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Fluorine in PDB 3wsp: Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan

Enzymatic activity of Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan

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

Protein crystallography data

The structure of Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan, PDB code: 3wsp 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) 19.96 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.875, 145.392, 63.029, 90.00, 97.06, 90.00
R / Rfree (%) 17.4 / 21.2

Other elements in 3wsp:

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

Iron (Fe) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan (pdb code 3wsp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 34 binding sites of Fluorine where determined in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan, PDB code: 3wsp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 34 in 3wsp

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Fluorine binding site 1 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:45.1
occ:1.00
FBN A:W09502 0.0 45.1 1.0
CAY A:W09502 1.4 46.0 1.0
FBO A:W09502 2.2 43.8 1.0
FBP A:W09502 2.2 46.2 1.0
CAX A:W09502 2.4 43.9 1.0
FBM A:W09502 2.8 42.4 1.0
FBL A:W09502 2.8 43.5 1.0
CZ A:PHE87 3.1 22.7 1.0
CAW A:W09502 3.7 43.7 1.0
O A:HOH660 3.9 19.0 1.0
CE1 A:PHE87 3.9 20.6 1.0
CE2 A:PHE87 4.0 21.6 1.0
FBJ A:W09502 4.0 44.7 1.0
FBK A:W09502 4.1 38.1 1.0
C1 A:DMS503 4.1 27.9 1.0
CB A:ALA328 4.3 15.4 1.0
O A:LEU437 4.3 21.5 0.4
CD2 A:LEU75 4.7 22.7 1.0
CA A:ALA328 4.8 14.1 1.0
CAV A:W09502 4.9 41.7 1.0

Fluorine binding site 2 out of 34 in 3wsp

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Fluorine binding site 2 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:43.8
occ:1.00
FBO A:W09502 0.0 43.8 1.0
CAY A:W09502 1.3 46.0 1.0
FBN A:W09502 2.2 45.1 1.0
FBP A:W09502 2.2 46.2 1.0
CAX A:W09502 2.3 43.9 1.0
O A:LEU437 2.5 21.5 0.4
FBK A:W09502 2.6 38.1 1.0
CAW A:W09502 2.8 43.7 1.0
FBM A:W09502 2.8 42.4 1.0
FBJ A:W09502 3.0 44.7 1.0
FBL A:W09502 3.5 43.5 1.0
CA A:ALA328 3.6 14.1 1.0
C A:LEU437 3.7 23.9 0.4
CB A:ALA328 3.8 15.4 1.0
CG2 A:THR438 3.8 22.7 0.6
CD A:PRO329 3.9 12.6 1.0
CG2 A:THR438 3.9 23.6 0.4
C A:ALA328 4.2 14.0 1.0
C A:LEU437 4.2 23.8 0.6
N A:THR438 4.2 23.0 0.6
O A:LEU437 4.3 21.4 0.6
CAV A:W09502 4.3 41.7 1.0
N A:PRO329 4.3 12.4 1.0
CB A:LEU437 4.5 26.8 0.6
CA A:THR438 4.5 20.9 0.6
CA A:LEU437 4.6 25.9 0.4
O A:THR327 4.6 16.9 1.0
N A:THR438 4.6 23.4 0.4
FBI A:W09502 4.7 42.4 1.0
CA A:THR438 4.7 22.0 0.4
CB A:LEU437 4.7 27.4 0.4
CB A:THR438 4.8 22.4 0.6
N A:ALA328 4.9 13.7 1.0
CB A:THR438 4.9 23.2 0.4
CA A:LEU437 4.9 25.3 0.6

Fluorine binding site 3 out of 34 in 3wsp

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Fluorine binding site 3 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:46.2
occ:1.00
FBP A:W09502 0.0 46.2 1.0
CAY A:W09502 1.4 46.0 1.0
FBO A:W09502 2.2 43.8 1.0
FBN A:W09502 2.2 45.1 1.0
CAX A:W09502 2.4 43.9 1.0
FBJ A:W09502 2.6 44.7 1.0
FBL A:W09502 2.8 43.5 1.0
CAW A:W09502 2.9 43.7 1.0
O A:ALA330 3.1 12.1 1.0
O A:HOH660 3.2 19.0 1.0
CB A:ALA328 3.4 15.4 1.0
FBK A:W09502 3.5 38.1 1.0
FBM A:W09502 3.6 42.4 1.0
C A:ALA328 3.7 14.0 1.0
CA A:ALA328 3.7 14.1 1.0
O A:ALA328 4.0 16.6 1.0
N A:PRO329 4.1 12.4 1.0
N A:ALA330 4.2 12.6 1.0
C A:ALA330 4.2 11.8 1.0
CAV A:W09502 4.3 41.7 1.0
CD A:PRO329 4.3 12.6 1.0
FBH A:W09502 4.4 43.2 1.0
O A:LEU437 4.6 21.5 0.4
CA A:ALA330 4.8 12.8 1.0
CZ A:PHE87 4.8 22.7 1.0
FBI A:W09502 4.9 42.4 1.0
C1 A:DMS503 4.9 27.9 1.0

Fluorine binding site 4 out of 34 in 3wsp

Go back to Fluorine Binding Sites List in 3wsp
Fluorine binding site 4 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:43.5
occ:1.00
FBL A:W09502 0.0 43.5 1.0
CAX A:W09502 1.3 43.9 1.0
FBM A:W09502 2.2 42.4 1.0
CAW A:W09502 2.4 43.7 1.0
CAY A:W09502 2.4 46.0 1.0
FBJ A:W09502 2.7 44.7 1.0
O A:HOH660 2.7 19.0 1.0
FBH A:W09502 2.8 43.2 1.0
FBP A:W09502 2.8 46.2 1.0
CAV A:W09502 2.8 41.7 1.0
FBN A:W09502 2.8 45.1 1.0
FBI A:W09502 2.9 42.4 1.0
FBK A:W09502 3.4 38.1 1.0
O A:HOH735 3.5 25.7 1.0
FBO A:W09502 3.5 43.8 1.0
CD2 A:LEU75 4.0 22.7 1.0
O A:ALA330 4.0 12.1 1.0
CAU A:W09502 4.3 40.7 1.0
CG A:LEU75 4.4 19.2 1.0
OG A:SER72 4.5 20.3 1.0
CZ A:PHE87 4.6 22.7 1.0
FBG A:W09502 4.8 37.8 1.0
FBF A:W09502 4.9 45.6 1.0
CD1 A:LEU75 4.9 19.6 1.0

Fluorine binding site 5 out of 34 in 3wsp

Go back to Fluorine Binding Sites List in 3wsp
Fluorine binding site 5 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:42.4
occ:1.00
FBM A:W09502 0.0 42.4 1.0
CAX A:W09502 1.4 43.9 1.0
FBL A:W09502 2.2 43.5 1.0
CAW A:W09502 2.4 43.7 1.0
CAY A:W09502 2.4 46.0 1.0
FBI A:W09502 2.6 42.4 1.0
FBK A:W09502 2.6 38.1 1.0
FBO A:W09502 2.8 43.8 1.0
FBN A:W09502 2.8 45.1 1.0
CAV A:W09502 3.0 41.7 1.0
FBJ A:W09502 3.3 44.7 1.0
O A:LEU437 3.5 21.5 0.4
CB A:LEU437 3.5 26.8 0.6
CB A:LEU437 3.6 27.4 0.4
FBP A:W09502 3.6 46.2 1.0
FBH A:W09502 3.8 43.2 1.0
CD1 A:LEU437 4.0 29.0 0.6
FBF A:W09502 4.1 45.6 1.0
CA A:LEU437 4.2 25.9 0.4
CG A:LEU437 4.2 28.2 0.6
CAU A:W09502 4.2 40.7 1.0
C A:LEU437 4.3 23.9 0.4
CG A:LEU437 4.5 28.9 0.4
CD2 A:LEU75 4.5 22.7 1.0
CD2 A:LEU437 4.5 28.4 0.6
CA A:LEU437 4.5 25.3 0.6
CD2 A:LEU437 4.6 28.9 0.4
CD1 A:LEU437 4.6 30.1 0.4
CB A:ALA74 4.7 18.7 1.0
C A:LEU437 4.8 23.8 0.6
O A:HOH660 4.8 19.0 1.0
CZ A:PHE87 4.9 22.7 1.0
FBG A:W09502 5.0 37.8 1.0

Fluorine binding site 6 out of 34 in 3wsp

Go back to Fluorine Binding Sites List in 3wsp
Fluorine binding site 6 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:44.7
occ:1.00
FBJ A:W09502 0.0 44.7 1.0
CAW A:W09502 1.0 43.7 1.0
FBK A:W09502 1.8 38.1 1.0
CAV A:W09502 2.1 41.7 1.0
CAX A:W09502 2.2 43.9 1.0
FBH A:W09502 2.5 43.2 1.0
FBP A:W09502 2.6 46.2 1.0
FBG A:W09502 2.7 37.8 1.0
CAY A:W09502 2.7 46.0 1.0
FBL A:W09502 2.7 43.5 1.0
CAU A:W09502 2.9 40.7 1.0
FBO A:W09502 3.0 43.8 1.0
FBI A:W09502 3.2 42.4 1.0
FBM A:W09502 3.3 42.4 1.0
O A:ALA330 3.4 12.1 1.0
FBF A:W09502 3.5 45.6 1.0
N A:ALA330 3.5 12.6 1.0
CD A:PRO329 3.7 12.6 1.0
CB A:ALA330 3.9 13.4 1.0
FBN A:W09502 4.0 45.1 1.0
CA A:ALA330 4.0 12.8 1.0
C A:ALA330 4.1 11.8 1.0
N A:PRO329 4.1 12.4 1.0
CAT A:W09502 4.2 38.9 1.0
CG A:PRO329 4.3 11.4 1.0
FBD A:W09502 4.3 35.4 1.0
O A:LEU437 4.3 21.5 0.4
O A:HOH660 4.3 19.0 1.0
C A:ALA328 4.5 14.0 1.0
C A:PRO329 4.5 12.0 1.0
O A:LEU437 4.6 21.4 0.6
CA A:PRO329 4.8 11.8 1.0
FBE A:W09502 4.9 37.8 1.0
CA A:ALA328 4.9 14.1 1.0

Fluorine binding site 7 out of 34 in 3wsp

Go back to Fluorine Binding Sites List in 3wsp
Fluorine binding site 7 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:38.1
occ:1.00
FBK A:W09502 0.0 38.1 1.0
CAW A:W09502 1.2 43.7 1.0
FBJ A:W09502 1.8 44.7 1.0
CAV A:W09502 2.2 41.7 1.0
CAX A:W09502 2.2 43.9 1.0
FBF A:W09502 2.5 45.6 1.0
FBM A:W09502 2.6 42.4 1.0
FBO A:W09502 2.6 43.8 1.0
CAU A:W09502 2.6 40.7 1.0
O A:LEU437 2.8 21.5 0.4
FBI A:W09502 2.8 42.4 1.0
CAY A:W09502 2.9 46.0 1.0
FBG A:W09502 2.9 37.8 1.0
O A:LEU437 3.1 21.4 0.6
FBL A:W09502 3.4 43.5 1.0
FBH A:W09502 3.4 43.2 1.0
C A:LEU437 3.4 23.8 0.6
C A:LEU437 3.4 23.9 0.4
FBP A:W09502 3.5 46.2 1.0
CA A:LEU437 3.6 25.9 0.4
CB A:LEU437 3.6 26.8 0.6
CA A:LEU437 3.6 25.3 0.6
CD A:PRO329 3.8 12.6 1.0
CB A:LEU437 4.0 27.4 0.4
FBN A:W09502 4.1 45.1 1.0
CAT A:W09502 4.2 38.9 1.0
N A:THR438 4.2 23.0 0.6
CG A:PRO329 4.4 11.4 1.0
N A:THR438 4.5 23.4 0.4
FBE A:W09502 4.6 37.8 1.0
N A:PRO329 4.7 12.4 1.0
CG A:LEU437 4.8 28.2 0.6
FBD A:W09502 4.8 35.4 1.0
O A:HOH676 4.9 20.1 1.0
N A:LEU437 4.9 24.2 0.4
CD2 A:LEU437 4.9 28.4 0.6
CA A:THR438 4.9 20.9 0.6
FBB A:W09502 5.0 37.7 1.0

Fluorine binding site 8 out of 34 in 3wsp

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Fluorine binding site 8 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:43.2
occ:1.00
FBH A:W09502 0.0 43.2 1.0
CAV A:W09502 1.4 41.7 1.0
FBI A:W09502 2.2 42.4 1.0
CAW A:W09502 2.4 43.7 1.0
CAU A:W09502 2.4 40.7 1.0
FBD A:W09502 2.4 35.4 1.0
FBJ A:W09502 2.5 44.7 1.0
FBL A:W09502 2.8 43.5 1.0
CAT A:W09502 2.8 38.9 1.0
FBG A:W09502 2.9 37.8 1.0
CAX A:W09502 3.1 43.9 1.0
FBE A:W09502 3.3 37.8 1.0
FBK A:W09502 3.4 38.1 1.0
FBF A:W09502 3.5 45.6 1.0
O A:HOH735 3.7 25.7 1.0
FBM A:W09502 3.8 42.4 1.0
CB A:ALA330 4.0 13.4 1.0
O A:ALA330 4.2 12.1 1.0
OG A:SER72 4.3 20.3 1.0
CAS A:W09502 4.3 40.0 1.0
CE A:MET354 4.3 22.0 1.0
CAY A:W09502 4.4 46.0 1.0
O A:HOH660 4.4 19.0 1.0
FBP A:W09502 4.4 46.2 1.0
C A:ALA330 4.5 11.8 1.0
FBC A:W09502 4.5 39.2 1.0
CB A:ALA74 4.7 18.7 1.0
CA A:ALA330 4.7 12.8 1.0
CB A:SER72 4.8 18.5 1.0
N A:ALA330 5.0 12.6 1.0

Fluorine binding site 9 out of 34 in 3wsp

Go back to Fluorine Binding Sites List in 3wsp
Fluorine binding site 9 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:42.4
occ:1.00
FBI A:W09502 0.0 42.4 1.0
CAV A:W09502 1.3 41.7 1.0
FBH A:W09502 2.2 43.2 1.0
CAU A:W09502 2.3 40.7 1.0
CAW A:W09502 2.4 43.7 1.0
FBM A:W09502 2.6 42.4 1.0
FBE A:W09502 2.6 37.8 1.0
FBF A:W09502 2.6 45.6 1.0
CAX A:W09502 2.7 43.9 1.0
FBK A:W09502 2.8 38.1 1.0
FBL A:W09502 2.9 43.5 1.0
CAT A:W09502 2.9 38.9 1.0
FBJ A:W09502 3.2 44.7 1.0
CB A:ALA74 3.3 18.7 1.0
FBD A:W09502 3.4 35.4 1.0
FBG A:W09502 3.5 37.8 1.0
CD2 A:LEU437 4.1 28.4 0.6
CD2 A:LEU437 4.2 28.9 0.4
CAY A:W09502 4.2 46.0 1.0
CB A:LEU437 4.3 26.8 0.6
CAS A:W09502 4.3 40.0 1.0
CB A:LEU437 4.5 27.4 0.4
OG A:SER72 4.5 20.3 1.0
FBB A:W09502 4.6 37.7 1.0
CG A:LEU437 4.6 28.2 0.6
FBO A:W09502 4.7 43.8 1.0
CA A:LEU437 4.7 25.9 0.4
CA A:ALA74 4.7 17.8 1.0
CA A:LEU437 4.8 25.3 0.6
FBP A:W09502 4.9 46.2 1.0
CG A:LEU437 4.9 28.9 0.4
O A:HOH735 4.9 25.7 1.0
O A:LEU437 5.0 21.5 0.4
CD1 A:LEU437 5.0 29.0 0.6

Fluorine binding site 10 out of 34 in 3wsp

Go back to Fluorine Binding Sites List in 3wsp
Fluorine binding site 10 out of 34 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-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-Perfluorononanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:45.6
occ:1.00
FBF A:W09502 0.0 45.6 1.0
CAU A:W09502 1.3 40.7 1.0
FBG A:W09502 2.1 37.8 1.0
CAV A:W09502 2.3 41.7 1.0
CAT A:W09502 2.3 38.9 1.0
FBK A:W09502 2.5 38.1 1.0
FBB A:W09502 2.5 37.7 1.0
FBI A:W09502 2.6 42.4 1.0
FBE A:W09502 2.7 37.8 1.0
CAS A:W09502 2.9 40.0 1.0
CAW A:W09502 2.9 43.7 1.0
O A:HOH676 3.4 20.1 1.0
FBJ A:W09502 3.5 44.7 1.0
CA A:LEU437 3.5 25.3 0.6
FBH A:W09502 3.5 43.2 1.0
FBD A:W09502 3.5 35.4 1.0
O A:LEU437 3.6 21.4 0.6
FBC A:W09502 3.7 39.2 1.0
CA A:LEU437 3.7 25.9 0.4
CB A:LEU437 3.9 26.8 0.6
C A:LEU437 4.0 23.8 0.6
CD2 A:LEU437 4.0 28.4 0.6
FBM A:W09502 4.1 42.4 1.0
CAX A:W09502 4.2 43.9 1.0
CD2 A:LEU437 4.2 28.9 0.4
CAR A:W09502 4.3 40.7 1.0
CB A:LEU437 4.3 27.4 0.4
FAZ A:W09502 4.4 44.6 1.0
C A:LEU437 4.4 23.9 0.4
O A:LEU437 4.5 21.5 0.4
CG2 A:VAL26 4.5 15.9 1.0
CG A:LEU437 4.6 28.2 0.6
N A:LEU437 4.6 24.2 0.4
N A:LEU437 4.6 22.8 0.6
O A:HOH842 4.7 34.1 1.0
FBL A:W09502 4.9 43.5 1.0
CG A:LEU437 4.9 28.9 0.4

Reference:

Z.Cong, O.Shoji, C.Kasai, N.Kawakami, H.Sugimoto, Y.Shiro, Y.Watanabe. Activation of Wild-Type Cytochrome P450BM3 By the Next Generation of Decoy Molecules: Enhanced Hydroxylation of Gaseous Alkanes and Crystallographic Evidence. Acs Catalysis.
ISSN: ESSN 2155-5435
DOI: 10.1021/CS501592F
Page generated: Sun Dec 13 11:57:49 2020

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