Fluorine in PDB 7arr: The De Novo Designed Hybrid Alpha/Beta-Miniprotein

The structure of The De Novo Designed Hybrid Alpha/Beta-Miniprotein, PDB code: 7arr was solved by M.Bejger, P.Fortuna, M.Drewniak-Switalska, W.Rypniewski, L.Berlicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.02 / 1.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.937, 32.068, 43.087, 114.16, 91.88, 109.86
R / Rfree (%)	12.9 / 16.1

The structure of The De Novo Designed Hybrid Alpha/Beta-Miniprotein also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	4 atoms

The binding sites of Fluorine atom in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein (pdb code 7arr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein, PDB code: 7arr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:14.1 occ:0.50 F1 A:TFA101 0.0 14.1 0.5 F2 A:TFA101 1.1 14.0 0.5 C2 A:TFA101 1.3 13.9 0.5 F1 A:TFA101 1.5 15.3 0.5 C2 A:TFA101 1.6 15.7 0.5 F3 A:TFA101 2.0 14.6 0.5 F2 A:TFA101 2.1 15.8 0.5 C1 A:TFA101 2.4 13.5 0.5 F3 A:TFA101 2.5 15.0 0.5 O A:TFA101 2.8 16.7 0.5 C1 A:TFA101 2.9 15.1 0.5 CD1 A:LEU35 3.2 14.3 1.0 OXT A:TFA101 3.4 17.0 0.5 OXT A:TFA101 3.4 15.1 0.5 CE1 B:TYR25 3.4 9.9 1.0 CD1 B:TYR25 3.6 10.2 1.0 O A:TFA101 3.7 22.8 0.5 CG2 B:VAL29 3.7 7.2 1.0 CG B:LYS26 3.9 15.2 1.0 CG2 A:VAL29 4.0 9.6 1.0 CG1 A:VAL29 4.3 8.3 1.0 CG A:LEU35 4.4 12.2 1.0 CB B:VAL29 4.4 7.9 1.0 CB A:VAL29 4.5 9.4 1.0 CA B:LYS26 4.5 10.0 1.0 CE1 A:TYR25 4.5 7.0 1.0 CZ B:TYR25 4.7 8.4 1.0 CB B:LYS26 4.7 10.3 1.0 O A:HOH223 4.7 15.5 0.5 CG1 B:VAL29 4.8 8.0 1.0 CG B:TYR25 4.9 9.2 1.0 N B:LYS26 5.0 7.5 1.0 CD B:LYS26 5.0 20.5 1.0

Fluorine binding site 2 out of 6 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:15.3 occ:0.50 F1 A:TFA101 0.0 15.3 0.5 C2 A:TFA101 1.2 13.9 0.5 C2 A:TFA101 1.3 15.7 0.5 C1 A:TFA101 1.4 13.5 0.5 O A:TFA101 1.5 16.7 0.5 F3 A:TFA101 1.5 14.6 0.5 F1 A:TFA101 1.5 14.1 0.5 F2 A:TFA101 2.1 14.0 0.5 F3 A:TFA101 2.1 15.0 0.5 C1 A:TFA101 2.4 15.1 0.5 OXT A:TFA101 2.5 15.1 0.5 F2 A:TFA101 2.6 15.8 0.5 OXT A:TFA101 2.6 17.0 0.5 CD1 A:LEU35 3.4 14.3 1.0 O A:TFA101 3.5 22.8 0.5 O A:HOH223 3.6 15.5 0.5 CG A:LYS26 3.8 7.9 1.0 CG2 A:VAL29 3.9 9.6 1.0 CB A:LYS26 4.3 7.4 1.0 CA A:LYS26 4.3 6.8 1.0 O A:HOH233 4.3 18.5 1.0 CB A:VAL29 4.3 9.4 1.0 CG1 A:VAL29 4.5 8.3 1.0 CE1 A:TYR25 4.5 7.0 1.0 CD A:LYS26 4.6 11.0 1.0 CG B:LYS26 4.7 15.2 1.0 CD1 A:TYR25 4.7 10.1 1.0 CE1 B:TYR25 4.7 9.9 1.0 CG A:LEU35 4.8 12.2 1.0 CG2 B:VAL29 4.9 7.2 1.0 CE A:LYS26 4.9 13.9 1.0 CD1 B:TYR25 5.0 10.2 1.0

Fluorine binding site 3 out of 6 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:15.8 occ:0.50 F2 A:TFA101 0.0 15.8 0.5 F2 A:TFA101 1.2 14.0 0.5 C2 A:TFA101 1.4 15.7 0.5 C2 A:TFA101 1.4 13.9 0.5 F3 A:TFA101 1.8 15.0 0.5 C1 A:TFA101 1.9 15.1 0.5 O A:TFA101 2.0 22.8 0.5 F1 A:TFA101 2.1 14.1 0.5 F3 A:TFA101 2.2 14.6 0.5 F1 A:TFA101 2.6 15.3 0.5 C1 A:TFA101 2.6 13.5 0.5 OXT A:TFA101 2.8 17.0 0.5 OXT A:TFA101 3.0 15.1 0.5 O B:HOH232 3.1 12.4 1.0 CB B:VAL29 3.6 7.9 1.0 CG2 B:VAL29 3.6 7.2 1.0 O A:TFA101 3.6 16.7 0.5 CG1 B:VAL29 3.6 8.0 1.0 CG B:LYS26 3.7 15.2 1.0 CA B:LYS26 3.9 10.0 1.0 CB B:LYS26 4.0 10.3 1.0 O B:LYS26 4.3 7.5 1.0 C B:LYS26 4.6 7.7 1.0 CD1 B:LEU35 4.7 11.2 1.0 O A:HOH238 4.7 35.8 1.0 CD B:LYS26 4.7 20.5 1.0 CD1 A:LEU35 4.9 14.3 1.0 CD1 B:TYR25 4.9 10.2 1.0 N B:LYS26 4.9 7.5 1.0 CE1 A:TYR25 4.9 7.0 1.0 CE1 B:TYR25 5.0 9.9 1.0

Fluorine binding site 4 out of 6 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:14.0 occ:0.50 F2 A:TFA101 0.0 14.0 0.5 F1 A:TFA101 1.1 14.1 0.5 F2 A:TFA101 1.2 15.8 0.5 C2 A:TFA101 1.2 13.9 0.5 C2 A:TFA101 1.4 15.7 0.5 F1 A:TFA101 2.1 15.3 0.5 F3 A:TFA101 2.1 14.6 0.5 F3 A:TFA101 2.2 15.0 0.5 C1 A:TFA101 2.4 15.1 0.5 C1 A:TFA101 2.5 13.5 0.5 O A:TFA101 2.9 22.8 0.5 OXT A:TFA101 3.1 17.0 0.5 OXT A:TFA101 3.2 15.1 0.5 O A:TFA101 3.3 16.7 0.5 CG2 B:VAL29 3.4 7.2 1.0 CG B:LYS26 3.5 15.2 1.0 CA B:LYS26 3.8 10.0 1.0 CB B:VAL29 3.8 7.9 1.0 CD1 B:TYR25 3.9 10.2 1.0 CD1 A:LEU35 3.9 14.3 1.0 CE1 B:TYR25 4.0 9.9 1.0 CB B:LYS26 4.0 10.3 1.0 CG1 B:VAL29 4.1 8.0 1.0 O B:HOH232 4.1 12.4 1.0 N B:LYS26 4.5 7.5 1.0 CD B:LYS26 4.6 20.5 1.0 O B:TYR25 4.6 6.8 1.0 O B:LYS26 4.7 7.5 1.0 CE1 A:TYR25 4.8 7.0 1.0 C B:LYS26 4.8 7.7 1.0 C B:TYR25 4.9 7.9 1.0 CG2 A:VAL29 4.9 9.6 1.0 CE B:LYS26 5.0 18.5 1.0

Fluorine binding site 5 out of 6 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:14.6 occ:0.50 F3 A:TFA101 0.0 14.6 0.5 F3 A:TFA101 0.9 15.0 0.5 C2 A:TFA101 1.3 13.9 0.5 C2 A:TFA101 1.4 15.7 0.5 F1 A:TFA101 1.5 15.3 0.5 F1 A:TFA101 2.0 14.1 0.5 F2 A:TFA101 2.1 14.0 0.5 F2 A:TFA101 2.2 15.8 0.5 C1 A:TFA101 2.4 13.5 0.5 C1 A:TFA101 2.7 15.1 0.5 O A:TFA101 2.8 16.7 0.5 CE1 A:TYR25 3.3 7.0 1.0 OXT A:TFA101 3.3 15.1 0.5 OXT A:TFA101 3.4 17.0 0.5 O A:TFA101 3.5 22.8 0.5 CD1 A:TYR25 3.6 10.1 1.0 CG A:LYS26 3.7 7.9 1.0 CG2 A:VAL29 4.0 9.6 1.0 CG2 B:VAL29 4.1 7.2 1.0 CD1 B:LEU35 4.1 11.2 1.0 CG1 B:VAL29 4.1 8.0 1.0 CB B:VAL29 4.5 7.9 1.0 CA A:LYS26 4.5 6.8 1.0 CZ A:TYR25 4.5 7.9 1.0 CB A:LYS26 4.6 7.4 1.0 CD A:LYS26 4.7 11.0 1.0 CE A:LYS26 4.7 13.9 1.0 CD1 A:LEU35 4.8 14.3 1.0 CB A:VAL29 4.8 9.4 1.0 CE1 B:TYR25 4.9 9.9 1.0 CG A:TYR25 4.9 12.1 1.0 O A:HOH223 4.9 15.5 0.5 OH A:TYR25 5.0 8.7 1.0

Fluorine binding site 6 out of 6 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:15.0 occ:0.50 F3 A:TFA101 0.0 15.0 0.5 F3 A:TFA101 0.9 14.6 0.5 C2 A:TFA101 1.3 15.7 0.5 C2 A:TFA101 1.5 13.9 0.5 F2 A:TFA101 1.8 15.8 0.5 F1 A:TFA101 2.1 15.3 0.5 F2 A:TFA101 2.2 14.0 0.5 C1 A:TFA101 2.2 15.1 0.5 C1 A:TFA101 2.5 13.5 0.5 F1 A:TFA101 2.5 14.1 0.5 O A:TFA101 2.8 22.8 0.5 OXT A:TFA101 3.1 15.1 0.5 OXT A:TFA101 3.1 17.0 0.5 O A:TFA101 3.2 16.7 0.5 CD1 B:LEU35 3.5 11.2 1.0 CE1 A:TYR25 3.7 7.0 1.0 CG1 B:VAL29 3.7 8.0 1.0 CG A:LYS26 3.8 7.9 1.0 CD1 A:TYR25 4.0 10.1 1.0 CG2 B:VAL29 4.2 7.2 1.0 CB B:VAL29 4.2 7.9 1.0 CE A:LYS26 4.3 13.9 1.0 O B:HOH232 4.3 12.4 1.0 CD A:LYS26 4.5 11.0 1.0 CG B:LEU35 4.8 9.9 1.0 CZ A:TYR25 4.9 7.9 1.0 CG2 A:VAL29 4.9 9.6 1.0 CB A:LYS26 4.9 7.4 1.0 O A:HOH238 4.9 35.8 1.0

M.Bejger, P.Fortuna, M.Drewniak-Switalska, J.Plewka, W.Rypniewski, L.Berlicki. A Computationally Designed Beta-Amino Acid-Containing Miniprotein. Chem.Commun.(Camb.) V. 57 6015 2021.
ISSN: ESSN 1364-548X
PubMed: 34032224
DOI: 10.1039/D1CC02192C