Fluorine in PDB 3nk8: Trypsin in Complex with Fluorine-Containing Fragment

All present enzymatic activity of Trypsin in Complex with Fluorine-Containing Fragment:
3.4.21.4;

The structure of Trypsin in Complex with Fluorine-Containing Fragment, PDB code: 3nk8 was solved by N.Schiering, A.Vulpetti, C.Dalvit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.30 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.720, 58.266, 66.770, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 14.3

The structure of Trypsin in Complex with Fluorine-Containing Fragment also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Fluorine atom in the Trypsin in Complex with Fluorine-Containing Fragment (pdb code 3nk8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Trypsin in Complex with Fluorine-Containing Fragment, PDB code: 3nk8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Trypsin in Complex with Fluorine-Containing Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trypsin in Complex with Fluorine-Containing Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:13.0 occ:1.00 F1 A:JKZ1 0.0 13.0 1.0 C2 A:JKZ1 1.3 12.5 1.0 F3 A:JKZ1 2.1 10.9 1.0 F4 A:JKZ1 2.2 14.8 1.0 C5 A:JKZ1 2.4 11.8 1.0 O A:SER214 2.9 5.3 1.0 C6 A:JKZ1 3.0 11.2 1.0 C A:SER214 3.2 4.1 1.0 C20 A:JKZ1 3.3 11.4 1.0 O A:HOH428 3.4 10.7 1.0 OG A:SER195 3.4 7.0 1.0 C10 A:JKZ1 3.5 12.4 1.0 N A:TRP215 3.5 4.2 1.0 CA A:TRP215 3.5 4.5 1.0 CG1 A:VAL213 3.9 5.0 1.0 CE1 A:HIS57 4.1 6.1 1.0 CA A:SER214 4.1 3.8 1.0 N A:SER214 4.2 3.6 1.0 NE2 A:HIS57 4.2 6.4 1.0 C7 A:JKZ1 4.3 11.9 1.0 C A:TRP215 4.3 5.0 1.0 CA A:SER195 4.4 4.8 1.0 CB A:SER195 4.4 5.6 1.0 O A:HOH68 4.4 8.0 0.5 C A:VAL213 4.5 3.7 1.0 O A:HOH317 4.5 29.9 1.0 O A:VAL213 4.5 4.0 1.0 O A:HOH592 4.6 17.5 1.0 C17 A:JKZ1 4.6 11.5 1.0 C9 A:JKZ1 4.6 13.2 1.0 N A:SER195 4.6 4.4 1.0 CB A:TRP215 4.7 4.7 1.0 N A:GLY216 4.8 5.8 1.0 O A:TRP215 4.9 5.5 1.0 N8 A:JKZ1 5.0 11.9 1.0

Fluorine binding site 2 out of 3 in the Trypsin in Complex with Fluorine-Containing Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trypsin in Complex with Fluorine-Containing Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:10.9 occ:1.00 F3 A:JKZ1 0.0 10.9 1.0 C2 A:JKZ1 1.3 12.5 1.0 F1 A:JKZ1 2.1 13.0 1.0 F4 A:JKZ1 2.2 14.8 1.0 C5 A:JKZ1 2.3 11.8 1.0 C6 A:JKZ1 3.0 11.2 1.0 O A:CYS191 3.1 7.7 1.0 OG A:SER195 3.2 7.0 1.0 C20 A:JKZ1 3.2 11.4 1.0 N A:SER195 3.4 4.4 1.0 C10 A:JKZ1 3.4 12.4 1.0 CG1 A:VAL213 3.6 5.0 1.0 C A:CYS191 3.7 6.4 1.0 CA A:SER195 3.8 4.8 1.0 CB A:SER195 4.0 5.6 1.0 O A:HOH455 4.1 11.1 1.0 CA A:GLN192 4.1 7.6 1.0 N A:GLN192 4.2 7.2 1.0 C A:ASP194 4.2 4.1 1.0 N A:ASP194 4.2 4.8 1.0 C7 A:JKZ1 4.3 11.9 1.0 N A:GLY193 4.4 6.4 1.0 CB A:ASP194 4.5 4.5 1.0 CA A:ASP194 4.5 4.6 1.0 CA A:CYS191 4.6 6.2 1.0 C9 A:JKZ1 4.6 13.2 1.0 C A:GLN192 4.6 6.8 1.0 N A:CYS191 4.7 5.7 1.0 C17 A:JKZ1 4.7 11.5 1.0 O A:HOH611 4.8 20.7 1.0 O A:SER214 4.9 5.3 1.0 N8 A:JKZ1 4.9 11.9 1.0 CB A:VAL213 4.9 4.1 1.0

Fluorine binding site 3 out of 3 in the Trypsin in Complex with Fluorine-Containing Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trypsin in Complex with Fluorine-Containing Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:14.8 occ:1.00 F4 A:JKZ1 0.0 14.8 1.0 C2 A:JKZ1 1.4 12.5 1.0 F3 A:JKZ1 2.2 10.9 1.0 F1 A:JKZ1 2.2 13.0 1.0 C5 A:JKZ1 2.4 11.8 1.0 OG A:SER195 2.7 7.0 1.0 C10 A:JKZ1 2.7 12.4 1.0 O A:HOH317 2.9 29.9 1.0 O A:HOH611 3.2 20.7 1.0 O A:HOH455 3.2 11.1 1.0 O A:HOH428 3.4 10.7 1.0 C6 A:JKZ1 3.7 11.2 1.0 NE2 A:HIS57 4.0 6.4 1.0 CB A:SER195 4.0 5.6 1.0 C9 A:JKZ1 4.1 13.2 1.0 CA A:GLN192 4.4 7.6 1.0 O A:SER214 4.4 5.3 1.0 CA A:SER195 4.5 4.8 1.0 O A:HOH68 4.6 8.0 0.5 C20 A:JKZ1 4.6 11.4 1.0 CE1 A:HIS57 4.6 6.1 1.0 N A:SER195 4.6 4.4 1.0 O A:CYS191 4.6 7.7 1.0 N A:GLY193 4.8 6.4 1.0 C7 A:JKZ1 4.8 11.9 1.0 N A:GLN192 4.8 7.2 1.0 O12 A:JKZ1 4.9 15.0 1.0 N8 A:JKZ1 4.9 11.9 1.0 C A:CYS191 5.0 6.4 1.0 CD2 A:HIS57 5.0 6.0 1.0

A.Vulpetti, N.Schiering, C.Dalvit. Combined Use of Computational Chemistry, uc(Nmr) Screening, and X-Ray Crystallography For Identification and Characterization of Fluorophilic Protein Environments. Proteins V. 78 3281 2010.
ISSN: ISSN 0887-3585
PubMed: 20886466
DOI: 10.1002/PROT.22836