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Fluorine in PDB 5b2w: Crystal Structure of P450BM3 with N-Perfluorododecanoyl-L-Tryptophan

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

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

Protein crystallography data

The structure of Crystal Structure of P450BM3 with N-Perfluorododecanoyl-L-Tryptophan, PDB code: 5b2w 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) 38.65 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.646, 145.829, 62.771, 90.00, 97.58, 90.00
R / Rfree (%) 18.5 / 20.8

Other elements in 5b2w:

The structure of Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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 - 40; Page 5, Binding sites: 41 - 46;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-L-Tryptophan (pdb code 5b2w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 46 binding sites of Fluorine where determined in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-L-Tryptophan, PDB code: 5b2w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 46 in 5b2w

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Fluorine binding site 1 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:53.8
occ:0.70
 FBS A:W1Z502 0.0 53.8 0.7
CBR A:W1Z502 1.3 52.0 0.7
CBQ A:W1Z502 2.2 50.0 0.7
FBT A:W1Z502 2.2 54.3 0.7
FBU A:W1Z502 2.2 53.7 0.7
FBW A:W1Z502 2.5 50.2 0.7
FBV A:W1Z502 2.6 49.2 0.7
CG2 A:ILE263 3.3 18.3 1.0
CAZ A:W1Z502 3.6 48.1 0.7
CB A:ILE263 3.7 17.8 1.0
N A:ALA264 3.7 15.9 1.0
FBY A:W1Z502 4.0 48.6 0.7
CB A:ALA264 4.0 16.4 1.0
FBX A:W1Z502 4.1 49.1 0.7
CA A:ALA264 4.1 16.0 1.0
O A:THR260 4.3 14.8 1.0
C A:ILE263 4.3 16.3 1.0
FBP A:W1Z502 4.6 47.0 0.7
CA A:ILE263 4.7 17.1 1.0
CD1 A:ILE263 4.7 18.5 1.0
CAY A:W1Z502 4.7 45.6 0.7
CG1 A:ILE263 4.8 18.4 1.0
CG1 A:VAL78 4.8 22.0 1.0
CD2 A:PHE87 4.8 16.5 1.0
CG A:PHE87 4.8 15.7 1.0

Fluorine binding site 2 out of 46 in 5b2w

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Fluorine binding site 2 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:54.3
occ:0.70
 FBT A:W1Z502 0.0 54.3 0.7
CBR A:W1Z502 1.3 52.0 0.7
CBQ A:W1Z502 2.2 50.0 0.7
FBS A:W1Z502 2.2 53.8 0.7
FBU A:W1Z502 2.2 53.7 0.7
FBY A:W1Z502 2.4 48.6 0.7
FBV A:W1Z502 2.5 49.2 0.7
CAZ A:W1Z502 2.8 48.1 0.7
CG1 A:VAL78 3.3 22.0 1.0
FBW A:W1Z502 3.4 50.2 0.7
FBX A:W1Z502 3.4 49.1 0.7
CG2 A:VAL78 4.0 22.1 1.0
CAY A:W1Z502 4.1 45.6 0.7
CD2 A:LEU181 4.1 39.9 1.0
CB A:VAL78 4.2 21.9 1.0
FBO A:W1Z502 4.2 47.2 0.7
CG2 A:ILE263 4.3 18.3 1.0
FBP A:W1Z502 4.6 47.0 0.7
FBD A:W1Z502 4.9 41.1 0.7

Fluorine binding site 3 out of 46 in 5b2w

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Fluorine binding site 3 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:53.7
occ:0.70
 FBU A:W1Z502 0.0 53.7 0.7
CBR A:W1Z502 1.3 52.0 0.7
CBQ A:W1Z502 2.2 50.0 0.7
FBS A:W1Z502 2.2 53.8 0.7
FBT A:W1Z502 2.2 54.3 0.7
FBX A:W1Z502 2.5 49.1 0.7
FBW A:W1Z502 2.6 50.2 0.7
CAZ A:W1Z502 2.7 48.1 0.7
FBY A:W1Z502 3.1 48.6 0.7
CD1 A:PHE87 3.2 16.3 1.0
CG A:PHE87 3.3 15.7 1.0
FBV A:W1Z502 3.4 49.2 0.7
CE1 A:PHE87 3.6 16.6 1.0
CD2 A:PHE87 3.7 16.5 1.0
CB A:PHE87 3.7 14.7 1.0
CZ A:PHE87 4.0 17.3 1.0
CE2 A:PHE87 4.1 17.0 1.0
CAY A:W1Z502 4.2 45.6 0.7
CG1 A:VAL78 4.3 22.0 1.0
FBP A:W1Z502 4.4 47.0 0.7
CD2 A:LEU75 4.4 20.7 1.0
CG2 A:THR88 4.7 14.8 1.0
FBO A:W1Z502 4.9 47.2 0.7
CB A:ALA264 4.9 16.4 1.0
FBA A:W1Z502 5.0 39.9 0.7

Fluorine binding site 4 out of 46 in 5b2w

Go back to Fluorine Binding Sites List in 5b2w
Fluorine binding site 4 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:49.2
occ:0.70
 FBV A:W1Z502 0.0 49.2 0.7
CBQ A:W1Z502 1.3 50.0 0.7
FBW A:W1Z502 2.2 50.2 0.7
CBR A:W1Z502 2.3 52.0 0.7
CAZ A:W1Z502 2.3 48.1 0.7
FBT A:W1Z502 2.5 54.3 0.7
FBS A:W1Z502 2.6 53.8 0.7
FBP A:W1Z502 2.7 47.0 0.7
FBO A:W1Z502 2.8 47.2 0.7
CAY A:W1Z502 2.8 45.6 0.7
FBY A:W1Z502 2.8 48.6 0.7
FBU A:W1Z502 3.4 53.7 0.7
CG2 A:ILE263 3.4 18.3 1.0
FBX A:W1Z502 3.5 49.1 0.7
CAX A:W1Z502 4.3 41.9 0.7
CD2 A:LEU181 4.4 39.9 1.0
FBD A:W1Z502 4.5 41.1 0.7
CB A:ILE263 4.6 17.8 1.0
N A:ALA264 4.7 15.9 1.0
CA A:ALA264 4.7 16.0 1.0
CG2 A:THR438 4.8 18.8 1.0
C A:ILE263 4.8 16.3 1.0
CD1 A:LEU181 4.9 40.5 1.0
O A:ILE263 4.9 16.9 1.0
CAW A:W1Z502 5.0 39.5 0.7
FBA A:W1Z502 5.0 39.9 0.7

Fluorine binding site 5 out of 46 in 5b2w

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Fluorine binding site 5 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:50.2
occ:0.70
 FBW A:W1Z502 0.0 50.2 0.7
CBQ A:W1Z502 1.3 50.0 0.7
FBV A:W1Z502 2.2 49.2 0.7
CBR A:W1Z502 2.3 52.0 0.7
CAZ A:W1Z502 2.3 48.1 0.7
FBP A:W1Z502 2.4 47.0 0.7
FBS A:W1Z502 2.5 53.8 0.7
FBU A:W1Z502 2.6 53.7 0.7
FBX A:W1Z502 2.7 49.1 0.7
CAY A:W1Z502 2.9 45.6 0.7
FBT A:W1Z502 3.4 54.3 0.7
FBY A:W1Z502 3.5 48.6 0.7
CE2 A:PHE87 3.5 17.0 1.0
CB A:ALA264 3.6 16.4 1.0
CA A:ALA264 3.7 16.0 1.0
CZ A:PHE87 3.7 17.3 1.0
FBO A:W1Z502 3.7 47.2 0.7
CD2 A:PHE87 3.8 16.5 1.0
CAX A:W1Z502 4.1 41.9 0.7
O A:HOH626 4.1 21.2 1.0
N A:ALA264 4.2 15.9 1.0
CE1 A:PHE87 4.2 16.6 1.0
FBA A:W1Z502 4.2 39.9 0.7
CG A:PHE87 4.3 15.7 1.0
CD1 A:PHE87 4.5 16.3 1.0
CG2 A:ILE263 4.6 18.3 1.0
C A:ILE263 4.9 16.3 1.0

Fluorine binding site 6 out of 46 in 5b2w

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Fluorine binding site 6 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:49.1
occ:0.70
 FBX A:W1Z502 0.0 49.1 0.7
CAZ A:W1Z502 1.3 48.1 0.7
FBY A:W1Z502 2.2 48.6 0.7
CBQ A:W1Z502 2.3 50.0 0.7
CAY A:W1Z502 2.3 45.6 0.7
FBU A:W1Z502 2.5 53.7 0.7
FBA A:W1Z502 2.5 39.9 0.7
CE1 A:PHE87 2.6 16.6 1.0
FBW A:W1Z502 2.7 50.2 0.7
CAX A:W1Z502 2.8 41.9 0.7
FBC A:W1Z502 2.8 41.2 0.7
CZ A:PHE87 2.9 17.3 1.0
FBP A:W1Z502 3.0 47.0 0.7
CBR A:W1Z502 3.0 52.0 0.7
CAW A:W1Z502 3.2 39.5 0.7
CD1 A:PHE87 3.2 16.3 1.0
FBO A:W1Z502 3.4 47.2 0.7
FBT A:W1Z502 3.4 54.3 0.7
FBV A:W1Z502 3.5 49.2 0.7
FBD A:W1Z502 3.6 41.1 0.7
CE2 A:PHE87 3.6 17.0 1.0
CD2 A:LEU75 3.7 20.7 1.0
CG A:PHE87 3.9 15.7 1.0
FBS A:W1Z502 4.1 53.8 0.7
CD2 A:PHE87 4.1 16.5 1.0
FBB A:W1Z502 4.1 39.4 0.7
CAV A:W1Z502 4.7 36.9 0.7
O A:HOH815 4.8 18.6 1.0

Fluorine binding site 7 out of 46 in 5b2w

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Fluorine binding site 7 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:48.6
occ:0.70
 FBY A:W1Z502 0.0 48.6 0.7
CAZ A:W1Z502 1.3 48.1 0.7
FBX A:W1Z502 2.2 49.1 0.7
CAY A:W1Z502 2.3 45.6 0.7
CBQ A:W1Z502 2.4 50.0 0.7
FBT A:W1Z502 2.4 54.3 0.7
FBO A:W1Z502 2.5 47.2 0.7
FBD A:W1Z502 2.5 41.1 0.7
FBV A:W1Z502 2.8 49.2 0.7
CBR A:W1Z502 2.9 52.0 0.7
FBC A:W1Z502 3.1 41.2 0.7
CAW A:W1Z502 3.1 39.5 0.7
FBU A:W1Z502 3.1 53.7 0.7
CAX A:W1Z502 3.3 41.9 0.7
FBP A:W1Z502 3.4 47.0 0.7
FBW A:W1Z502 3.5 50.2 0.7
FBA A:W1Z502 3.7 39.9 0.7
FBS A:W1Z502 4.0 53.8 0.7
CD2 A:LEU75 4.1 20.7 1.0
CD1 A:LEU437 4.3 23.6 1.0
CG2 A:VAL78 4.3 22.1 1.0
FBB A:W1Z502 4.3 39.4 0.7
CAV A:W1Z502 4.6 36.9 0.7
FBH A:W1Z502 4.6 36.5 0.7
CD2 A:LEU181 4.6 39.9 1.0
CE1 A:PHE87 4.7 16.6 1.0
CG1 A:VAL78 4.8 22.0 1.0
CB A:LEU437 4.9 22.5 1.0
CB A:VAL78 5.0 21.9 1.0

Fluorine binding site 8 out of 46 in 5b2w

Go back to Fluorine Binding Sites List in 5b2w
Fluorine binding site 8 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:47.2
occ:0.70
 FBO A:W1Z502 0.0 47.2 0.7
CAY A:W1Z502 1.3 45.6 0.7
FBP A:W1Z502 2.1 47.0 0.7
FBD A:W1Z502 2.2 41.1 0.7
CAZ A:W1Z502 2.3 48.1 0.7
CAX A:W1Z502 2.4 41.9 0.7
FBY A:W1Z502 2.5 48.6 0.7
FBB A:W1Z502 2.7 39.4 0.7
FBV A:W1Z502 2.8 49.2 0.7
CAW A:W1Z502 2.8 39.5 0.7
CG2 A:THR438 3.0 18.8 1.0
CBQ A:W1Z502 3.1 50.0 0.7
FBX A:W1Z502 3.4 49.1 0.7
FBA A:W1Z502 3.5 39.9 0.7
FBC A:W1Z502 3.7 41.2 0.7
FBW A:W1Z502 3.7 50.2 0.7
FBE A:W1Z502 3.8 34.5 0.7
CAV A:W1Z502 3.9 36.9 0.7
CB A:LEU437 4.1 22.5 1.0
FBT A:W1Z502 4.2 54.3 0.7
N A:THR438 4.2 19.1 1.0
CB A:THR438 4.3 18.9 1.0
CBR A:W1Z502 4.4 52.0 0.7
FBF A:W1Z502 4.7 34.5 0.7
CA A:THR438 4.7 18.3 1.0
CD1 A:LEU437 4.7 23.6 1.0
C A:LEU437 4.8 21.4 1.0
OG1 A:THR438 4.8 18.8 1.0
FBH A:W1Z502 4.8 36.5 0.7
FBU A:W1Z502 4.9 53.7 0.7
O A:THR436 4.9 21.3 1.0
CD2 A:LEU181 4.9 39.9 1.0

Fluorine binding site 9 out of 46 in 5b2w

Go back to Fluorine Binding Sites List in 5b2w
Fluorine binding site 9 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:47.0
occ:0.70
 FBP A:W1Z502 0.0 47.0 0.7
CAY A:W1Z502 1.3 45.6 0.7
FBO A:W1Z502 2.1 47.2 0.7
CAX A:W1Z502 2.3 41.9 0.7
CAZ A:W1Z502 2.3 48.1 0.7
FBW A:W1Z502 2.4 50.2 0.7
CBQ A:W1Z502 2.6 50.0 0.7
FBV A:W1Z502 2.7 49.2 0.7
FBB A:W1Z502 2.8 39.4 0.7
FBA A:W1Z502 3.0 39.9 0.7
FBX A:W1Z502 3.0 49.1 0.7
FBY A:W1Z502 3.4 48.6 0.7
CG2 A:THR438 3.6 18.8 1.0
CAW A:W1Z502 3.6 39.5 0.7
FBD A:W1Z502 3.8 41.1 0.7
O A:HOH626 4.0 21.2 1.0
CG2 A:THR268 4.1 15.3 1.0
CBR A:W1Z502 4.1 52.0 0.7
CZ A:PHE87 4.2 17.3 1.0
FBC A:W1Z502 4.3 41.2 0.7
FBU A:W1Z502 4.4 53.7 0.7
CE2 A:PHE87 4.5 17.0 1.0
CB A:ALA328 4.5 14.6 1.0
FBS A:W1Z502 4.6 53.8 0.7
FBT A:W1Z502 4.6 54.3 0.7
CAV A:W1Z502 4.8 36.9 0.7
CE1 A:PHE87 4.8 16.6 1.0
FBE A:W1Z502 4.9 34.5 0.7

Fluorine binding site 10 out of 46 in 5b2w

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Fluorine binding site 10 out of 46 in the Crystal Structure of P450BM3 with N-Perfluorododecanoyl-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-Perfluorododecanoyl-L-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:39.9
occ:0.70
 FBA A:W1Z502 0.0 39.9 0.7
CAX A:W1Z502 1.3 41.9 0.7
CAW A:W1Z502 2.1 39.5 0.7
FBC A:W1Z502 2.2 41.2 0.7
FBB A:W1Z502 2.2 39.4 0.7
CAY A:W1Z502 2.4 45.6 0.7
FBX A:W1Z502 2.5 49.1 0.7
FBF A:W1Z502 2.8 34.5 0.7
FBP A:W1Z502 3.0 47.0 0.7
CAZ A:W1Z502 3.0 48.1 0.7
CAV A:W1Z502 3.0 36.9 0.7
CZ A:PHE87 3.1 17.3 1.0
FBD A:W1Z502 3.3 41.1 0.7
CE1 A:PHE87 3.4 16.6 1.0
O A:HOH815 3.4 18.6 1.0
FBO A:W1Z502 3.5 47.2 0.7
FBY A:W1Z502 3.7 48.6 0.7
CB A:ALA328 3.9 14.6 1.0
FBE A:W1Z502 3.9 34.5 0.7
FBG A:W1Z502 4.1 35.6 0.7
CAU A:W1Z502 4.1 36.1 0.7
CE2 A:PHE87 4.2 17.0 1.0
FBW A:W1Z502 4.2 50.2 0.7
CBQ A:W1Z502 4.3 50.0 0.7
FBH A:W1Z502 4.6 36.5 0.7
CD1 A:PHE87 4.6 16.3 1.0
CA A:ALA328 4.7 14.2 1.0
O A:ALA330 4.9 13.5 1.0
CD2 A:LEU75 4.9 20.7 1.0
CBA A:HEM501 4.9 12.8 1.0
FBU A:W1Z502 5.0 53.7 0.7
FBV A:W1Z502 5.0 49.2 0.7

Reference:

Z.Cong, O.Shoji, C.Kasai, H.Sugimoto, Y.Shiro, Y.Watanabe. Crystal Structure of P450BM3 with Decoy Molecules To Be Published.
Page generated: Thu Aug 1 08:01:29 2024

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