Fluorine in PDB 6qoy: Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf

The structure of Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf, PDB code: 6qoy was solved by A.Gabdulkhakov, S.Tishchenko, I.Kudryakova, A.Afoshin, N.Vasilyeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.855, 122.553, 78.988, 90.00, 98.64, 90.00
R / Rfree (%)	20 / 24

The structure of Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf (pdb code 6qoy). 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 L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf, PDB code: 6qoy:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf


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 L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:38.4 occ:0.50 F B:AES202 0.0 38.4 0.5 O09 B:JAT203 0.1 34.0 0.5 S07 B:JAT203 1.5 53.0 0.5 S B:AES202 1.6 57.4 0.5 OG B:SER144 2.3 43.3 1.0 O10 B:JAT203 2.4 40.3 0.5 O1S B:AES202 2.4 50.6 0.5 O2S B:AES202 2.5 41.9 0.5 O08 B:JAT203 2.5 48.6 0.5 C1 B:AES202 2.6 43.7 0.5 C04 B:JAT203 2.8 41.2 0.5 N B:SER144 3.0 18.4 1.0 N B:GLY142 3.1 17.2 1.0 C2 B:AES202 3.1 37.2 0.5 CB B:SER144 3.2 29.8 1.0 C03 B:JAT203 3.2 36.0 0.5 CA B:ARG141 3.3 20.1 1.0 O B:GLY140 3.4 17.2 1.0 CA B:SER144 3.4 23.9 1.0 N B:ASP143 3.6 23.1 1.0 C B:ARG141 3.6 21.4 1.0 C6 B:AES202 3.9 34.1 0.5 C B:GLY140 3.9 22.3 1.0 N B:ARG141 3.9 21.9 1.0 C05 B:JAT203 4.0 32.9 0.5 O B:HOH318 4.0 32.1 1.0 C B:ASP143 4.0 21.9 1.0 CA B:GLY142 4.0 15.9 1.0 C B:GLY142 4.1 21.6 1.0 CA B:ASP143 4.2 20.7 1.0 C3 B:AES202 4.4 31.7 0.5 CB B:ARG141 4.5 25.0 1.0 C02 B:JAT203 4.6 30.5 0.5 CB B:ASP143 4.6 24.4 1.0 O B:ARG141 4.8 22.7 1.0 C B:SER144 4.9 22.6 1.0 CG B:ARG141 4.9 33.5 1.0 CG B:MET159 5.0 16.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf


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 L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ C:F202 b:49.5 occ:0.50 F C:AES202 0.0 49.5 0.5 O10 C:JAT203 0.1 44.3 0.5 S07 C:JAT203 1.5 57.0 0.5 S C:AES202 1.6 66.9 0.5 O09 C:JAT203 2.3 41.0 0.5 OG C:SER144 2.3 49.3 1.0 O1S C:AES202 2.4 52.8 0.5 O2S C:AES202 2.5 42.8 0.5 O08 C:JAT203 2.5 52.2 0.5 C1 C:AES202 2.6 54.3 0.5 C04 C:JAT203 2.7 48.1 0.5 C6 C:AES202 2.8 47.6 0.5 N C:GLY142 3.0 22.3 1.0 C05 C:JAT203 3.0 42.8 0.5 CB C:SER144 3.2 37.8 1.0 N C:SER144 3.4 20.8 1.0 CA C:ARG141 3.4 27.4 1.0 O C:HOH320 3.5 30.5 1.0 C C:ARG141 3.7 31.1 1.0 CA C:SER144 3.7 26.7 1.0 O C:GLY140 3.9 23.1 1.0 C2 C:AES202 3.9 47.1 0.5 C03 C:JAT203 4.0 41.5 0.5 CA C:GLY142 4.0 25.2 1.0 N C:ASP143 4.0 21.7 1.0 C5 C:AES202 4.2 44.6 0.5 N C:ARG141 4.2 25.0 1.0 C C:GLY142 4.3 25.4 1.0 CB C:ARG141 4.3 21.6 1.0 C C:GLY140 4.4 31.9 1.0 C06 C:JAT203 4.4 41.3 0.5 C C:ASP143 4.4 21.9 1.0 CG C:ARG141 4.6 28.6 1.0 NE2 C:HIS36 4.7 33.9 1.0 CA C:ASP143 4.8 23.2 1.0 O C:ARG141 4.9 28.8 1.0 C3 C:AES202 5.0 39.9 0.5

Fluorine binding site 3 out of 3 in the Crystal Structure of L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf


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 L1 Protease Lysobacter Sp. XL1 in Complex with Aebsf within 5.0Å range: probe atom residue distance (Å) B Occ D:F203 b:38.8 occ:0.50 F D:AES203 0.0 38.8 0.5 O08 D:JAT204 0.1 35.2 0.5 S07 D:JAT204 1.5 37.0 0.5 S D:AES203 1.6 46.8 0.5 O1S D:AES203 2.4 37.8 0.5 O09 D:JAT204 2.4 40.3 0.5 OG D:SER144 2.5 45.6 1.0 O2S D:AES203 2.5 41.4 0.5 O10 D:JAT204 2.6 39.7 0.5 C1 D:AES203 2.6 40.3 0.5 C04 D:JAT204 2.8 37.0 0.5 N D:SER144 3.0 27.4 1.0 C2 D:AES203 3.1 31.7 0.5 N D:GLY142 3.1 23.0 1.0 CB D:SER144 3.2 31.4 1.0 C03 D:JAT204 3.3 28.5 0.5 CA D:ARG141 3.5 27.3 1.0 O D:GLY140 3.5 21.1 1.0 CA D:SER144 3.6 25.7 1.0 N D:ASP143 3.6 19.5 1.0 C6 D:AES203 3.8 40.6 0.5 C D:ARG141 3.8 26.1 1.0 O D:HOH348 3.9 26.9 1.0 C05 D:JAT204 3.9 36.6 0.5 C D:ASP143 4.0 22.1 1.0 C D:GLY142 4.1 21.9 1.0 C D:GLY140 4.1 24.9 1.0 CA D:GLY142 4.1 19.1 1.0 N D:ARG141 4.1 25.1 1.0 CA D:ASP143 4.3 23.3 1.0 C3 D:AES203 4.4 35.6 0.5 C02 D:JAT204 4.6 33.3 0.5 CB D:ARG141 4.6 23.6 1.0 CB D:ASP143 4.7 17.2 1.0 C5 D:AES203 4.9 44.5 0.5 O D:GLY142 5.0 21.2 1.0 O D:ARG141 5.0 27.7 1.0

I.Kudryakova, A.Gabdulkhakov, S.Tishchenko, A.Afoshin, N.Vasilyeva. Serine Bacteriolytic Protease L1 of Lysobacter Sp. XL1 Complexed with Protease Inhibitor Aebsf: Features of Interaction Process Biochem 2019.
ISSN: ESSN 1873-3298
DOI: 10.1016/J.PROCBIO.2019.02.013