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Iron 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:

Fluorine (F) 34 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan, PDB code: 3wsp:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3wsp

Go back to Iron Binding Sites List in 3wsp
Iron binding site 1 out of 2 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe501

b:12.7
occ:1.00
FE A:HEM501 0.0 12.7 1.0
ND A:HEM501 2.0 11.5 1.0
NA A:HEM501 2.0 12.2 1.0
NC A:HEM501 2.1 13.5 1.0
NB A:HEM501 2.1 12.1 1.0
SG A:CYS400 2.3 14.1 1.0
S A:DMS503 2.6 29.0 1.0
C1D A:HEM501 3.0 12.0 1.0
C4D A:HEM501 3.0 12.3 1.0
C1A A:HEM501 3.0 11.8 1.0
C4B A:HEM501 3.0 13.0 1.0
C4A A:HEM501 3.0 12.5 1.0
C4C A:HEM501 3.0 14.2 1.0
C1B A:HEM501 3.1 12.2 1.0
C1C A:HEM501 3.1 14.6 1.0
O A:DMS503 3.3 30.1 1.0
CB A:CYS400 3.4 12.5 1.0
CHA A:HEM501 3.4 12.4 1.0
CHD A:HEM501 3.4 12.5 1.0
CHC A:HEM501 3.4 13.4 1.0
CHB A:HEM501 3.4 11.8 1.0
C1 A:DMS503 3.6 27.9 1.0
C2 A:DMS503 3.8 30.1 1.0
CA A:CYS400 4.0 11.3 1.0
C2A A:HEM501 4.2 11.8 1.0
C3A A:HEM501 4.2 11.9 1.0
C2D A:HEM501 4.2 11.7 1.0
C3D A:HEM501 4.2 11.7 1.0
C3C A:HEM501 4.3 15.3 1.0
C2C A:HEM501 4.3 16.2 1.0
C3B A:HEM501 4.3 12.7 1.0
C2B A:HEM501 4.3 12.3 1.0
O A:ALA264 4.7 25.3 0.6
C A:CYS400 4.8 12.2 1.0
N A:GLY402 4.8 13.1 1.0
CB A:ALA264 4.9 22.2 0.6
N A:ILE401 5.0 11.7 1.0

Iron binding site 2 out of 2 in 3wsp

Go back to Iron Binding Sites List in 3wsp
Iron binding site 2 out of 2 in the Crystal Structure of P450BM3 with N-Perfluorononanoyl-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
B:Fe501

b:11.4
occ:1.00
FE B:HEM501 0.0 11.4 1.0
ND B:HEM501 1.9 10.0 1.0
NA B:HEM501 2.0 10.4 1.0
NC B:HEM501 2.0 11.7 1.0
NB B:HEM501 2.1 10.6 1.0
SG B:CYS400 2.3 12.8 1.0
S B:DMS503 2.4 25.0 1.0
C1D B:HEM501 3.0 10.7 1.0
C4D B:HEM501 3.0 10.5 1.0
C4C B:HEM501 3.0 12.3 1.0
C4B B:HEM501 3.0 11.3 1.0
C1A B:HEM501 3.1 10.7 1.0
C4A B:HEM501 3.1 11.0 1.0
C1B B:HEM501 3.1 11.2 1.0
C1C B:HEM501 3.1 12.2 1.0
O B:DMS503 3.3 27.0 1.0
CB B:CYS400 3.3 11.4 1.0
CHD B:HEM501 3.4 10.6 1.0
CHC B:HEM501 3.4 11.8 1.0
CHA B:HEM501 3.4 10.4 1.0
CHB B:HEM501 3.5 10.5 1.0
C1 B:DMS503 3.5 23.9 1.0
C2 B:DMS503 3.6 25.5 1.0
CA B:CYS400 4.0 11.7 1.0
C3C B:HEM501 4.2 14.3 1.0
C2D B:HEM501 4.2 10.5 1.0
C3A B:HEM501 4.2 10.9 1.0
C3D B:HEM501 4.2 10.3 1.0
C2A B:HEM501 4.2 10.9 1.0
C2C B:HEM501 4.2 13.5 1.0
C3B B:HEM501 4.3 11.7 1.0
C2B B:HEM501 4.3 11.0 1.0
N B:GLY402 4.8 12.5 1.0
C B:CYS400 4.8 11.7 1.0
N B:ILE401 5.0 12.3 1.0

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 15:26:20 2020

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