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Iron in PDB 6l1a: Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine

Enzymatic activity of Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine

All present enzymatic activity of Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine, PDB code: 6l1a was solved by O.Shoji, K.Yonemura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.62 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.828, 128.427, 148.889, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine (pdb code 6l1a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine, PDB code: 6l1a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6l1a

Go back to Iron Binding Sites List in 6l1a
Iron binding site 1 out of 4 in the Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine


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-Enanthoyl-L-Prolyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:18.6
occ:0.54
 FE A:HEM501 0.0 18.6 0.5
FE A:HEM501 0.1 20.4 0.5
ND A:HEM501 1.9 19.9 0.5
ND A:HEM501 1.9 18.1 0.5
NA A:HEM501 2.0 20.2 0.5
NA A:HEM501 2.0 18.1 0.5
NB A:HEM501 2.1 20.6 0.5
NC A:HEM501 2.1 18.5 0.5
NC A:HEM501 2.1 19.6 0.5
NB A:HEM501 2.1 18.2 0.5
SG A:CYS400 2.3 22.0 1.0
S A:DMS502 2.5 35.6 1.0
C1D A:HEM501 2.9 18.3 0.5
C4D A:HEM501 3.0 20.0 0.5
C1D A:HEM501 3.0 19.6 0.5
C4D A:HEM501 3.0 19.0 0.5
C4A A:HEM501 3.0 20.6 0.5
C1B A:HEM501 3.0 21.1 0.5
C4C A:HEM501 3.0 18.8 0.5
C4B A:HEM501 3.0 22.1 0.5
C4C A:HEM501 3.0 19.1 0.5
C4B A:HEM501 3.0 18.4 0.5
C1A A:HEM501 3.0 21.0 0.5
C1A A:HEM501 3.0 18.1 0.5
C1B A:HEM501 3.1 17.6 0.5
C4A A:HEM501 3.1 17.6 0.5
C1C A:HEM501 3.1 20.0 0.5
C1C A:HEM501 3.1 20.0 0.5
O A:DMS502 3.3 46.9 1.0
CHD A:HEM501 3.4 19.3 0.5
CB A:CYS400 3.4 19.3 1.0
CHD A:HEM501 3.4 20.2 0.5
CHB A:HEM501 3.4 21.5 0.5
CHA A:HEM501 3.4 21.1 0.5
CHA A:HEM501 3.4 19.2 0.5
CHC A:HEM501 3.4 18.6 0.5
CHB A:HEM501 3.5 18.5 0.5
CHC A:HEM501 3.5 20.4 0.5
C2 A:DMS502 3.7 37.1 1.0
C1 A:DMS502 3.8 35.4 1.0
CA A:CYS400 4.0 19.2 1.0
C2D A:HEM501 4.2 18.9 0.5
C3D A:HEM501 4.2 19.8 0.5
C2D A:HEM501 4.2 19.1 0.5
C3A A:HEM501 4.2 21.1 0.5
C2A A:HEM501 4.2 21.0 0.5
C3D A:HEM501 4.3 18.8 0.5
C3C A:HEM501 4.3 19.8 0.5
C2A A:HEM501 4.3 17.9 0.5
C2B A:HEM501 4.3 21.3 0.5
C3C A:HEM501 4.3 18.6 0.5
C3A A:HEM501 4.3 17.2 0.5
C2C A:HEM501 4.3 19.7 0.5
C2B A:HEM501 4.3 18.5 0.5
C2C A:HEM501 4.3 19.4 0.5
C3B A:HEM501 4.3 22.3 0.5
C3B A:HEM501 4.3 18.3 0.5
N A:GLY402 4.8 20.5 1.0
C A:CYS400 4.8 19.2 1.0
N A:ILE401 4.9 21.4 1.0

Iron binding site 2 out of 4 in 6l1a

Go back to Iron Binding Sites List in 6l1a
Iron binding site 2 out of 4 in the Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine


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-Enanthoyl-L-Prolyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:20.4
occ:0.46
 FE A:HEM501 0.0 20.4 0.5
FE A:HEM501 0.1 18.6 0.5
ND A:HEM501 1.9 19.9 0.5
ND A:HEM501 2.0 18.1 0.5
NA A:HEM501 2.0 18.1 0.5
NA A:HEM501 2.0 20.2 0.5
NB A:HEM501 2.1 18.2 0.5
NC A:HEM501 2.1 19.6 0.5
NB A:HEM501 2.1 20.6 0.5
NC A:HEM501 2.1 18.5 0.5
SG A:CYS400 2.3 22.0 1.0
S A:DMS502 2.5 35.6 1.0
C1D A:HEM501 2.9 19.6 0.5
C4D A:HEM501 2.9 20.0 0.5
C1D A:HEM501 3.0 18.3 0.5
C4D A:HEM501 3.0 19.0 0.5
C4C A:HEM501 3.0 19.1 0.5
C1B A:HEM501 3.0 17.6 0.5
C1A A:HEM501 3.0 18.1 0.5
C4B A:HEM501 3.0 18.4 0.5
C4A A:HEM501 3.0 17.6 0.5
C1A A:HEM501 3.0 21.0 0.5
C4B A:HEM501 3.1 22.1 0.5
C4A A:HEM501 3.1 20.6 0.5
C1B A:HEM501 3.1 21.1 0.5
C4C A:HEM501 3.1 18.8 0.5
C1C A:HEM501 3.1 20.0 0.5
C1C A:HEM501 3.1 20.0 0.5
O A:DMS502 3.3 46.9 1.0
CB A:CYS400 3.4 19.3 1.0
CHD A:HEM501 3.4 20.2 0.5
CHD A:HEM501 3.4 19.3 0.5
CHA A:HEM501 3.4 21.1 0.5
CHB A:HEM501 3.4 18.5 0.5
CHA A:HEM501 3.4 19.2 0.5
CHC A:HEM501 3.5 18.6 0.5
CHB A:HEM501 3.5 21.5 0.5
CHC A:HEM501 3.5 20.4 0.5
C2 A:DMS502 3.8 37.1 1.0
C1 A:DMS502 3.8 35.4 1.0
CA A:CYS400 4.0 19.2 1.0
C2D A:HEM501 4.2 19.1 0.5
C3D A:HEM501 4.2 19.8 0.5
C3C A:HEM501 4.2 19.8 0.5
C2A A:HEM501 4.2 17.9 0.5
C3A A:HEM501 4.2 17.2 0.5
C2B A:HEM501 4.2 18.5 0.5
C2D A:HEM501 4.3 18.9 0.5
C2C A:HEM501 4.3 19.4 0.5
C3A A:HEM501 4.3 21.1 0.5
C2A A:HEM501 4.3 21.0 0.5
C3D A:HEM501 4.3 18.8 0.5
C3B A:HEM501 4.3 18.3 0.5
C2B A:HEM501 4.3 21.3 0.5
C3C A:HEM501 4.3 18.6 0.5
C2C A:HEM501 4.3 19.7 0.5
C3B A:HEM501 4.3 22.3 0.5
N A:GLY402 4.8 20.5 1.0
C A:CYS400 4.8 19.2 1.0
N A:ILE401 4.9 21.4 1.0

Iron binding site 3 out of 4 in 6l1a

Go back to Iron Binding Sites List in 6l1a
Iron binding site 3 out of 4 in the Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:16.9
occ:0.52
 FE B:HEM501 0.0 16.9 0.5
FE B:HEM501 0.0 20.0 0.5
ND B:HEM501 1.9 19.6 0.5
ND B:HEM501 1.9 14.9 0.5
NA B:HEM501 2.0 17.9 0.5
NA B:HEM501 2.0 16.2 0.5
NC B:HEM501 2.1 16.0 0.5
NB B:HEM501 2.1 16.4 0.5
NC B:HEM501 2.1 19.9 0.5
NB B:HEM501 2.1 19.6 0.5
SG B:CYS400 2.3 20.0 1.0
S B:DMS502 2.4 35.1 1.0
C1D B:HEM501 2.9 15.1 0.5
C4D B:HEM501 2.9 19.9 0.5
C1D B:HEM501 3.0 20.3 0.5
C4D B:HEM501 3.0 15.5 0.5
C4C B:HEM501 3.0 20.1 0.5
C1B B:HEM501 3.0 16.3 0.5
C1A B:HEM501 3.0 16.5 0.5
C4C B:HEM501 3.0 15.3 0.5
C1A B:HEM501 3.0 18.5 0.5
C4A B:HEM501 3.0 18.4 0.5
C4B B:HEM501 3.0 16.8 0.5
C1B B:HEM501 3.1 18.9 0.5
C4B B:HEM501 3.1 19.6 0.5
C4A B:HEM501 3.1 16.6 0.5
C1C B:HEM501 3.1 15.9 0.5
C1C B:HEM501 3.1 20.3 0.5
O B:DMS502 3.2 37.1 1.0
CB B:CYS400 3.4 17.7 1.0
CHD B:HEM501 3.4 15.2 0.5
CHD B:HEM501 3.4 20.9 0.5
CHA B:HEM501 3.4 19.6 0.5
CHA B:HEM501 3.4 16.4 0.5
CHB B:HEM501 3.4 18.5 0.5
CHB B:HEM501 3.4 17.1 0.5
CHC B:HEM501 3.5 17.1 0.5
CHC B:HEM501 3.5 20.8 0.5
C1 B:DMS502 3.6 37.8 1.0
C2 B:DMS502 3.7 36.2 1.0
CA B:CYS400 4.0 19.1 1.0
C2D B:HEM501 4.2 20.5 0.5
C3D B:HEM501 4.2 21.1 0.5
C2D B:HEM501 4.2 15.8 0.5
C3A B:HEM501 4.2 19.0 0.5
C3C B:HEM501 4.2 20.9 0.5
C2A B:HEM501 4.2 18.8 0.5
C3D B:HEM501 4.2 15.8 0.5
C2B B:HEM501 4.3 16.6 0.5
C3C B:HEM501 4.3 16.1 0.5
C2A B:HEM501 4.3 17.4 0.5
C2C B:HEM501 4.3 15.7 0.5
C3A B:HEM501 4.3 16.9 0.5
C2C B:HEM501 4.3 20.3 0.5
C2B B:HEM501 4.3 20.1 0.5
C3B B:HEM501 4.3 16.7 0.5
C3B B:HEM501 4.3 19.5 0.5
C B:CYS400 4.8 18.6 1.0
N B:GLY402 4.8 18.1 1.0
N B:ILE401 5.0 18.7 1.0

Iron binding site 4 out of 4 in 6l1a

Go back to Iron Binding Sites List in 6l1a
Iron binding site 4 out of 4 in the Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.0
occ:0.48
 FE B:HEM501 0.0 20.0 0.5
FE B:HEM501 0.0 16.9 0.5
ND B:HEM501 1.9 19.6 0.5
ND B:HEM501 2.0 14.9 0.5
NA B:HEM501 2.0 16.2 0.5
NA B:HEM501 2.0 17.9 0.5
NB B:HEM501 2.0 16.4 0.5
NC B:HEM501 2.1 19.9 0.5
NC B:HEM501 2.1 16.0 0.5
NB B:HEM501 2.1 19.6 0.5
SG B:CYS400 2.3 20.0 1.0
S B:DMS502 2.4 35.1 1.0
C1D B:HEM501 2.9 20.3 0.5
C4D B:HEM501 2.9 19.9 0.5
C1D B:HEM501 3.0 15.1 0.5
C4C B:HEM501 3.0 20.1 0.5
C1B B:HEM501 3.0 16.3 0.5
C4D B:HEM501 3.0 15.5 0.5
C1A B:HEM501 3.0 16.5 0.5
C4B B:HEM501 3.0 16.8 0.5
C1A B:HEM501 3.1 18.5 0.5
C4A B:HEM501 3.1 16.6 0.5
C4C B:HEM501 3.1 15.3 0.5
C4A B:HEM501 3.1 18.4 0.5
C4B B:HEM501 3.1 19.6 0.5
C1B B:HEM501 3.1 18.9 0.5
C1C B:HEM501 3.1 15.9 0.5
C1C B:HEM501 3.1 20.3 0.5
O B:DMS502 3.2 37.1 1.0
CB B:CYS400 3.3 17.7 1.0
CHD B:HEM501 3.4 20.9 0.5
CHA B:HEM501 3.4 19.6 0.5
CHA B:HEM501 3.4 16.4 0.5
CHB B:HEM501 3.4 17.1 0.5
CHD B:HEM501 3.4 15.2 0.5
CHC B:HEM501 3.4 17.1 0.5
CHB B:HEM501 3.5 18.5 0.5
CHC B:HEM501 3.5 20.8 0.5
C1 B:DMS502 3.7 37.8 1.0
C2 B:DMS502 3.7 36.2 1.0
CA B:CYS400 4.0 19.1 1.0
C2D B:HEM501 4.2 20.5 0.5
C3D B:HEM501 4.2 21.1 0.5
C3C B:HEM501 4.2 20.9 0.5
C2B B:HEM501 4.2 16.6 0.5
C2A B:HEM501 4.2 17.4 0.5
C3A B:HEM501 4.2 16.9 0.5
C2D B:HEM501 4.3 15.8 0.5
C3A B:HEM501 4.3 19.0 0.5
C2C B:HEM501 4.3 20.3 0.5
C2A B:HEM501 4.3 18.8 0.5
C3D B:HEM501 4.3 15.8 0.5
C3B B:HEM501 4.3 16.7 0.5
C2C B:HEM501 4.3 15.7 0.5
C3C B:HEM501 4.3 16.1 0.5
C2B B:HEM501 4.3 20.1 0.5
C3B B:HEM501 4.3 19.5 0.5
C B:CYS400 4.8 18.6 1.0
N B:GLY402 4.8 18.1 1.0
N B:ILE401 5.0 18.7 1.0

Reference:

O.Shoji, K.Yonemura. Crystal Structure of P450BM3 with N-Enanthoyl-L-Prolyl-L-Phenylalanine To Be Published.
Page generated: Wed Aug 7 00:29:22 2024

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