Fluorine in PDB 3d6v: Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase

All present enzymatic activity of Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase:
6.1.1.1;

The structure of Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase, PDB code: 3d6v was solved by W.Liu, E.Tippmann, A.V.Mack, P.G.Schultz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.92 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.155, 104.155, 70.826, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 27

The binding sites of Fluorine atom in the Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase (pdb code 3d6v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase, PDB code: 3d6v:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:67.1 occ:1.00 F16 A:TFQ400 0.0 67.1 1.0 C14 A:TFQ400 1.3 65.9 1.0 F17 A:TFQ400 2.1 66.9 1.0 F15 A:TFQ400 2.2 65.8 1.0 C13 A:TFQ400 2.3 55.2 1.0 C1 A:TFQ400 2.6 51.7 1.0 CD2 A:LEU65 2.8 48.6 1.0 C6 A:TFQ400 3.2 52.9 1.0 C2 A:TFQ400 3.3 50.4 1.0 CB A:LEU65 3.5 43.1 1.0 CG A:LEU65 3.8 45.7 1.0 CA A:GLY34 4.0 41.0 1.0 O A:HOH412 4.1 47.6 1.0 N A:GLY34 4.1 38.6 1.0 CD1 A:ILE32 4.2 40.2 1.0 CG1 A:ILE32 4.2 38.6 1.0 C5 A:TFQ400 4.3 49.1 1.0 C3 A:TFQ400 4.3 50.0 1.0 ND1 A:HIS160 4.3 45.9 1.0 C A:ILE33 4.5 37.4 1.0 CG A:HIS160 4.6 46.2 1.0 O A:ILE33 4.6 35.6 1.0 CB A:HIS160 4.8 48.2 1.0 CD1 A:LEU65 4.8 40.3 1.0 C4 A:TFQ400 4.8 50.3 1.0 CE1 A:HIS160 4.9 44.5 1.0 CG2 A:ILE32 5.0 34.1 1.0 CA A:LEU65 5.0 42.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:66.9 occ:1.00 F17 A:TFQ400 0.0 66.9 1.0 C14 A:TFQ400 1.3 65.9 1.0 F16 A:TFQ400 2.1 67.1 1.0 F15 A:TFQ400 2.1 65.8 1.0 C13 A:TFQ400 2.4 55.2 1.0 CD1 A:ILE32 3.5 40.2 1.0 CB A:HIS160 3.5 48.2 1.0 CE1 A:TYR161 3.6 54.8 1.0 C1 A:TFQ400 3.6 51.7 1.0 CG2 A:ILE32 3.7 34.1 1.0 CZ A:TYR161 3.7 51.4 1.0 O A:HIS160 3.8 52.2 1.0 OH A:TYR161 3.8 53.2 1.0 CG1 A:ILE32 3.8 38.6 1.0 O A:HOH412 3.9 47.6 1.0 CG A:HIS160 4.0 46.2 1.0 ND1 A:HIS160 4.2 45.9 1.0 CD1 A:TYR161 4.3 51.9 1.0 C2 A:TFQ400 4.3 50.4 1.0 C A:HIS160 4.3 51.2 1.0 CB A:ILE32 4.4 39.4 1.0 CE2 A:TYR161 4.4 51.1 1.0 CA A:HIS160 4.5 49.4 1.0 CD2 A:LEU65 4.6 48.6 1.0 C6 A:TFQ400 4.6 52.9 1.0 CD2 A:HIS160 4.9 44.0 1.0 CG A:TYR161 4.9 53.9 1.0 CD2 A:TYR161 5.0 50.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:F400 b:65.8 occ:1.00 F15 A:TFQ400 0.0 65.8 1.0 C14 A:TFQ400 1.3 65.9 1.0 F17 A:TFQ400 2.1 66.9 1.0 F16 A:TFQ400 2.2 67.1 1.0 C13 A:TFQ400 2.4 55.2 1.0 C2 A:TFQ400 2.8 50.4 1.0 C1 A:TFQ400 2.9 51.7 1.0 N A:GLY34 3.7 38.6 1.0 O A:HOH405 3.8 46.8 1.0 CG2 A:ILE32 3.8 34.1 1.0 OH A:TYR161 4.0 53.2 1.0 C3 A:TFQ400 4.1 50.0 1.0 C A:ILE33 4.1 37.4 1.0 C6 A:TFQ400 4.1 52.9 1.0 CG1 A:ILE32 4.2 38.6 1.0 CA A:GLY34 4.3 41.0 1.0 CE1 A:TYR161 4.3 54.8 1.0 CA A:ILE33 4.4 37.2 1.0 CZ A:TYR161 4.5 51.4 1.0 CB A:ILE32 4.6 39.4 1.0 CD1 A:ILE32 4.6 40.2 1.0 N A:ILE33 4.7 37.8 1.0 O A:ILE33 4.7 35.6 1.0 C A:ILE32 4.7 38.0 1.0 O A:ILE32 4.8 36.7 1.0 CD2 A:LEU65 4.9 48.6 1.0

E.Tippmann, W.Liu, D.Summerer, A.V.Mack, P.G.Schultz. A Genetically Encoded Diazirine Photocrosslinker in Escherichia Coli Chembiochem V. 8 2210 2007.
ISSN: ISSN 1439-4227
PubMed: 18000916
DOI: 10.1002/CBIC.200700460