Fluorine in PDB 5b2y: Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan

All present enzymatic activity of Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan:
1.14.14.1; 1.6.2.4;

The structure of Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan, PDB code: 5b2y was solved by Z.Cong, O.Shoji, C.Kasai, H.Sugimoto, Y.Shiro, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.734, 145.724, 63.193, 90.00, 82.85, 90.00
R / Rfree (%)	18.3 / 22

The structure of Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan (pdb code 5b2y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 38 binding sites of Fluorine where determined in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan, PDB code: 5b2y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:85.0 occ:1.00 FBQ A:W10502 0.0 85.0 1.0 CAZ A:W10502 1.3 81.7 1.0 FBS A:W10502 2.2 81.8 1.0 FBR A:W10502 2.2 83.5 1.0 CAY A:W10502 2.4 80.5 1.0 FBA A:W10502 2.6 73.1 1.0 CAX A:W10502 2.8 75.1 1.0 FBD A:W10502 2.9 70.0 1.0 CB A:LEU437 3.0 35.3 1.0 CG2 A:THR438 3.0 28.5 1.0 FBE A:W10502 3.1 66.6 1.0 N A:THR438 3.1 29.9 1.0 FBO A:W10502 3.1 81.3 1.0 CAW A:W10502 3.3 71.1 1.0 FBP A:W10502 3.4 81.4 1.0 C A:LEU437 3.5 33.2 1.0 CAV A:W10502 3.7 68.5 1.0 CA A:LEU437 3.8 32.7 1.0 O A:THR436 3.9 32.5 1.0 CA A:THR438 3.9 27.1 1.0 CB A:THR438 3.9 27.8 1.0 FBB A:W10502 4.1 68.3 1.0 CG A:LEU437 4.2 36.4 1.0 CD1 A:LEU437 4.2 36.6 1.0 O A:LEU437 4.4 32.9 1.0 OG1 A:THR438 4.4 28.7 1.0 FBC A:W10502 4.5 68.3 1.0 FBF A:W10502 4.6 64.8 1.0 C A:THR436 4.7 29.4 1.0 N A:LEU437 4.8 30.1 1.0 FBH A:W10502 4.8 67.9 1.0 CAU A:W10502 4.9 67.3 1.0

Fluorine binding site 2 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:83.5 occ:1.00 FBR A:W10502 0.0 83.5 1.0 CAZ A:W10502 1.3 81.7 1.0 FBS A:W10502 2.1 81.8 1.0 FBQ A:W10502 2.2 85.0 1.0 CAY A:W10502 2.3 80.5 1.0 FBO A:W10502 2.5 81.3 1.0 FBP A:W10502 3.0 81.4 1.0 CG2 A:THR438 3.5 28.5 1.0 CAX A:W10502 3.7 75.1 1.0 FBA A:W10502 3.9 73.1 1.0 FBD A:W10502 4.1 70.0 1.0 CG2 A:ILE263 4.2 35.6 1.0 CD2 A:LEU181 4.3 42.8 1.0 CAW A:W10502 4.5 71.1 1.0 FBB A:W10502 4.6 68.3 1.0 CB A:THR438 4.7 27.8 1.0 CB A:LEU437 4.7 35.3 1.0 N A:THR438 4.8 29.9 1.0 OG1 A:THR438 4.8 28.7 1.0 O A:THR436 4.9 32.5 1.0

Fluorine binding site 3 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:81.8 occ:1.00 FBS A:W10502 0.0 81.8 1.0 CAZ A:W10502 1.3 81.7 1.0 FBR A:W10502 2.1 83.5 1.0 FBQ A:W10502 2.2 85.0 1.0 CAY A:W10502 2.4 80.5 1.0 FBP A:W10502 2.4 81.4 1.0 FBD A:W10502 2.5 70.0 1.0 CD1 A:LEU437 3.3 36.6 1.0 CAX A:W10502 3.4 75.1 1.0 FBO A:W10502 3.4 81.3 1.0 CAW A:W10502 3.4 71.1 1.0 CB A:LEU437 3.6 35.3 1.0 CD2 A:LEU181 3.9 42.8 1.0 FBA A:W10502 3.9 73.1 1.0 CG A:LEU437 4.1 36.4 1.0 FBE A:W10502 4.3 66.6 1.0 FBC A:W10502 4.3 68.3 1.0 FBB A:W10502 4.5 68.3 1.0 CAV A:W10502 4.5 68.5 1.0 CG2 A:VAL78 4.5 28.6 1.0 CE2 A:PHE87 4.7 25.8 1.0 FBH A:W10502 4.7 67.9 1.0 O A:THR436 4.8 32.5 1.0 CG2 A:THR438 4.9 28.5 1.0 CZ A:PHE87 4.9 26.2 1.0 CA A:LEU437 5.0 32.7 1.0

Fluorine binding site 4 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:81.3 occ:1.00 FBO A:W10502 0.0 81.3 1.0 CAY A:W10502 1.3 80.5 1.0 FBP A:W10502 2.1 81.4 1.0 CAX A:W10502 2.4 75.1 1.0 CAZ A:W10502 2.4 81.7 1.0 FBR A:W10502 2.5 83.5 1.0 FBB A:W10502 2.6 68.3 1.0 FBA A:W10502 2.8 73.1 1.0 FBQ A:W10502 3.1 85.0 1.0 FBS A:W10502 3.4 81.8 1.0 CAW A:W10502 3.8 71.1 1.0 CZ A:PHE87 3.8 26.2 1.0 CG2 A:THR438 3.9 28.5 1.0 FBD A:W10502 4.0 70.0 1.0 CE2 A:PHE87 4.2 25.8 1.0 CG2 A:THR268 4.2 26.0 1.0 O A:HOH800 4.2 23.0 1.0 FBC A:W10502 4.4 68.3 1.0 CB A:ALA264 4.5 49.2 1.0 CE1 A:PHE87 4.6 24.6 1.0 CB A:ALA328 4.7 17.8 1.0 CAV A:W10502 4.9 68.5 1.0 CA A:ALA264 4.9 48.8 1.0 FBE A:W10502 4.9 66.6 1.0

Fluorine binding site 5 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:81.4 occ:1.00 FBP A:W10502 0.0 81.4 1.0 CAY A:W10502 1.3 80.5 1.0 FBO A:W10502 2.1 81.3 1.0 CAZ A:W10502 2.3 81.7 1.0 CAX A:W10502 2.4 75.1 1.0 FBS A:W10502 2.4 81.8 1.0 CZ A:PHE87 2.6 26.2 1.0 CE2 A:PHE87 2.7 25.8 1.0 FBD A:W10502 2.7 70.0 1.0 FBB A:W10502 2.9 68.3 1.0 CAW A:W10502 2.9 71.1 1.0 FBR A:W10502 3.0 83.5 1.0 FBC A:W10502 3.2 68.3 1.0 FBQ A:W10502 3.4 85.0 1.0 FBA A:W10502 3.5 73.1 1.0 CE1 A:PHE87 3.9 24.6 1.0 CD2 A:PHE87 3.9 25.1 1.0 CD2 A:LEU75 4.2 30.0 1.0 CAV A:W10502 4.4 68.5 1.0 FBE A:W10502 4.8 66.6 1.0 CD1 A:PHE87 4.8 23.2 1.0 CG A:PHE87 4.9 21.1 1.0

Fluorine binding site 6 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:73.1 occ:1.00 FBA A:W10502 0.0 73.1 1.0 CAX A:W10502 1.3 75.1 1.0 FBB A:W10502 2.1 68.3 1.0 CAW A:W10502 2.4 71.1 1.0 CAY A:W10502 2.4 80.5 1.0 FBE A:W10502 2.5 66.6 1.0 FBQ A:W10502 2.6 85.0 1.0 CAV A:W10502 2.6 68.5 1.0 FBF A:W10502 2.7 64.8 1.0 FBO A:W10502 2.8 81.3 1.0 CAZ A:W10502 3.0 81.7 1.0 FBD A:W10502 3.2 70.0 1.0 FBC A:W10502 3.4 68.3 1.0 CG2 A:THR438 3.4 28.5 1.0 CB A:ALA328 3.5 17.8 1.0 FBP A:W10502 3.5 81.4 1.0 CA A:ALA328 3.6 17.7 1.0 FBR A:W10502 3.9 83.5 1.0 FBS A:W10502 3.9 81.8 1.0 CAU A:W10502 4.2 67.3 1.0 N A:THR438 4.2 29.9 1.0 CA A:THR438 4.4 27.1 1.0 C A:LEU437 4.4 33.2 1.0 O A:THR327 4.5 17.5 1.0 C A:ALA328 4.5 17.5 1.0 CD A:PRO329 4.5 16.7 1.0 CB A:THR438 4.5 27.8 1.0 O A:LEU437 4.6 32.9 1.0 FBH A:W10502 4.7 67.9 1.0 N A:ALA328 4.7 17.4 1.0 CB A:LEU437 4.7 35.3 1.0 CG2 A:THR268 4.7 26.0 1.0 FBG A:W10502 4.8 67.0 1.0 N A:PRO329 4.8 16.1 1.0 FBJ A:W10502 5.0 63.5 1.0

Fluorine binding site 7 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:68.3 occ:1.00 FBB A:W10502 0.0 68.3 1.0 CAX A:W10502 1.3 75.1 1.0 FBA A:W10502 2.1 73.1 1.0 CAW A:W10502 2.3 71.1 1.0 CAY A:W10502 2.4 80.5 1.0 FBC A:W10502 2.4 68.3 1.0 FBO A:W10502 2.6 81.3 1.0 FBP A:W10502 2.9 81.4 1.0 FBF A:W10502 3.1 64.8 1.0 CAV A:W10502 3.3 68.5 1.0 CZ A:PHE87 3.3 26.2 1.0 FBD A:W10502 3.4 70.0 1.0 CB A:ALA328 3.6 17.8 1.0 CE1 A:PHE87 3.8 24.6 1.0 CAZ A:W10502 3.8 81.7 1.0 O A:HOH634 3.9 24.0 1.0 FBE A:W10502 3.9 66.6 1.0 FBQ A:W10502 4.1 85.0 1.0 CE2 A:PHE87 4.3 25.8 1.0 CA A:ALA328 4.4 17.7 1.0 FBS A:W10502 4.5 81.8 1.0 CAU A:W10502 4.5 67.3 1.0 FBG A:W10502 4.6 67.0 1.0 FBR A:W10502 4.6 83.5 1.0 O A:HOH800 4.9 23.0 1.0 CBA A:HEM501 4.9 15.0 1.0

Fluorine binding site 8 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:68.3 occ:1.00 FBC A:W10502 0.0 68.3 1.0 CAW A:W10502 1.3 71.1 1.0 FBD A:W10502 2.2 70.0 1.0 CAV A:W10502 2.3 68.5 1.0 CAX A:W10502 2.4 75.1 1.0 FBB A:W10502 2.4 68.3 1.0 FBG A:W10502 2.6 67.0 1.0 FBF A:W10502 2.7 64.8 1.0 O A:HOH634 2.8 24.0 1.0 CAU A:W10502 2.8 67.3 1.0 FBH A:W10502 3.0 67.9 1.0 FBP A:W10502 3.2 81.4 1.0 CAY A:W10502 3.4 80.5 1.0 FBA A:W10502 3.4 73.1 1.0 FBE A:W10502 3.5 66.6 1.0 CZ A:PHE87 3.5 26.2 1.0 CD2 A:LEU75 3.5 30.0 1.0 O A:HOH848 4.2 36.0 1.0 CAZ A:W10502 4.3 81.7 1.0 FBS A:W10502 4.3 81.8 1.0 CE1 A:PHE87 4.3 24.6 1.0 CAT A:W10502 4.3 64.9 1.0 FBO A:W10502 4.4 81.3 1.0 CG A:LEU75 4.4 29.0 1.0 CE2 A:PHE87 4.4 25.8 1.0 O A:ALA330 4.5 20.0 1.0 FBQ A:W10502 4.5 85.0 1.0 FBJ A:W10502 4.7 63.5 1.0 CD1 A:LEU75 4.8 28.7 1.0 FBI A:W10502 5.0 64.3 1.0

Fluorine binding site 9 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:70.0 occ:1.00 FBD A:W10502 0.0 70.0 1.0 CAW A:W10502 1.3 71.1 1.0 FBC A:W10502 2.2 68.3 1.0 CAV A:W10502 2.4 68.5 1.0 CAX A:W10502 2.4 75.1 1.0 FBH A:W10502 2.4 67.9 1.0 FBS A:W10502 2.5 81.8 1.0 CAY A:W10502 2.7 80.5 1.0 FBP A:W10502 2.7 81.4 1.0 FBE A:W10502 2.8 66.6 1.0 CAZ A:W10502 2.8 81.7 1.0 CAU A:W10502 2.9 67.3 1.0 FBQ A:W10502 2.9 85.0 1.0 FBA A:W10502 3.2 73.1 1.0 FBB A:W10502 3.4 68.3 1.0 FBF A:W10502 3.5 64.8 1.0 FBG A:W10502 3.6 67.0 1.0 CB A:LEU437 3.7 35.3 1.0 CD1 A:LEU437 4.0 36.6 1.0 FBO A:W10502 4.0 81.3 1.0 CD2 A:LEU75 4.1 30.0 1.0 FBR A:W10502 4.1 83.5 1.0 CAT A:W10502 4.2 64.9 1.0 FBI A:W10502 4.3 64.3 1.0 CG A:LEU437 4.3 36.4 1.0 CZ A:PHE87 4.4 26.2 1.0 CE2 A:PHE87 4.7 25.8 1.0 CA A:LEU437 4.8 32.7 1.0 CB A:ALA74 4.8 29.7 1.0 CD2 A:LEU437 4.9 37.1 1.0 O A:HOH634 5.0 24.0 1.0 FBJ A:W10502 5.0 63.5 1.0 FBL A:W10502 5.0 62.5 1.0

Fluorine binding site 10 out of 38 in the Crystal Structure of P450BM3 with N-Perfluorodecanoyl-L-Tryptophan


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 P450BM3 with N-Perfluorodecanoyl-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:66.6 occ:1.00 FBE A:W10502 0.0 66.6 1.0 CAV A:W10502 1.3 68.5 1.0 FBF A:W10502 2.2 64.8 1.0 CAW A:W10502 2.4 71.1 1.0 CAU A:W10502 2.4 67.3 1.0 FBA A:W10502 2.5 73.1 1.0 FBI A:W10502 2.6 64.3 1.0 FBD A:W10502 2.8 70.0 1.0 CAT A:W10502 2.8 64.9 1.0 FBH A:W10502 2.9 67.9 1.0 CAX A:W10502 2.9 75.1 1.0 FBJ A:W10502 3.0 63.5 1.0 O A:LEU437 3.0 32.9 1.0 FBQ A:W10502 3.1 85.0 1.0 C A:LEU437 3.1 33.2 1.0 CB A:LEU437 3.3 35.3 1.0 CA A:LEU437 3.4 32.7 1.0 FBG A:W10502 3.5 67.0 1.0 FBC A:W10502 3.5 68.3 1.0 N A:THR438 3.7 29.9 1.0 FBB A:W10502 3.9 68.3 1.0 CAZ A:W10502 4.0 81.7 1.0 CAY A:W10502 4.0 80.5 1.0 CD A:PRO329 4.0 16.7 1.0 CAS A:W10502 4.3 61.4 1.0 FBS A:W10502 4.3 81.8 1.0 CA A:THR438 4.4 27.1 1.0 CG A:LEU437 4.6 36.4 1.0 FBL A:W10502 4.6 62.5 1.0 CG A:PRO329 4.8 16.1 1.0 CG2 A:THR438 4.8 28.5 1.0 FBP A:W10502 4.8 81.4 1.0 N A:PRO329 4.8 16.1 1.0 CA A:ALA328 4.8 17.7 1.0 N A:LEU437 4.9 30.1 1.0 CD2 A:LEU437 4.9 37.1 1.0 FBK A:W10502 4.9 60.5 1.0 FBO A:W10502 4.9 81.3 1.0

Z.Cong, O.Shoji, C.Kasai, H.Sugimoto, Y.Shiro, Y.Watanabe. Crystal Structure of P450BM3 with Decoy Molecules To Be Published.