Fluorine in PDB 3d6u: 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: 3d6u 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)	45.98 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.779, 102.779, 70.780, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 27.4

The binding sites of Fluorine atom in the Crystal Structure of 4-(Trifluoromethyldiazirinyl) Phenylalanyl-Trna Synthetase (pdb code 3d6u). 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: 3d6u:
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:F315 b:39.2 occ:1.00 F17 A:T11315 0.0 39.2 1.0 C14 A:T11315 1.3 37.9 1.0 F15 A:T11315 2.1 36.9 1.0 F16 A:T11315 2.2 43.2 1.0 C13 A:T11315 2.4 30.7 1.0 N19 A:T11315 2.8 34.9 1.0 N18 A:T11315 2.9 36.1 1.0 CD1 A:ILE32 3.4 24.8 1.0 CB A:HIS160 3.5 29.2 1.0 CE1 A:TYR161 3.7 29.7 1.0 C1 A:T11315 3.7 29.3 1.0 CG1 A:ILE32 3.7 22.9 1.0 O A:HOH318 3.8 31.3 1.0 CZ A:TYR161 3.8 29.1 1.0 OH A:TYR161 3.8 31.0 1.0 CG2 A:ILE32 3.9 20.1 1.0 O A:HIS160 3.9 30.8 1.0 CG A:HIS160 3.9 26.2 1.0 ND1 A:HIS160 4.2 24.8 1.0 CD2 A:LEU65 4.4 25.5 1.0 CD1 A:TYR161 4.4 28.9 1.0 CB A:ILE32 4.4 26.0 1.0 C2 A:T11315 4.4 25.1 1.0 C A:HIS160 4.4 31.2 1.0 CA A:HIS160 4.5 30.5 1.0 CE2 A:TYR161 4.6 30.5 1.0 C6 A:T11315 4.6 29.6 1.0 O A:HOH361 4.7 37.4 1.0 CB A:LEU65 4.9 26.2 1.0 CD2 A:HIS160 4.9 23.5 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:F315 b:36.9 occ:1.00 F15 A:T11315 0.0 36.9 1.0 C14 A:T11315 1.3 37.9 1.0 F16 A:T11315 2.1 43.2 1.0 F17 A:T11315 2.1 39.2 1.0 C13 A:T11315 2.2 30.7 1.0 O A:HOH361 2.9 37.4 1.0 C1 A:T11315 3.0 29.3 1.0 C2 A:T11315 3.0 25.1 1.0 N19 A:T11315 3.2 34.9 1.0 OH A:TYR161 3.4 31.0 1.0 N18 A:T11315 3.5 36.1 1.0 O A:HOH320 3.6 25.5 1.0 CG2 A:ILE32 3.7 20.1 1.0 CE1 A:TYR161 3.8 29.7 1.0 N A:GLY34 3.9 24.8 1.0 CZ A:TYR161 3.9 29.1 1.0 CG1 A:ILE32 4.1 22.9 1.0 C A:ILE33 4.3 25.2 1.0 C3 A:T11315 4.3 25.2 1.0 C6 A:T11315 4.3 29.6 1.0 CD1 A:ILE32 4.5 24.8 1.0 CB A:ILE32 4.5 26.0 1.0 CA A:ILE33 4.5 23.8 1.0 CA A:GLY34 4.5 24.6 1.0 CB A:ALA167 4.7 25.8 1.0 N A:ILE33 4.8 24.5 1.0 C A:ILE32 4.9 24.5 1.0 CD1 A:TYR161 4.9 28.9 1.0 O A:ILE32 4.9 25.0 1.0 O A:ILE33 5.0 24.7 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:F315 b:43.2 occ:1.00 F16 A:T11315 0.0 43.2 1.0 C14 A:T11315 1.3 37.9 1.0 F15 A:T11315 2.1 36.9 1.0 F17 A:T11315 2.2 39.2 1.0 C13 A:T11315 2.4 30.7 1.0 C1 A:T11315 2.8 29.3 1.0 N18 A:T11315 3.3 36.1 1.0 N A:GLY34 3.3 24.8 1.0 C2 A:T11315 3.3 25.1 1.0 CD2 A:LEU65 3.4 25.5 1.0 CA A:GLY34 3.4 24.6 1.0 CB A:LEU65 3.5 26.2 1.0 C6 A:T11315 3.6 29.6 1.0 N19 A:T11315 3.6 34.9 1.0 C A:ILE33 3.6 25.2 1.0 CG1 A:ILE32 3.7 22.9 1.0 CD1 A:ILE32 3.9 24.8 1.0 O A:ILE33 3.9 24.7 1.0 CG A:LEU65 4.1 25.5 1.0 C3 A:T11315 4.3 25.2 1.0 CA A:ILE33 4.5 23.8 1.0 C5 A:T11315 4.5 24.5 1.0 O A:HOH320 4.6 25.5 1.0 CG2 A:ILE32 4.6 20.1 1.0 O A:HOH318 4.7 31.3 1.0 N A:ILE33 4.7 24.5 1.0 CA A:LEU65 4.8 25.3 1.0 O A:HOH361 4.8 37.4 1.0 CB A:ILE32 4.8 26.0 1.0 C A:GLY34 4.8 25.2 1.0 C4 A:T11315 4.8 26.8 1.0 N A:LEU65 4.9 25.7 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