Fluorine in PDB 6d0j: Crystal Structure of A Clc-Type Fluoride/Proton Antiporter

The structure of Crystal Structure of A Clc-Type Fluoride/Proton Antiporter, PDB code: 6d0j was solved by N.B.Last, R.B.Stockbridge, A.E.Wilson, T.Shane, L.Kolmakova-Partensky, A.Koide, S.Koide, C.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.972, 126.421, 133.947, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 26

The binding sites of Fluorine atom in the Crystal Structure of A Clc-Type Fluoride/Proton Antiporter (pdb code 6d0j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of A Clc-Type Fluoride/Proton Antiporter, PDB code: 6d0j:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of A Clc-Type Fluoride/Proton Antiporter


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 Clc-Type Fluoride/Proton Antiporter within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:0.6 occ:1.00 N A:ARG117 2.4 0.1 1.0 N A:GLU118 2.5 0.8 1.0 N A:GLY119 3.0 0.0 1.0 C A:GLY116 3.1 0.1 1.0 C A:ARG117 3.1 0.5 1.0 CA A:GLY116 3.2 0.5 1.0 CA A:ARG117 3.2 0.3 1.0 CA A:GLY317 3.3 0.8 1.0 N A:VAL319 3.4 0.4 1.0 CA A:GLU118 3.5 0.3 1.0 C A:GLY317 3.5 0.8 1.0 CB A:VAL319 3.6 0.7 1.0 N A:GLY317 3.6 0.7 1.0 C A:GLU118 3.7 0.1 1.0 N A:GLU318 3.7 0.8 1.0 CB A:GLU118 3.9 0.0 1.0 N A:THR320 3.9 1.0 1.0 CG2 A:VAL319 3.9 1.0 1.0 CA A:VAL319 4.0 0.5 1.0 O A:GLY116 4.0 0.9 1.0 CA A:GLY119 4.1 0.4 1.0 O A:ARG117 4.1 0.8 1.0 O A:GLY317 4.1 0.7 1.0 N A:GLY116 4.3 0.6 1.0 OG1 A:THR320 4.3 0.5 1.0 CG A:GLU118 4.3 0.8 1.0 C A:GLU318 4.4 0.8 1.0 CB A:ARG117 4.5 0.6 1.0 C A:VAL319 4.5 0.7 1.0 CA A:GLU318 4.5 0.9 1.0 CG A:ARG117 4.6 0.4 1.0 N A:VAL120 4.7 0.8 1.0 CB A:THR320 4.8 0.8 1.0 C A:GLY316 4.9 0.3 1.0 CG1 A:VAL319 4.9 0.7 1.0 O A:GLU118 4.9 0.8 1.0 C A:GLY119 5.0 0.5 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of A Clc-Type Fluoride/Proton Antiporter


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 Clc-Type Fluoride/Proton Antiporter within 5.0Å range: probe atom residue distance (Å) B Occ A:F506 b:0.2 occ:1.00 OE1 A:GLU318 3.0 0.6 1.0 OH A:TYR396 3.0 0.5 1.0 CE1 A:TYR396 3.4 0.1 1.0 CZ A:TYR396 3.6 0.9 1.0 CA A:GLY119 3.8 0.4 1.0 CD1 A:ILE395 4.0 0.9 1.0 CG2 A:VAL319 4.1 1.0 1.0 N A:GLU318 4.1 0.8 1.0 CE A:MET79 4.1 0.4 1.0 CD A:GLU318 4.2 0.4 1.0 CA A:GLY317 4.4 0.8 1.0 CD1 A:TYR396 4.6 0.3 1.0 N A:GLY119 4.6 0.0 1.0 OE2 A:GLU318 4.8 0.5 1.0 C A:GLY317 4.8 0.8 1.0 C A:GLY119 4.8 0.5 1.0 CE2 A:TYR396 4.9 0.3 1.0 N A:VAL319 4.9 0.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of A Clc-Type Fluoride/Proton Antiporter


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 Clc-Type Fluoride/Proton Antiporter within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:0.3 occ:1.00 N B:GLU118 2.3 0.8 1.0 N B:ARG117 2.4 0.1 1.0 C B:ARG117 3.0 0.9 1.0 C B:GLY116 3.1 0.9 1.0 N B:GLY119 3.1 0.4 1.0 CA B:ARG117 3.1 0.0 1.0 CA B:GLY116 3.2 0.5 1.0 CA B:GLU118 3.3 0.9 1.0 N B:VAL319 3.5 0.6 1.0 CB B:VAL319 3.6 0.6 1.0 CB B:GLU118 3.7 1.0 1.0 CA B:GLY317 3.7 0.1 1.0 C B:GLU118 3.7 0.6 1.0 N B:THR320 3.8 0.8 1.0 C B:GLY317 3.8 0.2 1.0 N B:GLY317 4.0 0.8 1.0 OG1 B:THR320 4.0 0.2 1.0 O B:ARG117 4.0 0.1 1.0 N B:GLU318 4.0 0.7 1.0 CA B:VAL319 4.0 0.2 1.0 CG2 B:VAL319 4.0 0.2 1.0 CG B:GLU118 4.0 0.8 1.0 O B:GLY116 4.1 0.2 1.0 CA B:GLY119 4.2 0.4 1.0 CB B:ARG117 4.3 0.8 1.0 O B:GLY317 4.4 0.5 1.0 N B:GLY116 4.4 0.1 1.0 CG B:ARG117 4.4 1.0 1.0 C B:VAL319 4.4 0.1 1.0 C B:GLU318 4.5 0.5 1.0 CB B:THR320 4.6 0.4 1.0 CA B:GLU318 4.7 0.1 1.0 CG1 B:VAL319 4.8 1.0 1.0 N B:VAL120 4.8 0.2 1.0 CA B:THR320 4.8 0.7 1.0 O B:GLU118 4.9 0.1 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of A Clc-Type Fluoride/Proton Antiporter


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of A Clc-Type Fluoride/Proton Antiporter within 5.0Å range: probe atom residue distance (Å) B Occ B:F504 b:0.6 occ:1.00 OH B:TYR396 3.0 0.7 1.0 CE1 B:TYR396 3.3 1.0 1.0 OE1 B:GLU318 3.5 0.6 1.0 CZ B:TYR396 3.6 0.1 1.0 CA B:GLY119 3.6 0.4 1.0 CE B:MET79 3.8 0.6 1.0 CG2 B:VAL319 4.1 0.2 1.0 N B:GLU318 4.4 0.7 1.0 N B:GLY119 4.5 0.4 1.0 CD1 B:TYR396 4.5 0.5 1.0 CA B:GLY317 4.5 0.1 1.0 C B:GLY119 4.6 0.1 1.0 CD B:GLU318 4.7 0.8 1.0 O B:GLY119 4.9 0.9 1.0 CE2 B:TYR396 4.9 0.7 1.0

N.B.Last, R.B.Stockbridge, A.E.Wilson, T.Shane, L.Kolmakova-Partensky, A.Koide, S.Koide, C.Miller. A Clc-Type F-/H+Antiporter in Ion-Swapped Conformations. Nat. Struct. Mol. Biol. V. 25 601 2018.
ISSN: ESSN 1545-9985
PubMed: 29941917
DOI: 10.1038/S41594-018-0082-0