Fluorine in PDB 5zab: Crystal Structure of CF3-Aequorin

The structure of Crystal Structure of CF3-Aequorin, PDB code: 5zab was solved by S.Inouye, Y.Tomabechi, S.I.Sekine, M.Shirouzu, T.Hosoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	91.800, 97.550, 121.840, 77.62, 73.06, 75.17
R / Rfree (%)	19.6 / 23

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of CF3-Aequorin (pdb code 5zab). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 48 binding sites of Fluorine where determined in the Crystal Structure of CF3-Aequorin, PDB code: 5zab:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 48 in the Crystal Structure of CF3-Aequorin


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 CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:37.7 occ:1.00 F01 A:9A3201 0.0 37.7 1.0 C08 A:9A3201 1.4 37.9 1.0 F03 A:9A3201 2.2 39.0 1.0 F02 A:9A3201 2.2 42.0 1.0 C07 A:9A3201 2.4 32.0 1.0 C06 A:9A3201 2.7 32.2 1.0 O A:ILE105 2.9 32.2 1.0 OG1 A:THR166 3.3 34.2 1.0 C A:ILE105 3.6 29.6 1.0 CA A:GLY109 3.6 33.2 1.0 C09 A:9A3201 3.7 35.2 1.0 N A:GLY109 3.8 28.6 1.0 CA A:ARG106 3.9 28.9 1.0 CG1 A:ILE105 3.9 35.6 1.0 N A:ARG106 4.0 32.5 1.0 CA A:THR166 4.1 39.0 1.0 C05 A:9A3201 4.1 34.1 1.0 CB A:THR166 4.2 37.1 1.0 N A:THR166 4.4 34.9 1.0 O A:ARG106 4.5 27.1 1.0 C A:ARG106 4.5 25.8 1.0 CD1 A:ILE105 4.5 33.8 1.0 CA A:ILE105 4.6 30.4 1.0 CB A:ILE105 4.7 34.8 1.0 CG2 A:THR166 4.7 35.4 1.0 CG1 A:VAL162 4.7 38.6 1.0 C10 A:9A3201 4.8 37.2 1.0 C A:MET165 4.8 34.2 1.0 CB A:HIS169 4.9 33.3 1.0 CG2 A:ILE105 4.9 29.7 1.0 O A:VAL162 4.9 38.6 1.0 C A:GLY109 4.9 37.5 1.0 O A:MET165 4.9 36.3 1.0 CG A:HIS169 5.0 33.5 1.0 C04 A:9A3201 5.0 31.0 1.0 CB A:ARG106 5.0 35.1 1.0

Fluorine binding site 2 out of 48 in the Crystal Structure of CF3-Aequorin


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 CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:42.0 occ:1.00 F02 A:9A3201 0.0 42.0 1.0 C08 A:9A3201 1.4 37.9 1.0 F03 A:9A3201 2.2 39.0 1.0 F01 A:9A3201 2.2 37.7 1.0 C07 A:9A3201 2.5 32.0 1.0 C09 A:9A3201 3.1 35.2 1.0 CA A:GLY109 3.5 33.2 1.0 C06 A:9A3201 3.5 32.2 1.0 OG1 A:THR166 3.7 34.2 1.0 CB A:MET165 3.7 39.1 1.0 CG1 A:VAL162 3.8 38.6 1.0 O A:VAL162 3.9 38.6 1.0 N A:THR166 4.0 34.9 1.0 CA A:VAL162 4.1 39.1 1.0 CE1 A:PHE113 4.1 45.0 1.0 CB A:VAL162 4.3 40.9 1.0 CZ A:PHE113 4.3 43.1 1.0 C A:MET165 4.3 34.2 1.0 CG2 A:VAL162 4.3 41.6 1.0 C A:GLY109 4.4 37.5 1.0 C10 A:9A3201 4.4 37.2 1.0 C A:VAL162 4.4 38.9 1.0 N A:GLY109 4.5 28.6 1.0 CA A:THR166 4.5 39.0 1.0 CA A:MET165 4.6 37.5 1.0 CD1 A:PHE113 4.7 45.6 1.0 CB A:THR166 4.7 37.1 1.0 C05 A:9A3201 4.8 34.1 1.0 O A:MET165 4.8 36.3 1.0 CG A:MET165 4.8 48.0 1.0 O A:GLY109 4.8 37.3 1.0 O A:ILE105 4.8 32.2 1.0

Fluorine binding site 3 out of 48 in the Crystal Structure of CF3-Aequorin


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 CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:39.0 occ:1.00 F03 A:9A3201 0.0 39.0 1.0 C08 A:9A3201 1.4 37.9 1.0 F02 A:9A3201 2.2 42.0 1.0 F01 A:9A3201 2.2 37.7 1.0 C07 A:9A3201 2.5 32.0 1.0 O A:MET165 3.0 36.3 1.0 C A:MET165 3.0 34.2 1.0 C09 A:9A3201 3.1 35.2 1.0 N A:THR166 3.1 34.9 1.0 CA A:THR166 3.3 39.0 1.0 CB A:MET165 3.4 39.1 1.0 ND1 A:HIS169 3.5 41.2 1.0 C06 A:9A3201 3.5 32.2 1.0 CG A:HIS169 3.5 33.5 1.0 CB A:HIS169 3.7 33.3 1.0 OG1 A:THR166 3.7 34.2 1.0 CA A:MET165 3.8 37.5 1.0 CE1 A:HIS169 4.1 42.5 1.0 CD2 A:HIS169 4.2 38.8 1.0 CB A:THR166 4.2 37.1 1.0 C10 A:9A3201 4.4 37.2 1.0 O A:VAL162 4.4 38.6 1.0 NE2 A:HIS169 4.5 38.7 1.0 C A:THR166 4.5 35.1 1.0 CG A:MET165 4.7 48.0 1.0 C05 A:9A3201 4.7 34.1 1.0 CG1 A:ILE105 4.8 35.6 1.0 O A:THR166 4.8 32.6 1.0 CE A:MET165 4.9 42.0 1.0 N A:MET165 5.0 39.9 1.0

Fluorine binding site 4 out of 48 in the Crystal Structure of CF3-Aequorin


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 CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:36.4 occ:1.00 F01 B:9A3201 0.0 36.4 1.0 C08 B:9A3201 1.4 36.1 1.0 F03 B:9A3201 2.2 39.7 1.0 F02 B:9A3201 2.2 36.6 1.0 C07 B:9A3201 2.4 32.9 1.0 C06 B:9A3201 2.8 30.0 1.0 O B:ILE105 3.0 29.8 1.0 OG1 B:THR166 3.2 36.9 1.0 CA B:GLY109 3.6 27.0 1.0 C B:ILE105 3.7 28.2 1.0 C09 B:9A3201 3.7 35.2 1.0 CA B:ARG106 3.7 28.8 1.0 N B:GLY109 3.9 27.9 1.0 N B:ARG106 4.0 29.4 1.0 C05 B:9A3201 4.2 37.4 1.0 CG1 B:ILE105 4.2 33.6 1.0 CG1 B:VAL162 4.2 33.6 1.0 CA B:THR166 4.2 36.8 1.0 O B:ARG106 4.2 27.4 1.0 CB B:THR166 4.2 36.8 1.0 C B:ARG106 4.4 22.0 1.0 N B:THR166 4.4 38.9 1.0 O B:VAL162 4.7 34.7 1.0 C B:GLY109 4.8 26.1 1.0 CA B:ILE105 4.8 26.1 1.0 CB B:ARG106 4.8 27.5 1.0 CG2 B:THR166 4.8 30.4 1.0 C10 B:9A3201 4.8 35.3 1.0 CG2 B:ILE105 4.9 34.7 1.0 CB B:ILE105 4.9 31.4 1.0 C B:MET165 4.9 39.3 1.0 CD1 B:ILE105 5.0 34.9 1.0

Fluorine binding site 5 out of 48 in the Crystal Structure of CF3-Aequorin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:36.6 occ:1.00 F02 B:9A3201 0.0 36.6 1.0 C08 B:9A3201 1.4 36.1 1.0 F01 B:9A3201 2.2 36.4 1.0 F03 B:9A3201 2.3 39.7 1.0 C07 B:9A3201 2.4 32.9 1.0 C09 B:9A3201 2.9 35.2 1.0 C06 B:9A3201 3.5 30.0 1.0 CB B:MET165 3.6 38.4 1.0 CA B:GLY109 3.8 27.0 1.0 OG1 B:THR166 4.0 36.9 1.0 CA B:VAL162 4.0 36.2 1.0 CG2 B:VAL162 4.0 38.1 1.0 O B:VAL162 4.0 34.7 1.0 CG1 B:VAL162 4.0 33.6 1.0 CZ B:PHE113 4.1 39.5 1.0 N B:THR166 4.2 38.9 1.0 CB B:VAL162 4.2 37.1 1.0 CG B:MET165 4.2 49.0 1.0 C10 B:9A3201 4.2 35.3 1.0 CE1 B:PHE113 4.3 40.2 1.0 C B:MET165 4.4 39.3 1.0 C B:VAL162 4.5 35.8 1.0 CA B:MET165 4.5 37.4 1.0 CE2 B:PHE113 4.6 37.7 1.0 C B:GLY109 4.6 26.1 1.0 C05 B:9A3201 4.7 37.4 1.0 CA B:THR166 4.7 36.8 1.0 N B:GLY109 4.7 27.9 1.0 SD B:MET165 4.7 58.8 1.0 CE B:MET165 4.8 43.8 1.0 O B:MET165 4.9 34.7 1.0 CD1 B:PHE113 5.0 36.0 1.0 O B:ILE105 5.0 29.8 1.0 C04 B:9A3201 5.0 34.5 1.0 CB B:THR166 5.0 36.8 1.0 O B:GLY109 5.0 29.4 1.0

Fluorine binding site 6 out of 48 in the Crystal Structure of CF3-Aequorin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:39.7 occ:1.00 F03 B:9A3201 0.0 39.7 1.0 C08 B:9A3201 1.4 36.1 1.0 F01 B:9A3201 2.2 36.4 1.0 F02 B:9A3201 2.3 36.6 1.0 C07 B:9A3201 2.5 32.9 1.0 C09 B:9A3201 3.2 35.2 1.0 N B:THR166 3.2 38.9 1.0 C B:MET165 3.2 39.3 1.0 O B:MET165 3.3 34.7 1.0 CA B:THR166 3.3 36.8 1.0 C06 B:9A3201 3.4 30.0 1.0 CG B:HIS169 3.5 37.0 1.0 ND1 B:HIS169 3.5 37.9 1.0 CB B:MET165 3.6 38.4 1.0 OG1 B:THR166 3.7 36.9 1.0 CB B:HIS169 3.7 36.0 1.0 CG B:MET165 3.9 49.0 1.0 CE1 B:HIS169 4.0 45.2 1.0 CA B:MET165 4.0 37.4 1.0 CD2 B:HIS169 4.1 36.4 1.0 CB B:THR166 4.1 36.8 1.0 NE2 B:HIS169 4.3 39.4 1.0 C10 B:9A3201 4.5 35.3 1.0 CG1 B:ILE105 4.5 33.6 1.0 C B:THR166 4.5 37.5 1.0 O B:VAL162 4.6 34.7 1.0 C05 B:9A3201 4.6 37.4 1.0 O B:ILE105 4.8 29.8 1.0 O B:THR166 4.8 35.0 1.0 CG2 B:THR166 5.0 30.4 1.0

Fluorine binding site 7 out of 48 in the Crystal Structure of CF3-Aequorin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:39.4 occ:1.00 F01 C:9A3201 0.0 39.4 1.0 C08 C:9A3201 1.4 38.4 1.0 F02 C:9A3201 2.2 41.2 1.0 F03 C:9A3201 2.2 42.3 1.0 C07 C:9A3201 2.4 38.6 1.0 C06 C:9A3201 2.7 36.5 1.0 O C:ILE105 3.1 32.7 1.0 OG1 C:THR166 3.2 34.7 1.0 CA C:GLY109 3.6 33.9 1.0 C09 C:9A3201 3.7 37.8 1.0 C C:ILE105 3.7 32.8 1.0 CA C:ARG106 3.8 29.9 1.0 N C:GLY109 3.9 30.5 1.0 N C:ARG106 4.0 32.2 1.0 CG1 C:ILE105 4.0 33.8 1.0 C05 C:9A3201 4.0 37.4 1.0 CA C:THR166 4.2 38.0 1.0 CB C:THR166 4.2 36.5 1.0 O C:ARG106 4.3 32.4 1.0 N C:THR166 4.4 34.6 1.0 C C:ARG106 4.4 26.1 1.0 CG2 C:VAL162 4.5 41.3 1.0 CD1 C:ILE105 4.7 36.0 1.0 C10 C:9A3201 4.7 40.8 1.0 C C:GLY109 4.8 38.6 1.0 CG2 C:THR166 4.8 29.2 1.0 CA C:ILE105 4.8 33.8 1.0 O C:VAL162 4.8 38.5 1.0 CB C:ILE105 4.9 35.9 1.0 CB C:ARG106 4.9 31.9 1.0 C C:MET165 4.9 37.6 1.0 C04 C:9A3201 4.9 36.6 1.0

Fluorine binding site 8 out of 48 in the Crystal Structure of CF3-Aequorin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:41.2 occ:1.00 F02 C:9A3201 0.0 41.2 1.0 C08 C:9A3201 1.4 38.4 1.0 F03 C:9A3201 2.2 42.3 1.0 F01 C:9A3201 2.2 39.4 1.0 C07 C:9A3201 2.5 38.6 1.0 C09 C:9A3201 3.0 37.8 1.0 CB C:MET165 3.4 35.8 1.0 C06 C:9A3201 3.5 36.5 1.0 OG1 C:THR166 3.6 34.7 1.0 CG2 C:VAL162 3.6 41.3 1.0 O C:VAL162 3.7 38.5 1.0 N C:THR166 3.8 34.6 1.0 CA C:GLY109 3.9 33.9 1.0 C C:MET165 4.1 37.6 1.0 CE1 C:PHE113 4.1 45.0 1.0 CA C:VAL162 4.1 41.2 1.0 CZ C:PHE113 4.2 44.4 1.0 CA C:THR166 4.3 38.0 1.0 C10 C:9A3201 4.4 40.8 1.0 CA C:MET165 4.4 36.7 1.0 C C:VAL162 4.4 42.2 1.0 CB C:VAL162 4.4 41.7 1.0 CG C:MET165 4.4 47.5 1.0 O C:MET165 4.5 36.6 1.0 CB C:THR166 4.6 36.5 1.0 CD1 C:PHE113 4.7 41.3 1.0 C C:GLY109 4.7 38.6 1.0 C05 C:9A3201 4.7 37.4 1.0 N C:GLY109 4.9 30.5 1.0 CE2 C:PHE113 4.9 46.1 1.0 CE C:MET165 4.9 48.8 1.0

Fluorine binding site 9 out of 48 in the Crystal Structure of CF3-Aequorin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:42.3 occ:1.00 F03 C:9A3201 0.0 42.3 1.0 C08 C:9A3201 1.4 38.4 1.0 F02 C:9A3201 2.2 41.2 1.0 F01 C:9A3201 2.2 39.4 1.0 C07 C:9A3201 2.4 38.6 1.0 C09 C:9A3201 3.0 37.8 1.0 O C:MET165 3.0 36.6 1.0 C C:MET165 3.1 37.6 1.0 N C:THR166 3.2 34.6 1.0 CA C:THR166 3.3 38.0 1.0 CG C:HIS169 3.4 40.1 1.0 C06 C:9A3201 3.4 36.5 1.0 ND1 C:HIS169 3.4 45.0 1.0 CB C:HIS169 3.6 37.8 1.0 CB C:MET165 3.6 35.8 1.0 OG1 C:THR166 3.7 34.7 1.0 CD2 C:HIS169 3.9 41.1 1.0 CE1 C:HIS169 4.0 41.4 1.0 CA C:MET165 4.0 36.7 1.0 CB C:THR166 4.2 36.5 1.0 NE2 C:HIS169 4.2 41.1 1.0 C10 C:9A3201 4.3 40.8 1.0 C C:THR166 4.4 35.5 1.0 C05 C:9A3201 4.6 37.4 1.0 O C:VAL162 4.6 38.5 1.0 CG1 C:ILE105 4.6 33.8 1.0 O C:THR166 4.7 37.8 1.0 CG C:MET165 4.8 47.5 1.0 CA C:HIS169 4.9 35.8 1.0 N C:HIS169 4.9 35.8 1.0 CE C:MET165 4.9 48.8 1.0 C04 C:9A3201 5.0 36.6 1.0

Fluorine binding site 10 out of 48 in the Crystal Structure of CF3-Aequorin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of CF3-Aequorin within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:40.9 occ:1.00 F01 D:9A3201 0.0 40.9 1.0 C08 D:9A3201 1.4 42.7 1.0 F03 D:9A3201 2.2 43.0 1.0 F02 D:9A3201 2.2 39.6 1.0 C07 D:9A3201 2.4 43.4 1.0 C06 D:9A3201 2.7 39.5 1.0 O D:ILE105 3.0 31.5 1.0 OG1 D:THR166 3.4 34.4 1.0 CA D:GLY109 3.7 30.5 1.0 C D:ILE105 3.7 37.5 1.0 C09 D:9A3201 3.7 45.8 1.0 CA D:ARG106 3.8 33.8 1.0 N D:GLY109 3.9 35.1 1.0 CG1 D:ILE105 3.9 38.8 1.0 N D:ARG106 4.1 33.5 1.0 CA D:THR166 4.1 39.0 1.0 C05 D:9A3201 4.1 40.9 1.0 CB D:THR166 4.2 33.4 1.0 N D:THR166 4.4 37.5 1.0 O D:ARG106 4.4 30.8 1.0 C D:ARG106 4.5 29.1 1.0 CG2 D:THR166 4.6 36.7 1.0 CD1 D:ILE105 4.6 37.9 1.0 CA D:ILE105 4.7 34.9 1.0 CB D:ILE105 4.7 37.8 1.0 C10 D:9A3201 4.8 45.8 1.0 C D:MET165 4.8 39.1 1.0 O D:VAL162 4.8 40.9 1.0 CG1 D:VAL162 4.9 48.6 1.0 CG2 D:ILE105 4.9 38.5 1.0 C D:GLY109 4.9 35.4 1.0 CB D:ARG106 5.0 38.5 1.0 C04 D:9A3201 5.0 42.1 1.0 O D:MET165 5.0 37.8 1.0

S.Inouye, Y.Tomabechi, T.Hosoya, S.I.Sekine, M.Shirouzu. Slow Luminescence Kinetics of Semi-Synthetic Aequorin: Expression, Purification and Structure Determination of CF3-Aequorin. J. Biochem. V. 164 247 2018.
ISSN: ISSN 1756-2651
PubMed: 29796619
DOI: 10.1093/JB/MVY049