Fluorine in PDB 3nkk: 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: 3nkk 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)	39.72 / 1.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.423, 58.088, 66.579, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 14.8

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 3nkk). 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: 3nkk:
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:8.7 occ:0.25 F1 A:JLZ1 0.0 8.7 0.2 C2 A:JLZ1 1.3 7.7 0.2 F1 A:JLZ1 1.5 8.7 0.5 C2 A:JLZ1 1.7 7.7 0.5 C4 A:JLZ1 1.7 8.6 0.2 C3 A:JLZ1 2.2 8.5 0.2 C3 A:JLZ1 2.3 7.4 0.5 C3 A:JLZ1 2.4 7.5 0.2 C9 A:JLZ1 2.4 7.3 0.2 C9 A:JLZ1 2.6 6.7 0.5 C6 A:JLZ1 2.7 8.6 0.2 C17 A:JLZ1 2.7 9.1 0.2 C17 A:JLZ1 2.7 8.8 0.5 C17 A:JLZ1 2.8 8.2 0.2 O A:SER214 3.0 5.8 1.0 C A:SER214 3.2 4.5 1.0 CG1 A:VAL213 3.3 5.2 1.0 C2 A:JLZ1 3.3 8.4 0.2 C4 A:JLZ1 3.4 7.3 0.5 OG A:SER195 3.6 6.6 1.0 N A:TRP215 3.6 4.6 1.0 C4 A:JLZ1 3.6 7.4 0.2 C8 A:JLZ1 3.6 5.8 0.5 C8 A:JLZ1 3.6 7.0 0.2 C8 A:JLZ1 3.7 8.5 0.2 CA A:TRP215 3.8 4.9 1.0 N A:SER214 3.8 4.1 1.0 C9 A:JLZ1 3.9 8.5 0.2 C6 A:JLZ1 3.9 6.9 0.5 CA A:SER214 4.0 4.5 1.0 C A:VAL213 4.1 4.0 1.0 O A:HOH345 4.1 7.8 1.0 C6 A:JLZ1 4.1 7.0 0.2 CA A:SER195 4.1 4.9 1.0 O A:VAL213 4.2 4.5 1.0 O A:HOH422 4.3 18.4 1.0 F1 A:JLZ1 4.3 8.0 0.2 N A:SER195 4.4 4.3 1.0 CE1 A:HIS57 4.4 6.5 1.0 CB A:SER195 4.4 5.7 1.0 NE2 A:HIS57 4.5 6.7 1.0 C A:TRP215 4.5 5.3 1.0 CB A:VAL213 4.5 4.5 1.0 O A:CYS191 4.7 6.8 1.0 O A:TRP215 4.8 5.8 1.0 CA A:VAL213 4.8 4.2 1.0 O A:HOH557 4.8 87.4 0.8 C11 A:JLZ1 4.9 5.6 0.5 C11 A:JLZ1 4.9 7.0 0.2 C11 A:JLZ1 4.9 8.7 0.2

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:8.7 occ:0.50 F1 A:JLZ1 0.0 8.7 0.5 C2 A:JLZ1 1.3 7.7 0.5 C4 A:JLZ1 1.4 8.6 0.2 F1 A:JLZ1 1.5 8.7 0.2 C2 A:JLZ1 1.7 7.7 0.2 C3 A:JLZ1 2.3 7.5 0.2 C3 A:JLZ1 2.3 8.5 0.2 C9 A:JLZ1 2.3 6.7 0.5 C3 A:JLZ1 2.4 7.4 0.5 C6 A:JLZ1 2.4 8.6 0.2 C9 A:JLZ1 2.6 7.3 0.2 C17 A:JLZ1 2.7 8.2 0.2 C17 A:JLZ1 2.8 9.1 0.2 C17 A:JLZ1 2.8 8.8 0.5 CG1 A:VAL213 3.1 5.2 1.0 O A:CYS191 3.1 6.8 1.0 OG A:SER195 3.4 6.6 1.0 C4 A:JLZ1 3.4 7.4 0.2 N A:SER195 3.5 4.3 1.0 C2 A:JLZ1 3.6 8.4 0.2 C4 A:JLZ1 3.6 7.3 0.5 C8 A:JLZ1 3.6 5.8 0.5 C8 A:JLZ1 3.6 7.0 0.2 C8 A:JLZ1 3.7 8.5 0.2 C A:CYS191 3.7 6.6 1.0 CA A:SER195 3.8 4.9 1.0 C6 A:JLZ1 3.9 7.0 0.2 C6 A:JLZ1 4.1 6.9 0.5 C9 A:JLZ1 4.1 8.5 0.2 CB A:SER195 4.1 5.7 1.0 C A:ASP194 4.2 4.3 1.0 N A:GLN192 4.3 7.3 1.0 CA A:GLN192 4.5 7.8 1.0 CB A:ASP194 4.5 4.6 1.0 CA A:CYS191 4.5 6.6 1.0 N A:CYS191 4.5 6.2 1.0 CB A:VAL213 4.5 4.5 1.0 N A:ASP194 4.5 4.9 1.0 O A:SER214 4.5 5.8 1.0 CA A:ASP194 4.6 4.6 1.0 O A:HOH365 4.6 9.3 1.0 F1 A:JLZ1 4.7 8.0 0.2 O A:HOH345 4.7 7.8 1.0 C A:SER214 4.8 4.5 1.0 C A:VAL213 4.9 4.0 1.0 OG A:SER190 4.9 6.7 1.0 N A:GLY193 4.9 6.8 1.0 C11 A:JLZ1 4.9 5.6 0.5 C11 A:JLZ1 4.9 7.0 0.2 N A:SER214 4.9 4.1 1.0 C11 A:JLZ1 4.9 8.7 0.2 O A:VAL213 5.0 4.5 1.0 O A:ASP194 5.0 4.5 1.0 C A:GLN192 5.0 6.9 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:8.0 occ:0.25 F1 A:JLZ1 0.0 8.0 0.2 C4 A:JLZ1 1.3 7.3 0.5 C2 A:JLZ1 1.3 8.4 0.2 C4 A:JLZ1 2.1 7.4 0.2 O A:HOH557 2.2 87.4 0.8 C6 A:JLZ1 2.3 6.9 0.5 C3 A:JLZ1 2.3 7.4 0.5 C9 A:JLZ1 2.4 8.5 0.2 C3 A:JLZ1 2.4 8.5 0.2 C3 A:JLZ1 2.5 7.5 0.2 C17 A:JLZ1 2.8 9.1 0.2 C6 A:JLZ1 2.8 7.0 0.2 C17 A:JLZ1 2.8 8.8 0.5 O A:HOH288 2.9 24.3 1.0 C17 A:JLZ1 3.0 8.2 0.2 NE2 A:GLN192 3.0 14.3 1.0 O A:HOH447 3.0 15.9 1.0 O A:GLY216 3.3 7.3 0.5 C2 A:JLZ1 3.4 7.7 0.2 O A:GLY216 3.4 6.8 0.5 C2 A:JLZ1 3.6 7.7 0.5 C8 A:JLZ1 3.6 5.8 0.5 C4 A:JLZ1 3.6 8.6 0.2 C8 A:JLZ1 3.6 8.5 0.2 C8 A:JLZ1 3.7 7.0 0.2 O A:HOH519 3.7 25.4 1.0 N A:GLY216 3.8 6.2 0.5 O A:HOH451 3.8 18.2 1.0 N A:GLY216 3.8 6.0 0.5 C9 A:JLZ1 3.9 7.3 0.2 O A:HOH422 4.1 18.4 1.0 C9 A:JLZ1 4.1 6.7 0.5 C6 A:JLZ1 4.1 8.6 0.2 CD A:GLN192 4.1 13.7 1.0 CA A:TRP215 4.2 4.9 1.0 F1 A:JLZ1 4.3 8.7 0.2 C A:GLY216 4.3 6.9 0.5 C A:TRP215 4.3 5.3 1.0 C A:GLY216 4.4 6.4 0.5 CA A:GLY216 4.6 6.5 0.5 CA A:GLY216 4.6 6.2 0.5 O A:GLY219 4.7 7.9 1.0 F1 A:JLZ1 4.7 8.7 0.5 CB A:TRP215 4.7 4.9 1.0 C11 A:JLZ1 4.8 5.6 0.5 OE1 A:GLN192 4.8 15.2 1.0 C11 A:JLZ1 4.9 7.0 0.2 C11 A:JLZ1 4.9 8.7 0.2 CG A:GLN192 4.9 12.0 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