7 1.0 O A:HOH2199 4.9 36.0 1.0

Fluorine binding site 3 out of 4 in the Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F1269 b:9.4 occ:1.00 F31 B:I241269 0.0 9.4 1.0 C26 B:I241269 1.4 8.8 1.0 C27 B:I241269 2.4 9.0 1.0 C25 B:I241269 2.4 8.9 1.0 C24 B:I241269 2.8 9.6 1.0 N1 B:I241269 3.3 8.0 1.0 CG1 B:VAL152 3.3 7.4 1.0 O B:VAL152 3.5 8.9 1.0 C20 B:I241269 3.6 7.7 1.0 C22 B:I241269 3.6 9.1 1.0 C30 B:I241269 3.6 10.4 1.0 C28 B:I241269 3.6 11.7 1.0 C21 B:I241269 3.7 7.7 1.0 N9 B:I241269 3.8 7.3 1.0 C5 B:I241269 3.9 8.8 1.0 CE2 B:TYR157 3.9 10.0 1.0 C29 B:I241269 4.1 10.8 1.0 C B:VAL152 4.2 7.5 1.0 CG B:LEU190 4.3 9.0 1.0 C2 B:I241269 4.3 9.2 1.0 CD2 B:TYR157 4.3 12.2 1.0 C23 B:I241269 4.5 9.9 1.0 O11 B:I241269 4.6 8.9 1.0 CB B:VAL152 4.6 7.7 1.0 CZ B:TYR157 4.7 11.3 1.0 F32 B:I241269 4.7 12.3 1.0 CA B:VAL152 4.8 7.3 1.0 CD2 B:LEU190 4.8 10.2 1.0 CD1 B:LEU190 4.9 9.1 1.0 OH B:TYR157 4.9 13.6 1.0 OD1 B:ASN155 4.9 13.8 1.0

Fluorine binding site 4 out of 4 in the Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Glutamate Racemase (Muri) From E. Faecalis in Complex with A 9-Benzyl Purine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F1269 b:12.3 occ:1.00 F32 B:I241269 0.0 12.3 1.0 C30 B:I241269 1.3 10.4 1.0 C25 B:I241269 2.3 8.9 1.0 C29 B:I241269 2.4 10.8 1.0 C24 B:I241269 2.8 9.6 1.0 N9 B:I241269 3.1 7.3 1.0 C8 B:I241269 3.2 8.2 1.0 O B:GLU153 3.3 10.9 1.0 O B:HOH2236 3.4 17.1 1.0 C26 B:I241269 3.6 8.8 1.0 C28 B:I241269 3.6 11.7 1.0 OE2 B:GLU153 3.8 14.4 1.0 CA B:GLU153 4.0 9.0 1.0 CD1 B:ILE250 4.1 10.1 1.0 C B:GLU153 4.1 9.9 1.0 C27 B:I241269 4.1 9.0 1.0 C5 B:I241269 4.2 8.8 1.0 N7 B:I241269 4.3 8.7 1.0 CD B:GLU153 4.4 12.1 1.0 O B:HOH2239 4.5 15.4 1.0 CB B:GLU153 4.7 9.4 1.0 F31 B:I241269 4.7 9.4 1.0 O B:VAL152 4.7 8.9 1.0 C6 B:I241269 4.9 8.1 1.0

B.Geng, G.Breault, J.Comita-Prevoir, R.Petrichko, C.Eyermann, T.Lundqvist, P.Doig, E.Gorseth, B.Noonan. Exploring 9-Benzyl Purines As Inhibitors of Glutamate Racemase (Muri) in Gram-Positive Bacteria. Bioorg.Med.Chem.Lett. V. 18 4368 2008.
ISSN: ISSN 0960-894X
PubMed: 18614367
DOI: 10.1016/J.BMCL.2008.06.068