Fluorine in PDB 4rm2: Crystal Structure of A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid

The structure of Crystal Structure of A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid, PDB code: 4rm2 was solved by S.Strom, M.Nosrati, C.Thornburg, K.D.Walker, J.H.Geiger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.61 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.885, 95.749, 98.605, 90.00, 110.43, 90.00
R / Rfree (%)	15.9 / 20.2

The binding sites of Fluorine atom in the Crystal Structure of A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid (pdb code 4rm2). 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 A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid, PDB code: 4rm2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid


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 A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1000 b:15.7 occ:1.00 F10 A:3U41000 0.0 15.7 1.0 C7 A:3U41000 1.3 13.2 1.0 C6 A:3U41000 2.3 11.4 1.0 C2 A:3U41000 2.4 11.8 1.0 O8 A:3U41000 2.8 14.8 1.0 C1 A:3U41000 2.8 12.9 1.0 O A:HOH1217 3.2 17.9 1.0 O A:HOH1218 3.2 18.6 1.0 O A:HOH1123 3.3 19.9 1.0 O A:HOH1386 3.4 25.4 1.0 CA A:SER328 3.5 10.7 1.0 C5 A:3U41000 3.5 12.1 1.0 O A:GLY327 3.5 11.4 1.0 O A:HOH1145 3.6 9.9 1.0 C3 A:3U41000 3.6 10.9 1.0 C A:GLY327 3.8 11.7 1.0 N A:SER328 3.8 11.4 1.0 O9 A:3U41000 3.8 12.7 1.0 C A:SER328 3.9 11.6 1.0 NZ A:LYS427 4.0 27.1 1.0 N A:THR329 4.0 10.0 1.0 C4 A:3U41000 4.0 12.4 1.0 O A:SER328 4.6 11.4 1.0 CA A:GLY327 4.7 10.6 1.0 CB A:SER328 4.8 11.5 1.0 CE A:LYS427 4.8 29.7 1.0 OG1 A:THR329 4.8 11.5 1.0 O A:HOH1102 5.0 4.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid


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 A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:32.3 occ:1.00 F10 A:3U41001 0.0 32.3 1.0 C7 A:3U41001 1.4 25.7 1.0 O9 A:3U41001 2.4 22.1 1.0 C6 A:3U41001 2.4 24.0 1.0 C2 A:3U41001 2.4 22.2 1.0 C1 A:3U41001 2.8 23.8 1.0 CZ A:PHE272 3.4 9.7 1.0 CB A:ALA221 3.4 11.0 1.0 CA A:GLY274 3.6 10.9 1.0 CE2 A:PHE272 3.6 9.4 1.0 C5 A:3U41001 3.7 22.2 1.0 C3 A:3U41001 3.7 24.3 1.0 CA A:GLY278 3.8 13.8 1.0 N A:ALA275 3.9 11.7 1.0 O8 A:3U41001 4.0 26.2 1.0 C4 A:3U41001 4.2 24.5 1.0 C A:GLY278 4.2 12.8 1.0 C A:GLY274 4.2 11.7 1.0 O A:ALA275 4.2 10.7 1.0 N A:TYR279 4.4 12.9 1.0 CE A:MET282 4.4 13.1 1.0 CE1 A:PHE272 4.6 9.3 1.0 O A:TYR273 4.6 9.2 1.0 N A:GLY274 4.6 9.5 1.0 N A:GLY278 4.7 13.2 1.0 O A:GLY278 4.8 16.5 1.0 CA A:ALA221 4.9 10.5 1.0 O A:HOH1438 4.9 21.0 1.0 C A:TYR273 4.9 9.8 1.0 CD2 A:PHE272 5.0 9.6 1.0 CA A:ALA275 5.0 11.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid


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 A Benzoate Coenzyme A Ligase with 2-Fluoro Benzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F1000 b:12.6 occ:1.00 F10 B:3U41000 0.0 12.6 1.0 C7 B:3U41000 1.4 9.7 1.0 C2 B:3U41000 2.3 9.7 1.0 C6 B:3U41000 2.4 8.7 1.0 O9 B:3U41000 2.7 12.6 1.0 C1 B:3U41000 2.8 11.1 1.0 O B:HOH1247 3.0 22.0 1.0 O B:HOH1260 3.3 22.0 1.0 O B:HOH1156 3.3 15.2 1.0 O B:HOH1134 3.5 15.2 1.0 O B:GLY327 3.5 11.2 1.0 O B:HOH1128 3.6 9.1 1.0 CA B:SER328 3.6 11.0 1.0 C3 B:3U41000 3.6 8.2 1.0 C5 B:3U41000 3.6 7.6 1.0 C B:GLY327 3.8 11.4 1.0 N B:SER328 3.9 11.3 1.0 O8 B:3U41000 3.9 12.2 1.0 C B:SER328 3.9 10.4 1.0 NZ B:LYS427 4.0 19.6 1.0 N B:THR329 4.0 10.2 1.0 C4 B:3U41000 4.1 7.7 1.0 CE B:LYS427 4.5 23.0 1.0 O B:SER328 4.7 10.8 1.0 CA B:GLY327 4.7 10.5 1.0 CB B:SER328 4.8 10.8 1.0 OG1 B:THR329 4.9 14.5 1.0

C.K.Thornburg, S.Wortas-Strom, M.Nosrati, J.H.Geiger, K.D.Walker. Kinetically and Crystallographically Guided Mutations of A Benzoate Coa Ligase (Bada) Elucidate Mechanism and Expand Substrate Permissivity. Biochemistry V. 54 6230 2015.
ISSN: ISSN 0006-2960
PubMed: 26378464
DOI: 10.1021/ACS.BIOCHEM.5B00899